Starting phenix.real_space_refine on Sun Aug 24 06:59:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxn_40855/08_2025/8sxn_40855_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxn_40855/08_2025/8sxn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sxn_40855/08_2025/8sxn_40855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxn_40855/08_2025/8sxn_40855.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxn_40855/08_2025/8sxn_40855_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxn_40855/08_2025/8sxn_40855_neut.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 4.04, 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: 1.56 Conformation dependent library (CDL) restraints added in 924.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.81 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: 3.63 Time building geometry restraints manager: 2.09 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.910 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- 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 aren 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 : 0.717 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: 0.6926 (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: 0.9283 (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: 0.7831 (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: 0.1430 time to fit residues: 86.5908 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 : 0.715 ------------------------------------------------------------------------------- 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 aren 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 : 0.657 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: 0.8743 (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: 0.1293 time to fit residues: 55.9847 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 : 0.695 ------------------------------------------------------------------------------- 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 aren 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 : 0.725 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 63 MET cc_start: 0.7877 (tmm) cc_final: 0.7665 (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: 0.1173 time to fit residues: 42.5700 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 : 0.706 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.077507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060907 restraints weight = 77810.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062815 restraints weight = 44846.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064105 restraints weight = 31031.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064924 restraints weight = 24207.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065286 restraints weight = 20622.656| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3573 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= 0.152 Angle : 0.577 9.857 24390 Z= 0.294 Chirality : 0.040 0.302 2728 Planarity : 0.004 0.034 3076 Dihedral : 10.068 149.000 2474 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.69 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.19), residues: 2176 helix: 0.96 (0.17), residues: 994 sheet: -0.76 (0.32), residues: 264 loop : -0.09 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 292 TYR 0.012 0.001 TYR A 263 PHE 0.038 0.002 PHE C 502 TRP 0.010 0.001 TRP C 478 HIS 0.005 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00334 (18064) covalent geometry : angle 0.57720 (24390) hydrogen bonds : bond 0.04312 ( 769) hydrogen bonds : angle 4.54197 ( 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 : 0.692 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 109 ILE cc_start: 0.8774 (mt) cc_final: 0.8049 (mt) REVERT: A 112 GLU cc_start: 0.7647 (tt0) cc_final: 0.7299 (tm-30) REVERT: A 158 MET cc_start: 0.6085 (mmm) cc_final: 0.5799 (mmm) REVERT: A 228 GLU cc_start: 0.9052 (tp30) cc_final: 0.8811 (mm-30) REVERT: B 158 MET cc_start: 0.6992 (mmm) cc_final: 0.6325 (mmt) REVERT: B 219 ILE cc_start: 0.9264 (mm) cc_final: 0.8954 (mm) REVERT: B 263 TYR cc_start: 0.8464 (m-80) cc_final: 0.8219 (m-80) REVERT: C 230 ILE cc_start: 0.9294 (mm) cc_final: 0.8927 (mt) REVERT: C 600 ILE cc_start: 0.9186 (mm) cc_final: 0.8683 (tp) REVERT: C 665 VAL cc_start: 0.9444 (t) cc_final: 0.9056 (p) REVERT: C 758 MET cc_start: 0.9265 (tpp) cc_final: 0.8886 (tpp) REVERT: C 943 LEU cc_start: 0.9221 (tp) cc_final: 0.9007 (tp) REVERT: D 230 ILE cc_start: 0.9239 (mm) cc_final: 0.8887 (mt) REVERT: D 240 MET cc_start: 0.8566 (mmm) cc_final: 0.8357 (tpt) REVERT: D 301 MET cc_start: 0.8155 (tpp) cc_final: 0.7947 (mmm) REVERT: