Starting phenix.real_space_refine on Thu Feb 5 13:19:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxn_40855/02_2026/8sxn_40855_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxn_40855/02_2026/8sxn_40855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sxn_40855/02_2026/8sxn_40855_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxn_40855/02_2026/8sxn_40855_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sxn_40855/02_2026/8sxn_40855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxn_40855/02_2026/8sxn_40855.map" } resolution = 4.04 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 154 5.16 5 C 11278 2.51 5 N 3008 2.21 5 O 3262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17708 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2284 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "B" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2284 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "C" Number of atoms: 6511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6511 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 23, 'TRANS': 792} Chain breaks: 4 Chain: "D" Number of atoms: 6511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6511 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 23, 'TRANS': 792} Chain breaks: 4 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.03, per 1000 atoms: 0.23 Number of scatterers: 17708 At special positions: 0 Unit cell: (135.616, 172.224, 98.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 6 15.00 O 3262 8.00 N 3008 7.00 C 11278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 694.3 milliseconds 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 12 sheets defined 49.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.566A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 134 through 154 removed outlier: 3.661A pdb=" N LYS A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 190 through 196 removed outlier: 4.168A pdb=" N SER A 195 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.922A pdb=" N ASP A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 284 through 300 removed outlier: 3.668A pdb=" N CYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.510A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 134 through 154 removed outlier: 3.705A pdb=" N LYS B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 190 through 196 removed outlier: 4.190A pdb=" N SER B 195 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 215 through 232 removed outlier: 3.573A pdb=" N ILE B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 284 through 297 Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.567A pdb=" N GLU C 356 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLN C 359 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N HIS C 360 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 438 through 452 Processing helix chain 'C' and resid 463 through 479 removed outlier: 4.090A pdb=" N GLY C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 522 through 534 removed outlier: 3.812A pdb=" N TYR C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 564 Processing helix chain 'C' and resid 567 through 571 Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 592 through 596 Processing helix chain 'C' and resid 597 through 616 Processing helix chain 'C' and resid 627 through 637 Processing helix chain 'C' and resid 639 through 647 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 659 through 672 Processing helix chain 'C' and resid 731 through 738 Processing helix chain 'C' and resid 754 through 765 Processing helix chain 'C' and resid 785 through 795 removed outlier: 4.196A pdb=" N ASP C 789 " --> pdb=" O GLU C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 824 removed outlier: 3.679A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 843 through 854 removed outlier: 3.949A pdb=" N SER C 849 " --> pdb=" O GLN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 880 removed outlier: 3.562A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 909 Processing helix chain 'C' and resid 924 through 937 Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 957 through 966 Processing helix chain 'C' and resid 982 through 994 removed outlier: 3.554A pdb=" N LYS C 994 " --> pdb=" O CYS C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1025 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 328 through 337 Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.968A pdb=" N GLU D 356 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN D 359 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N HIS D 360 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 388 through 402 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 411 through 428 Processing helix chain 'D' and resid 438 through 452 Processing helix chain 'D' and resid 463 through 479 removed outlier: 4.196A pdb=" N GLY D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 492 Processing helix chain 'D' and resid 496 through 505 Processing helix chain 'D' and resid 522 through 534 removed outlier: 3.942A pdb=" N TYR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 564 Processing helix chain 'D' and resid 567 through 571 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 592 through 596 Processing helix chain 'D' and resid 597 through 617 Processing helix chain 'D' and resid 627 through 637 Processing helix chain 'D' and resid 639 through 647 Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 659 through 672 Processing helix chain 'D' and resid 731 through 738 Processing helix chain 'D' and resid 754 through 765 Processing helix chain 'D' and resid 785 through 795 removed outlier: 4.095A pdb=" N ASP D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 824 removed outlier: 3.693A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 843 through 854 removed outlier: 3.757A pdb=" N SER D 849 " --> pdb=" O GLN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 880 removed outlier: 3.534A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 911 removed outlier: 4.477A pdb=" N ALA D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 937 Processing helix chain 'D' and resid 954 through 956 No H-bonds generated for 'chain 'D' and resid 954 through 956' Processing helix chain 'D' and resid 957 through 966 Processing helix chain 'D' and resid 982 through 994 removed outlier: 3.607A pdb=" N LYS D 994 " --> pdb=" O CYS D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1025 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 42 removed outlier: 5.399A pdb=" N ILE A 36 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 52 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG A 42 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 99 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 112 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR A 97 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 42 removed outlier: 5.345A pdb=" N ILE B 36 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 52 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG B 42 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 112 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 97 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AA5, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.675A pdb=" N ILE C 297 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU C 347 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE C 299 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR C 349 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET C 301 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 259 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA7, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AA8, first strand: chain 'C' and resid 652 through 655 removed outlier: 6.614A pdb=" N LEU C 679 " --> pdb=" O ASP C 747 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 889 " --> pdb=" O TYR C 918 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.663A pdb=" N TYR D 255 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU D 300 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE D 257 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP D 302 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE D 259 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AB2, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AB3, first strand: chain 'D' and resid 652 through 655 removed outlier: 6.611A pdb=" N ILE D 653 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU D 679 " --> pdb=" O ASP D 747 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU D 860 " --> pdb=" O GLY D 890 " (cutoff:3.500A) 769 hydrogen bonds defined for protein. 2148 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: 2.88 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2968 1.31 - 1.44: 4591 1.44 - 1.56: 10266 1.56 - 1.69: 23 1.69 - 1.82: 216 Bond restraints: 18064 Sorted by residual: bond pdb=" C08 7YN D1101 " pdb=" C09 7YN D1101 " ideal model delta sigma weight residual 1.340 1.521 -0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" C08 7YN C1101 " pdb=" C09 7YN C1101 " ideal model delta sigma weight residual 1.340 1.521 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" C14 7YN D1101 " pdb=" N13 7YN D1101 " ideal model delta sigma weight residual 1.349 1.469 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C14 7YN C1101 " pdb=" N13 7YN C1101 " ideal model delta sigma weight residual 1.349 1.463 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C06 7YN C1101 " pdb=" C09 7YN C1101 " ideal model delta sigma weight residual 1.461 1.544 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 18059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.09: 24311 6.09 - 12.19: 73 12.19 - 18.28: 0 18.28 - 24.37: 2 24.37 - 30.47: 4 Bond angle restraints: 24390 Sorted by residual: angle pdb=" PB ATP C1102 " pdb=" O3B ATP C1102 " pdb=" PG ATP C1102 " ideal model delta sigma weight residual 139.87 109.40 30.47 1.00e+00 1.00e+00 9.28e+02 angle pdb=" PB ATP D1102 " pdb=" O3B ATP D1102 " pdb=" PG ATP D1102 " ideal model delta sigma weight residual 139.87 109.46 30.41 1.00e+00 1.00e+00 9.25e+02 angle pdb=" PA ATP D1102 " pdb=" O3A ATP D1102 " pdb=" PB ATP D1102 " ideal model delta sigma weight residual 136.83 111.34 25.49 1.00e+00 1.00e+00 6.50e+02 angle pdb=" PA ATP C1102 " pdb=" O3A ATP C1102 " pdb=" PB ATP C1102 " ideal model delta sigma weight residual 136.83 111.39 25.44 1.00e+00 1.00e+00 6.47e+02 angle pdb=" C5' ATP D1102 " pdb=" O5' ATP D1102 " pdb=" PA ATP D1102 " ideal model delta sigma weight residual 121.27 113.22 8.05 1.00e+00 1.00e+00 6.48e+01 ... (remaining 24385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 10757 27.04 - 54.08: 180 54.08 - 81.12: 61 81.12 - 108.16: 12 108.16 - 135.20: 4 Dihedral angle restraints: 11014 sinusoidal: 4570 harmonic: 6444 Sorted by residual: dihedral pdb=" CA GLN C 624 " pdb=" C GLN C 624 " pdb=" N PRO C 625 " pdb=" CA PRO C 625 " ideal model delta harmonic sigma weight residual 180.00 151.50 28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" C14 7YN C1101 " pdb=" N15 7YN C1101 " pdb=" S17 7YN C1101 " pdb=" O18 7YN C1101 " ideal model delta sinusoidal sigma weight residual 196.22 61.02 135.20 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C14 7YN D1101 " pdb=" N15 7YN D1101 " pdb=" S17 7YN D1101 " pdb=" O18 7YN D1101 " ideal model delta sinusoidal sigma weight residual 196.22 64.01 132.21 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 11011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1554 0.044 - 0.088: 728 0.088 - 0.131: 332 0.131 - 0.175: 105 0.175 - 0.219: 9 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CA PRO A 134 " pdb=" N PRO A 134 " pdb=" C PRO A 134 " pdb=" CB PRO A 134 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C4' ATP C1102 " pdb=" C3' ATP C1102 " pdb=" C5' ATP C1102 " pdb=" O4' ATP C1102 " both_signs ideal model delta sigma weight residual False -2.49 -2.69 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" C4' ATP D1102 " pdb=" C3' ATP D1102 " pdb=" C5' ATP D1102 " pdb=" O4' ATP D1102 " both_signs ideal model delta sigma weight residual False -2.49 -2.69 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2725 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7YN D1101 " -0.077 2.00e-02 2.50e+03 2.02e-01 1.32e+03 pdb=" C02 7YN D1101 " -0.078 2.00e-02 2.50e+03 pdb=" C03 7YN D1101 " -0.103 2.00e-02 2.50e+03 pdb=" C04 7YN D1101 " -0.078 2.00e-02 2.50e+03 pdb=" C05 7YN D1101 " -0.124 2.00e-02 2.50e+03 pdb=" C06 7YN D1101 " -0.093 2.00e-02 2.50e+03 pdb=" C07 7YN D1101 " -0.059 2.00e-02 2.50e+03 pdb=" C08 7YN D1101 " 0.458 2.00e-02 2.50e+03 pdb=" C09 7YN D1101 " -0.096 2.00e-02 2.50e+03 pdb=" C10 7YN D1101 " -0.060 2.00e-02 2.50e+03 pdb=" C11 7YN D1101 " 0.483 2.00e-02 2.50e+03 pdb=" C12 7YN D1101 " -0.118 2.00e-02 2.50e+03 pdb=" N13 7YN D1101 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN C1101 " 0.075 2.00e-02 2.50e+03 1.97e-01 1.27e+03 pdb=" C02 7YN C1101 " 0.074 2.00e-02 2.50e+03 pdb=" C03 7YN C1101 " 0.108 2.00e-02 2.50e+03 pdb=" C04 7YN C1101 " 0.079 2.00e-02 2.50e+03 pdb=" C05 7YN C1101 " 0.105 2.00e-02 2.50e+03 pdb=" C06 7YN C1101 " 0.103 2.00e-02 2.50e+03 pdb=" C07 7YN C1101 " 0.065 2.00e-02 2.50e+03 pdb=" C08 7YN C1101 " -0.459 2.00e-02 2.50e+03 pdb=" C09 7YN C1101 " 0.096 2.00e-02 2.50e+03 pdb=" C10 7YN C1101 " 0.058 2.00e-02 2.50e+03 pdb=" C11 7YN C1101 " -0.463 2.00e-02 2.50e+03 pdb=" C12 7YN C1101 " 0.105 2.00e-02 2.50e+03 pdb=" N13 7YN C1101 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP C1102 " 0.222 2.00e-02 2.50e+03 8.84e-02 2.15e+02 pdb=" C2 ATP C1102 " -0.031 2.00e-02 2.50e+03 pdb=" C4 ATP C1102 " -0.062 2.00e-02 2.50e+03 pdb=" C5 ATP C1102 " -0.006 2.00e-02 2.50e+03 pdb=" C6 ATP C1102 " 0.036 2.00e-02 2.50e+03 pdb=" C8 ATP C1102 " -0.090 2.00e-02 2.50e+03 pdb=" N1 ATP C1102 " 0.028 2.00e-02 2.50e+03 pdb=" N3 ATP C1102 " -0.074 2.00e-02 2.50e+03 pdb=" N6 ATP C1102 " 0.089 2.00e-02 2.50e+03 pdb=" N7 ATP C1102 " -0.024 2.00e-02 2.50e+03 pdb=" N9 ATP C1102 " -0.089 2.00e-02 2.50e+03 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 6684 2.87 - 3.38: 17808 3.38 - 3.89: 30520 3.89 - 4.39: 36495 4.39 - 4.90: 57294 Nonbonded interactions: 148801 Sorted by model distance: nonbonded pdb=" OG SER B 187 " pdb=" OG1 THR B 190 " model vdw 2.369 3.040 nonbonded pdb=" OD2 ASP A 78 " pdb=" NZ LYS A 189 " model vdw 2.382 3.120 nonbonded pdb=" O ASP C 949 " pdb=" C ASN C 950 " model vdw 2.399 3.270 nonbonded pdb=" OD2 ASP B 78 " pdb=" NZ LYS B 189 " model vdw 2.400 3.120 nonbonded pdb=" OG SER D 555 " pdb=" N ARG D 556 " model vdw 2.403 3.120 ... (remaining 148796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.790 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.012 0.181 18064 Z= 0.693 Angle : 1.263 30.465 24390 Z= 0.904 Chirality : 0.062 0.219 2728 Planarity : 0.007 0.202 3076 Dihedral : 12.199 135.195 6834 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 1.15 % Allowed : 3.03 % Favored : 95.82 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % 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 are not related in a simple way. whole: -0.38 (0.17), residues: 2176 helix: -0.18 (0.15), residues: 1024 sheet: -0.51 (0.31), residues: 262 loop : -0.00 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.025 0.004 TYR D 443 PHE 0.020 0.003 PHE C 502 TRP 0.023 0.004 TRP D 611 HIS 0.006 0.001 HIS C 916 Details of bonding type rmsd covalent geometry : bond 0.01250 (18064) covalent geometry : angle 1.26254 (24390) hydrogen bonds : bond 0.17600 ( 769) hydrogen bonds : angle 6.58618 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.7339 (m-80) cc_final: 0.6927 (m-80) REVERT: A 62 LEU cc_start: 0.7750 (tp) cc_final: 0.3171 (mt) REVERT: A 65 VAL cc_start: 0.8073 (t) cc_final: 0.0643 (t) REVERT: A 109 ILE cc_start: 0.8069 (mt) cc_final: 0.6531 (mt) REVERT: A 140 LYS cc_start: 0.9343 (tttp) cc_final: 0.9104 (ttpt) REVERT: A 142 PHE cc_start: 0.8829 (t80) cc_final: 0.8526 (t80) REVERT: A 158 MET cc_start: 0.6681 (mtm) cc_final: 0.6202 (mtm) REVERT: A 186 PHE cc_start: 0.8800 (m-80) cc_final: 0.8340 (m-80) REVERT: A 226 LEU cc_start: 0.9685 (tp) cc_final: 0.9392 (tp) REVERT: A 236 PHE cc_start: 0.9030 (m-80) cc_final: 0.8773 (m-80) REVERT: A 247 CYS cc_start: 0.8516 (m) cc_final: 0.8229 (t) REVERT: A 286 THR cc_start: 0.9282 (m) cc_final: 0.8879 (t) REVERT: B 34 PHE cc_start: 0.6378 (m-80) cc_final: 0.6048 (m-80) REVERT: B 62 LEU cc_start: 0.7957 (tp) cc_final: 0.3796 (mp) REVERT: B 65 VAL cc_start: 0.8228 (t) cc_final: 0.2226 (t) REVERT: B 104 ASP cc_start: 0.9176 (m-30) cc_final: 0.8963 (t70) REVERT: B 176 LYS cc_start: 0.8552 (mttt) cc_final: 0.8332 (mtpp) REVERT: B 226 LEU cc_start: 0.9642 (tp) cc_final: 0.9356 (tt) REVERT: B 286 THR cc_start: 0.9264 (m) cc_final: 0.8887 (t) REVERT: C 230 ILE cc_start: 0.9210 (mm) cc_final: 0.8900 (mt) REVERT: C 248 LEU cc_start: 0.8082 (tp) cc_final: 0.7391 (mm) REVERT: C 521 ILE cc_start: 0.9156 (pt) cc_final: 0.8635 (mm) REVERT: C 536 LEU cc_start: 0.8468 (mt) cc_final: 0.8192 (pp) REVERT: C 591 TYR cc_start: 0.6877 (m-80) cc_final: 0.6472 (m-10) REVERT: C 637 MET cc_start: 0.8613 (ttm) cc_final: 0.8358 (ttm) REVERT: C 642 PHE cc_start: 0.8475 (t80) cc_final: 0.7625 (t80) REVERT: C 665 VAL cc_start: 0.9590 (t) cc_final: 0.9372 (p) REVERT: C 807 ASP cc_start: 0.8493 (m-30) cc_final: 0.8180 (t70) REVERT: C 846 ASP cc_start: 0.8354 (m-30) cc_final: 0.7832 (t0) REVERT: C 943 LEU cc_start: 0.9266 (tp) cc_final: 0.8958 (tt) REVERT: C 1021 LEU cc_start: 0.9609 (tp) cc_final: 0.9362 (mm) REVERT: C 1025 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8729 (mttp) REVERT: D 230 ILE cc_start: 0.9142 (mm) cc_final: 0.8837 (mt) REVERT: D 240 MET cc_start: 0.8651 (mmm) cc_final: 0.7986 (mmt) REVERT: D 248 LEU cc_start: 0.8089 (tp) cc_final: 0.7723 (mm) REVERT: D 508 PHE cc_start: 0.8130 (m-80) cc_final: 0.7861 (m-10) REVERT: D 521 ILE cc_start: 0.9310 (pt) cc_final: 0.8976 (tp) REVERT: D 591 TYR cc_start: 0.6880 (m-80) cc_final: 0.6650 (m-10) REVERT: D 595 LYS cc_start: 0.8643 (tptt) cc_final: 0.8433 (tptp) REVERT: D 624 GLN cc_start: 0.6675 (mp10) cc_final: 0.6399 (mp10) REVERT: D 807 ASP cc_start: 0.8625 (m-30) cc_final: 0.8235 (t70) REVERT: D 846 ASP cc_start: 0.8290 (m-30) cc_final: 0.7836 (t0) REVERT: D 957 CYS cc_start: 0.8165 (p) cc_final: 0.7551 (p) REVERT: D 961 LEU cc_start: 0.9490 (mt) cc_final: 0.9082 (mt) REVERT: D 1021 LEU cc_start: 0.9592 (tp) cc_final: 0.9361 (mm) outliers start: 1 outliers final: 1 residues processed: 410 average time/residue: 0.1219 time to fit residues: 74.5802 Evaluate side-chains 213 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN B 252 GLN C 269 GLN C1001 GLN D 622 GLN ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.079742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.062876 restraints weight = 77430.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064882 restraints weight = 44773.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066250 restraints weight = 30735.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.067043 restraints weight = 23745.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.067387 restraints weight = 20241.506| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 18064 Z= 0.155 Angle : 0.643 10.111 24390 Z= 0.333 Chirality : 0.041 0.207 2728 Planarity : 0.004 0.029 3076 Dihedral : 10.022 147.768 2474 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.95 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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 are not related in a simple way. whole: 0.43 (0.18), residues: 2176 helix: 0.80 (0.16), residues: 1016 sheet: -0.28 (0.33), residues: 248 loop : 0.03 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 294 TYR 0.022 0.002 TYR C 136 PHE 0.031 0.002 PHE C 502 TRP 0.007 0.001 TRP C 478 HIS 0.004 0.001 HIS D 784 Details of bonding type rmsd covalent geometry : bond 0.00336 (18064) covalent geometry : angle 0.64301 (24390) hydrogen bonds : bond 0.05597 ( 769) hydrogen bonds : angle 4.94604 ( 2148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8296 (tmm) cc_final: 0.8006 (ppp) REVERT: A 109 ILE cc_start: 0.8832 (mt) cc_final: 0.8129 (mt) REVERT: A 112 GLU cc_start: 0.7634 (tt0) cc_final: 0.7315 (tm-30) REVERT: A 140 LYS cc_start: 0.8971 (tttp) cc_final: 0.8744 (ttpt) REVERT: A 142 PHE cc_start: 0.8495 (t80) cc_final: 0.8286 (t80) REVERT: B 26 MET cc_start: 0.7853 (mmm) cc_final: 0.7464 (mpp) REVERT: B 63 MET cc_start: 0.8467 (tmm) cc_final: 0.8131 (ppp) REVERT: B 229 MET cc_start: 0.9076 (mtp) cc_final: 0.8828 (mtp) REVERT: B 263 TYR cc_start: 0.8453 (m-80) cc_final: 0.8194 (m-80) REVERT: C 205 MET cc_start: 0.8029 (ttp) cc_final: 0.7502 (tpp) REVERT: C 230 ILE cc_start: 0.9204 (mm) cc_final: 0.8895 (mt) REVERT: C 636 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8251 (tp30) REVERT: C 665 VAL cc_start: 0.9377 (t) cc_final: 0.9042 (p) REVERT: C 742 SER cc_start: 0.8141 (m) cc_final: 0.7904 (p) REVERT: C 943 LEU cc_start: 0.9247 (tp) cc_final: 0.8940 (tt) REVERT: C 1025 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8604 (mttp) REVERT: D 205 MET cc_start: 0.7578 (ttp) cc_final: 0.7020 (tpp) REVERT: D 230 ILE cc_start: 0.9174 (mm) cc_final: 0.8824 (mt) REVERT: D 240 MET cc_start: 0.8495 (mmm) cc_final: 0.8090 (mmt) REVERT: D 508 PHE cc_start: 0.8343 (m-80) cc_final: 0.8136 (m-10) REVERT: D 595 LYS cc_start: 0.8306 (tptt) cc_final: 0.8066 (tptp) REVERT: D 636 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8127 (tp30) REVERT: D 640 GLU cc_start: 0.8049 (pp20) cc_final: 0.7839 (pp20) REVERT: D 1025 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8816 (mmtp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1149 time to fit residues: 50.3784 Evaluate side-chains 174 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 73 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 60 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 108 ASN B 108 ASN C 360 HIS C 845 GLN D 824 HIS ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.078425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.061787 restraints weight = 76969.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.063757 restraints weight = 44033.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065084 restraints weight = 30190.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065856 restraints weight = 23343.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066485 restraints weight = 19838.480| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18064 Z= 0.146 Angle : 0.587 10.227 24390 Z= 0.303 Chirality : 0.039 0.144 2728 Planarity : 0.004 0.031 3076 Dihedral : 9.997 148.685 2474 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.46 % Favored : 95.08 % Rotamer: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.58 % 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 are not related in a simple way. whole: 0.39 (0.19), residues: 2176 helix: 0.91 (0.17), residues: 1004 sheet: -0.63 (0.32), residues: 266 loop : -0.04 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 779 TYR 0.011 0.001 TYR A 49 PHE 0.043 0.002 PHE C 382 TRP 0.010 0.001 TRP C 243 HIS 0.004 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00314 (18064) covalent geometry : angle 0.58707 (24390) hydrogen bonds : bond 0.04594 ( 769) hydrogen bonds : angle 4.65272 ( 2148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8006 (tmm) cc_final: 0.7672 (tmm) REVERT: A 109 ILE cc_start: 0.8771 (mt) cc_final: 0.8483 (mt) REVERT: A 112 GLU cc_start: 0.7620 (tt0) cc_final: 0.7272 (tm-30) REVERT: B 28 TYR cc_start: 0.6585 (m-10) cc_final: 0.6385 (m-10) REVERT: B 63 MET cc_start: 0.7877 (tmm) cc_final: 0.7666 (tmm) REVERT: B 263 TYR cc_start: 0.8385 (m-80) cc_final: 0.8165 (m-80) REVERT: C 230 ILE cc_start: 0.9285 (mm) cc_final: 0.8890 (mt) REVERT: C 600 ILE cc_start: 0.9156 (mm) cc_final: 0.8639 (tp) REVERT: C 636 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8317 (tp30) REVERT: C 665 VAL cc_start: 0.9469 (t) cc_final: 0.9049 (p) REVERT: C 943 LEU cc_start: 0.9210 (tp) cc_final: 0.8919 (tt) REVERT: D 230 ILE cc_start: 0.9224 (mm) cc_final: 0.8840 (mt) REVERT: D 240 MET cc_start: 0.8574 (mmm) cc_final: 0.8185 (mmt) REVERT: D 636 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8096 (tp30) REVERT: D 807 ASP cc_start: 0.8410 (t70) cc_final: 0.8073 (t0) REVERT: D 957 CYS cc_start: 0.8360 (p) cc_final: 0.7690 (p) REVERT: D 987 MET cc_start: 0.8410 (ppp) cc_final: 0.8161 (mmm) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1181 time to fit residues: 42.8959 Evaluate side-chains 164 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 169 optimal weight: 0.0980 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 164 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 HIS C 674 HIS D 215 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.077292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060676 restraints weight = 77887.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.062561 restraints weight = 45317.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.063862 restraints weight = 31311.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.064518 restraints weight = 24496.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065174 restraints weight = 20924.809| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18064 Z= 0.152 Angle : 0.578 9.788 24390 Z= 0.295 Chirality : 0.040 0.298 2728 Planarity : 0.004 0.034 3076 Dihedral : 10.089 149.081 2474 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.60 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 2176 helix: 0.96 (0.17), residues: 994 sheet: -0.77 (0.32), residues: 264 loop : -0.09 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 294 TYR 0.010 0.001 TYR A 263 PHE 0.041 0.002 PHE C 502 TRP 0.010 0.001 TRP C 478 HIS 0.006 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00332 (18064) covalent geometry : angle 0.57817 (24390) hydrogen bonds : bond 0.04265 ( 769) hydrogen bonds : angle 4.52910 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8764 (mt) cc_final: 0.8031 (mt) REVERT: A 112 GLU cc_start: 0.7679 (tt0) cc_final: 0.7317 (tm-30) REVERT: A 158 MET cc_start: 0.6134 (mmm) cc_final: 0.5875 (mmm) REVERT: A 228 GLU cc_start: 0.9064 (tp30) cc_final: 0.8813 (mm-30) REVERT: B 158 MET cc_start: 0.6976 (mmm) cc_final: 0.6286 (mmt) REVERT: B 219 ILE cc_start: 0.9260 (mm) cc_final: 0.8949 (mm) REVERT: B 263 TYR cc_start: 0.8471 (m-80) cc_final: 0.8218 (m-80) REVERT: C 230 ILE cc_start: 0.9298 (mm) cc_final: 0.8931 (mt) REVERT: C 600 ILE cc_start: 0.9189 (mm) cc_final: 0.8687 (tp) REVERT: C 665 VAL cc_start: 0.9440 (t) cc_final: 0.9066 (p) REVERT: C 943 LEU cc_start: 0.9226 (tp) cc_final: 0.9014 (tp) REVERT: D 230 ILE cc_start: 0.9251 (mm) cc_final: 0.8899 (mt) REVERT: D 382 PHE cc_start: 0.8422 (m-80) cc_final: 0.8061 (m-80) REVERT: D 636 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8225 (tp30) REVERT: D 807 ASP cc_start: 0.8496 (t70) cc_final: 0.8107 (t0) REVERT: D 810 LEU cc_start: 0.8457 (mt) cc_final: 0.8072 (mt) REVERT: D 957 CYS cc_start: 0.8385 (p) cc_final: 0.7594 (p) REVERT: D 961 LEU cc_start: 0.9478 (mt) cc_final: 0.9066 (mt) REVERT: D 987 MET cc_start: 0.8421 (ppp) cc_final: 0.8175 (mmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1037 time to fit residues: 34.9348 Evaluate side-chains 155 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 64 optimal weight: 7.9990 chunk 186 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN C 360 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.077317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059990 restraints weight = 76483.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.062065 restraints weight = 41924.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.063492 restraints weight = 28237.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064436 restraints weight = 21557.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064888 restraints weight = 18063.123| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18064 Z= 0.118 Angle : 0.551 7.878 24390 Z= 0.281 Chirality : 0.039 0.221 2728 Planarity : 0.003 0.033 3076 Dihedral : 10.102 150.067 2474 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.92 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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 are not related in a simple way. whole: 0.33 (0.19), residues: 2176 helix: 0.97 (0.17), residues: 1000 sheet: -0.76 (0.33), residues: 262 loop : -0.17 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 294 TYR 0.012 0.001 TYR C 136 PHE 0.045 0.002 PHE D 502 TRP 0.009 0.001 TRP C 243 HIS 0.004 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00254 (18064) covalent geometry : angle 0.55148 (24390) hydrogen bonds : bond 0.03907 ( 769) hydrogen bonds : angle 4.40068 ( 2148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7634 (tt0) cc_final: 0.7376 (tm-30) REVERT: A 158 MET cc_start: 0.6404 (mmm) cc_final: 0.5904 (mmm) REVERT: A 219 ILE cc_start: 0.9137 (mm) cc_final: 0.8881 (mm) REVERT: A 290 ASP cc_start: 0.8524 (t0) cc_final: 0.8239 (p0) REVERT: B 63 MET cc_start: 0.8188 (ppp) cc_final: 0.7772 (tmm) REVERT: B 65 VAL cc_start: 0.7952 (t) cc_final: 0.7523 (t) REVERT: B 158 MET cc_start: 0.6875 (mmm) cc_final: 0.6664 (mmm) REVERT: B 219 ILE cc_start: 0.9184 (mm) cc_final: 0.8904 (mm) REVERT: B 263 TYR cc_start: 0.8490 (m-80) cc_final: 0.8254 (m-80) REVERT: C 230 ILE cc_start: 0.9290 (mm) cc_final: 0.8935 (mt) REVERT: C 382 PHE cc_start: 0.8477 (m-80) cc_final: 0.8189 (m-80) REVERT: C 636 GLU cc_start: 0.8726 (tp30) cc_final: 0.8336 (tp30) REVERT: C 665 VAL cc_start: 0.9436 (t) cc_final: 0.8929 (p) REVERT: C 669 CYS cc_start: 0.8934 (m) cc_final: 0.8695 (m) REVERT: C 846 ASP cc_start: 0.7989 (t0) cc_final: 0.7505 (t0) REVERT: C 943 LEU cc_start: 0.9202 (tp) cc_final: 0.8921 (tt) REVERT: C 961 LEU cc_start: 0.9375 (mt) cc_final: 0.9088 (mt) REVERT: C 1008 MET cc_start: 0.7593 (mmm) cc_final: 0.7365 (mmm) REVERT: D 230 ILE cc_start: 0.9220 (mm) cc_final: 0.8855 (mt) REVERT: D 368 VAL cc_start: 0.9069 (t) cc_final: 0.8678 (m) REVERT: D 382 PHE cc_start: 0.8395 (m-80) cc_final: 0.8151 (m-80) REVERT: D 532 MET cc_start: 0.8765 (ttm) cc_final: 0.8543 (tpp) REVERT: D 636 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8122 (tp30) REVERT: D 807 ASP cc_start: 0.8526 (t70) cc_final: 0.8104 (t0) REVERT: D 810 LEU cc_start: 0.8482 (mt) cc_final: 0.8128 (mt) REVERT: D 864 GLU cc_start: 0.7866 (tp30) cc_final: 0.7455 (tp30) REVERT: D 957 CYS cc_start: 0.8521 (p) cc_final: 0.7585 (p) REVERT: D 961 LEU cc_start: 0.9385 (mt) cc_final: 0.8924 (mt) REVERT: D 987 MET cc_start: 0.8483 (ppp) cc_final: 0.8184 (mmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1102 time to fit residues: 36.8404 Evaluate side-chains 165 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 44 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS C 260 HIS C 360 HIS C 883 GLN D 165 ASN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 995 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.073972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056625 restraints weight = 77283.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.058549 restraints weight = 43931.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059800 restraints weight = 30109.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.060516 restraints weight = 23630.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.061177 restraints weight = 20300.057| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18064 Z= 0.229 Angle : 0.647 7.749 24390 Z= 0.325 Chirality : 0.041 0.182 2728 Planarity : 0.004 0.044 3076 Dihedral : 10.424 149.835 2474 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.84 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 are not related in a simple way. whole: -0.07 (0.19), residues: 2176 helix: 0.78 (0.17), residues: 1022 sheet: -1.13 (0.31), residues: 274 loop : -0.53 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 779 TYR 0.016 0.002 TYR A 49 PHE 0.035 0.002 PHE C 502 TRP 0.018 0.001 TRP C 478 HIS 0.007 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00504 (18064) covalent geometry : angle 0.64681 (24390) hydrogen bonds : bond 0.04305 ( 769) hydrogen bonds : angle 4.63513 ( 2148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7916 (tt0) cc_final: 0.7459 (tm-30) REVERT: A 158 MET cc_start: 0.6558 (mmm) cc_final: 0.6095 (mmt) REVERT: A 219 ILE cc_start: 0.9285 (mm) cc_final: 0.9047 (mm) REVERT: A 228 GLU cc_start: 0.9156 (tp30) cc_final: 0.8882 (mm-30) REVERT: A 295 MET cc_start: 0.8846 (mmm) cc_final: 0.8646 (mmp) REVERT: B 63 MET cc_start: 0.8137 (ppp) cc_final: 0.7699 (tmm) REVERT: B 65 VAL cc_start: 0.8035 (t) cc_final: 0.7554 (t) REVERT: B 158 MET cc_start: 0.6939 (mmm) cc_final: 0.6114 (mmm) REVERT: B 186 PHE cc_start: 0.7385 (m-10) cc_final: 0.7084 (m-80) REVERT: B 219 ILE cc_start: 0.9308 (mm) cc_final: 0.9029 (mm) REVERT: B 263 TYR cc_start: 0.8666 (m-80) cc_final: 0.8444 (m-80) REVERT: B 290 ASP cc_start: 0.8461 (t0) cc_final: 0.8210 (p0) REVERT: C 230 ILE cc_start: 0.9363 (mm) cc_final: 0.8982 (mt) REVERT: C 636 GLU cc_start: 0.8685 (tp30) cc_final: 0.8411 (tp30) REVERT: C 665 VAL cc_start: 0.9361 (t) cc_final: 0.9025 (p) REVERT: C 669 CYS cc_start: 0.9004 (m) cc_final: 0.8603 (m) REVERT: C 846 ASP cc_start: 0.8090 (t0) cc_final: 0.7591 (t0) REVERT: C 987 MET cc_start: 0.8281 (mmt) cc_final: 0.8066 (mmt) REVERT: D 230 ILE cc_start: 0.9297 (mm) cc_final: 0.8919 (mt) REVERT: D 382 PHE cc_start: 0.8344 (m-80) cc_final: 0.8085 (m-80) REVERT: D 484 PHE cc_start: 0.8625 (m-80) cc_final: 0.8409 (m-10) REVERT: D 636 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8194 (tp30) REVERT: D 669 CYS cc_start: 0.8963 (m) cc_final: 0.8755 (m) REVERT: D 807 ASP cc_start: 0.8576 (t70) cc_final: 0.8185 (t0) REVERT: D 864 GLU cc_start: 0.7932 (tp30) cc_final: 0.7614 (tp30) REVERT: D 957 CYS cc_start: 0.8630 (p) cc_final: 0.7922 (p) REVERT: D 987 MET cc_start: 0.8502 (ppp) cc_final: 0.8301 (mmt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1134 time to fit residues: 34.2789 Evaluate side-chains 151 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 149 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 188 optimal weight: 0.3980 chunk 147 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 HIS D 165 ASN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.076401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059488 restraints weight = 76670.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.061149 restraints weight = 43142.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.062713 restraints weight = 27618.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062775 restraints weight = 22769.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.062867 restraints weight = 20567.589| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18064 Z= 0.115 Angle : 0.552 8.133 24390 Z= 0.278 Chirality : 0.039 0.152 2728 Planarity : 0.003 0.039 3076 Dihedral : 10.393 152.030 2474 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.96 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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 are not related in a simple way. whole: 0.19 (0.19), residues: 2176 helix: 1.03 (0.17), residues: 1014 sheet: -1.20 (0.32), residues: 270 loop : -0.35 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 294 TYR 0.021 0.001 TYR C 632 PHE 0.037 0.002 PHE C 382 TRP 0.008 0.001 TRP C 478 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00242 (18064) covalent geometry : angle 0.55186 (24390) hydrogen bonds : bond 0.03705 ( 769) hydrogen bonds : angle 4.36159 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7836 (tt0) cc_final: 0.7459 (tm-30) REVERT: A 140 LYS cc_start: 0.9105 (tttp) cc_final: 0.8765 (ttpt) REVERT: A 158 MET cc_start: 0.6516 (mmm) cc_final: 0.5478 (mmt) REVERT: A 219 ILE cc_start: 0.9185 (mm) cc_final: 0.8931 (mm) REVERT: B 63 MET cc_start: 0.8252 (ppp) cc_final: 0.7767 (tmm) REVERT: B 65 VAL cc_start: 0.8029 (t) cc_final: 0.7461 (t) REVERT: B 152 MET cc_start: 0.8941 (ttm) cc_final: 0.8699 (ttt) REVERT: B 158 MET cc_start: 0.6950 (mmm) cc_final: 0.5665 (mmt) REVERT: B 219 ILE cc_start: 0.9206 (mm) cc_final: 0.8959 (mm) REVERT: B 263 TYR cc_start: 0.8565 (m-80) cc_final: 0.8346 (m-80) REVERT: B 269 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8650 (mp10) REVERT: C 205 MET cc_start: 0.7844 (ttm) cc_final: 0.7495 (tpp) REVERT: C 208 LEU cc_start: 0.9283 (mt) cc_final: 0.9065 (mt) REVERT: C 230 ILE cc_start: 0.9324 (mm) cc_final: 0.8989 (mt) REVERT: C 239 MET cc_start: 0.8867 (ttp) cc_final: 0.8556 (ttp) REVERT: C 405 LEU cc_start: 0.9074 (tp) cc_final: 0.8748 (tt) REVERT: C 409 CYS cc_start: 0.8345 (m) cc_final: 0.8128 (m) REVERT: C 636 GLU cc_start: 0.8714 (tp30) cc_final: 0.8415 (tp30) REVERT: C 665 VAL cc_start: 0.9393 (t) cc_final: 0.9032 (p) REVERT: C 669 CYS cc_start: 0.8880 (m) cc_final: 0.8634 (m) REVERT: C 846 ASP cc_start: 0.8216 (t0) cc_final: 0.7635 (t0) REVERT: D 230 ILE cc_start: 0.9255 (mm) cc_final: 0.8907 (mt) REVERT: D 256 LEU cc_start: 0.9328 (mt) cc_final: 0.9082 (mt) REVERT: D 277 MET cc_start: 0.8145 (mpp) cc_final: 0.7779 (ttp) REVERT: D 382 PHE cc_start: 0.8509 (m-80) cc_final: 0.8104 (m-80) REVERT: D 669 CYS cc_start: 0.8833 (m) cc_final: 0.8607 (m) REVERT: D 807 ASP cc_start: 0.8532 (t70) cc_final: 0.8108 (t0) REVERT: D 864 GLU cc_start: 0.7937 (tp30) cc_final: 0.7647 (tp30) REVERT: D 957 CYS cc_start: 0.8732 (p) cc_final: 0.7986 (p) REVERT: D 987 MET cc_start: 0.8558 (ppp) cc_final: 0.8296 (mmt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1167 time to fit residues: 38.7409 Evaluate side-chains 160 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 52 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 129 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.075931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058294 restraints weight = 77433.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.060298 restraints weight = 43468.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061656 restraints weight = 29693.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.062540 restraints weight = 22972.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.062983 restraints weight = 19463.250| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18064 Z= 0.125 Angle : 0.568 10.038 24390 Z= 0.285 Chirality : 0.039 0.184 2728 Planarity : 0.003 0.034 3076 Dihedral : 10.357 151.123 2474 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.15 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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 are not related in a simple way. whole: 0.18 (0.19), residues: 2176 helix: 1.03 (0.17), residues: 1016 sheet: -1.25 (0.32), residues: 270 loop : -0.37 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 294 TYR 0.015 0.001 TYR D 140 PHE 0.042 0.002 PHE C 502 TRP 0.008 0.001 TRP C 478 HIS 0.004 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00275 (18064) covalent geometry : angle 0.56795 (24390) hydrogen bonds : bond 0.03732 ( 769) hydrogen bonds : angle 4.37263 ( 2148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7866 (tt0) cc_final: 0.7572 (tm-30) REVERT: A 158 MET cc_start: 0.6705 (mmm) cc_final: 0.6240 (mmm) REVERT: A 219 ILE cc_start: 0.9179 (mm) cc_final: 0.8930 (mm) REVERT: A 295 MET cc_start: 0.8843 (mmm) cc_final: 0.8601 (mmp) REVERT: B 63 MET cc_start: 0.8273 (ppp) cc_final: 0.7767 (tmm) REVERT: B 152 MET cc_start: 0.8957 (ttm) cc_final: 0.8708 (ttt) REVERT: B 158 MET cc_start: 0.6898 (mmm) cc_final: 0.5624 (mmt) REVERT: B 219 ILE cc_start: 0.9193 (mm) cc_final: 0.8955 (mm) REVERT: B 263 TYR cc_start: 0.8618 (m-80) cc_final: 0.8400 (m-80) REVERT: C 205 MET cc_start: 0.7747 (ttm) cc_final: 0.7504 (tpp) REVERT: C 208 LEU cc_start: 0.9292 (mt) cc_final: 0.9084 (mt) REVERT: C 230 ILE cc_start: 0.9324 (mm) cc_final: 0.8954 (mt) REVERT: C 239 MET cc_start: 0.8878 (ttp) cc_final: 0.8617 (ttp) REVERT: C 405 LEU cc_start: 0.9118 (tp) cc_final: 0.8779 (tt) REVERT: C 409 CYS cc_start: 0.8369 (m) cc_final: 0.8149 (m) REVERT: C 626 SER cc_start: 0.8660 (p) cc_final: 0.8154 (t) REVERT: C 636 GLU cc_start: 0.8707 (tp30) cc_final: 0.8441 (tp30) REVERT: C 665 VAL cc_start: 0.9453 (t) cc_final: 0.9103 (p) REVERT: C 669 CYS cc_start: 0.8991 (m) cc_final: 0.8675 (m) REVERT: C 846 ASP cc_start: 0.8162 (t0) cc_final: 0.7558 (t0) REVERT: C 987 MET cc_start: 0.8255 (tmm) cc_final: 0.7731 (mmt) REVERT: D 230 ILE cc_start: 0.9243 (mm) cc_final: 0.8878 (mt) REVERT: D 239 MET cc_start: 0.8907 (ttp) cc_final: 0.8681 (ttp) REVERT: D 256 LEU cc_start: 0.9319 (mt) cc_final: 0.8984 (mt) REVERT: D 382 PHE cc_start: 0.8336 (m-80) cc_final: 0.8081 (m-80) REVERT: D 405 LEU cc_start: 0.9067 (tp) cc_final: 0.8716 (tt) REVERT: D 409 CYS cc_start: 0.8268 (m) cc_final: 0.8054 (m) REVERT: D 532 MET cc_start: 0.8986 (tpp) cc_final: 0.8723 (tpp) REVERT: D 669 CYS cc_start: 0.8789 (m) cc_final: 0.8549 (m) REVERT: D 807 ASP cc_start: 0.8510 (t70) cc_final: 0.8092 (t0) REVERT: D 864 GLU cc_start: 0.7925 (tp30) cc_final: 0.7650 (tp30) REVERT: D 957 CYS cc_start: 0.8687 (p) cc_final: 0.7914 (p) REVERT: D 987 MET cc_start: 0.8502 (ppp) cc_final: 0.8214 (mmm) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1225 time to fit residues: 39.3353 Evaluate side-chains 151 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 65 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS C 360 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN D 883 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.073750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057036 restraints weight = 77557.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058643 restraints weight = 43503.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.059417 restraints weight = 29641.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059626 restraints weight = 26522.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.059788 restraints weight = 24249.420| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18064 Z= 0.229 Angle : 0.658 10.564 24390 Z= 0.330 Chirality : 0.042 0.198 2728 Planarity : 0.004 0.033 3076 Dihedral : 10.577 150.578 2474 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.25 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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 are not related in a simple way. whole: -0.02 (0.19), residues: 2176 helix: 0.95 (0.17), residues: 1014 sheet: -1.46 (0.31), residues: 272 loop : -0.53 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 779 TYR 0.016 0.002 TYR A 202 PHE 0.025 0.002 PHE C 484 TRP 0.017 0.001 TRP C 478 HIS 0.008 0.001 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00500 (18064) covalent geometry : angle 0.65845 (24390) hydrogen bonds : bond 0.04149 ( 769) hydrogen bonds : angle 4.66403 ( 2148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8121 (tt0) cc_final: 0.7613 (tm-30) REVERT: A 158 MET cc_start: 0.6665 (mmm) cc_final: 0.6122 (mmm) REVERT: A 219 ILE cc_start: 0.9303 (mm) cc_final: 0.9069 (mm) REVERT: A 228 GLU cc_start: 0.9221 (tp30) cc_final: 0.8901 (mm-30) REVERT: A 263 TYR cc_start: 0.8738 (m-80) cc_final: 0.8522 (m-10) REVERT: A 295 MET cc_start: 0.8820 (mmm) cc_final: 0.8606 (mmp) REVERT: B 63 MET cc_start: 0.8143 (ppp) cc_final: 0.7931 (ppp) REVERT: B 158 MET cc_start: 0.6916 (mmm) cc_final: 0.6070 (mmt) REVERT: B 186 PHE cc_start: 0.7729 (m-80) cc_final: 0.7520 (m-10) REVERT: B 219 ILE cc_start: 0.9342 (mm) cc_final: 0.9100 (mm) REVERT: B 263 TYR cc_start: 0.8690 (m-80) cc_final: 0.8461 (m-80) REVERT: B 290 ASP cc_start: 0.8405 (t0) cc_final: 0.8204 (p0) REVERT: C 208 LEU cc_start: 0.9314 (mt) cc_final: 0.9090 (mt) REVERT: C 230 ILE cc_start: 0.9368 (mm) cc_final: 0.9013 (mt) REVERT: C 382 PHE cc_start: 0.8390 (m-80) cc_final: 0.8056 (m-80) REVERT: C 484 PHE cc_start: 0.8421 (m-10) cc_final: 0.8177 (m-10) REVERT: C 665 VAL cc_start: 0.9495 (t) cc_final: 0.9150 (p) REVERT: C 669 CYS cc_start: 0.9066 (m) cc_final: 0.8783 (m) REVERT: C 846 ASP cc_start: 0.8333 (t0) cc_final: 0.7748 (t0) REVERT: D 205 MET cc_start: 0.8244 (tpp) cc_final: 0.7675 (tpp) REVERT: D 208 LEU cc_start: 0.9448 (mt) cc_final: 0.9199 (mt) REVERT: D 230 ILE cc_start: 0.9322 (mm) cc_final: 0.8982 (mt) REVERT: D 382 PHE cc_start: 0.8407 (m-80) cc_final: 0.7922 (m-80) REVERT: D 484 PHE cc_start: 0.8870 (m-80) cc_final: 0.8460 (m-10) REVERT: D 532 MET cc_start: 0.8994 (tpp) cc_final: 0.8672 (tpp) REVERT: D 669 CYS cc_start: 0.8948 (m) cc_final: 0.8682 (m) REVERT: D 807 ASP cc_start: 0.8571 (t70) cc_final: 0.8172 (t0) REVERT: D 864 GLU cc_start: 0.7999 (tp30) cc_final: 0.7758 (tp30) REVERT: D 957 CYS cc_start: 0.8821 (p) cc_final: 0.8069 (p) REVERT: D 987 MET cc_start: 0.8632 (ppp) cc_final: 0.8325 (mmm) REVERT: D 1008 MET cc_start: 0.7109 (mmt) cc_final: 0.6766 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1198 time to fit residues: 35.9571 Evaluate side-chains 147 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 64 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN C 360 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.075872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.058359 restraints weight = 76125.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060357 restraints weight = 43213.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.061729 restraints weight = 29582.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.062458 restraints weight = 22792.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.063159 restraints weight = 19448.797| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18064 Z= 0.117 Angle : 0.590 11.212 24390 Z= 0.293 Chirality : 0.040 0.173 2728 Planarity : 0.003 0.039 3076 Dihedral : 10.487 151.006 2474 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.24 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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 are not related in a simple way. whole: 0.09 (0.19), residues: 2176 helix: 1.02 (0.17), residues: 1016 sheet: -1.40 (0.31), residues: 270 loop : -0.46 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 35 TYR 0.016 0.001 TYR A 202 PHE 0.022 0.002 PHE C 484 TRP 0.009 0.001 TRP D 478 HIS 0.006 0.001 HIS D 492 Details of bonding type rmsd covalent geometry : bond 0.00255 (18064) covalent geometry : angle 0.59034 (24390) hydrogen bonds : bond 0.03719 ( 769) hydrogen bonds : angle 4.41992 ( 2148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8052 (tt0) cc_final: 0.7657 (tm-30) REVERT: A 158 MET cc_start: 0.6743 (mmm) cc_final: 0.6290 (mmt) REVERT: A 263 TYR cc_start: 0.8740 (m-80) cc_final: 0.8523 (m-10) REVERT: A 295 MET cc_start: 0.8853 (mmm) cc_final: 0.8653 (mmp) REVERT: B 63 MET cc_start: 0.8204 (ppp) cc_final: 0.7657 (tmm) REVERT: B 152 MET cc_start: 0.8963 (ttm) cc_final: 0.8743 (ttt) REVERT: B 158 MET cc_start: 0.6906 (mmm) cc_final: 0.5646 (mmt) REVERT: B 219 ILE cc_start: 0.9251 (mm) cc_final: 0.9008 (mm) REVERT: B 263 TYR cc_start: 0.8616 (m-80) cc_final: 0.8401 (m-80) REVERT: C 230 ILE cc_start: 0.9314 (mm) cc_final: 0.8983 (mt) REVERT: C 484 PHE cc_start: 0.8191 (m-10) cc_final: 0.7975 (m-10) REVERT: C 626 SER cc_start: 0.8523 (p) cc_final: 0.8035 (t) REVERT: C 665 VAL cc_start: 0.9442 (t) cc_final: 0.9088 (p) REVERT: C 669 CYS cc_start: 0.8945 (m) cc_final: 0.8708 (m) REVERT: C 987 MET cc_start: 0.8135 (mmt) cc_final: 0.7866 (tmm) REVERT: D 205 MET cc_start: 0.8157 (tpp) cc_final: 0.7640 (tpp) REVERT: D 230 ILE cc_start: 0.9245 (mm) cc_final: 0.8898 (mt) REVERT: D 382 PHE cc_start: 0.8011 (m-80) cc_final: 0.7753 (m-80) REVERT: D 409 CYS cc_start: 0.8205 (t) cc_final: 0.7732 (t) REVERT: D 484 PHE cc_start: 0.8672 (m-80) cc_final: 0.8366 (m-10) REVERT: D 532 MET cc_start: 0.8983 (tpp) cc_final: 0.8631 (tpp) REVERT: D 636 GLU cc_start: 0.8790 (tp30) cc_final: 0.8480 (tp30) REVERT: D 647 MET cc_start: 0.8597 (tpp) cc_final: 0.8369 (ttm) REVERT: D 669 CYS cc_start: 0.8719 (m) cc_final: 0.8274 (m) REVERT: D 807 ASP cc_start: 0.8527 (t70) cc_final: 0.8127 (t0) REVERT: D 864 GLU cc_start: 0.7952 (tp30) cc_final: 0.7712 (tp30) REVERT: D 957 CYS cc_start: 0.8653 (p) cc_final: 0.7845 (p) REVERT: D 975 SER cc_start: 0.9129 (t) cc_final: 0.8927 (t) REVERT: D 987 MET cc_start: 0.8457 (ppp) cc_final: 0.8213 (mmm) REVERT: D 1008 MET cc_start: 0.6820 (mmt) cc_final: 0.6500 (mmm) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1117 time to fit residues: 35.7432 Evaluate side-chains 161 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 138 optimal weight: 0.2980 chunk 91 optimal weight: 0.0570 chunk 177 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 17 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.076494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.058990 restraints weight = 77008.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.061010 restraints weight = 43426.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.062314 restraints weight = 29637.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.063089 restraints weight = 23005.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.063812 restraints weight = 19552.092| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18064 Z= 0.113 Angle : 0.590 11.384 24390 Z= 0.293 Chirality : 0.040 0.205 2728 Planarity : 0.003 0.037 3076 Dihedral : 10.396 151.393 2474 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.42 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 2176 helix: 0.99 (0.17), residues: 1018 sheet: -1.43 (0.31), residues: 270 loop : -0.41 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 35 TYR 0.013 0.001 TYR A 202 PHE 0.041 0.002 PHE C 382 TRP 0.006 0.001 TRP D 478 HIS 0.006 0.001 HIS D 492 Details of bonding type rmsd covalent geometry : bond 0.00243 (18064) covalent geometry : angle 0.58977 (24390) hydrogen bonds : bond 0.03615 ( 769) hydrogen bonds : angle 4.38049 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.25 seconds wall clock time: 46 minutes 32.92 seconds (2792.92 seconds total)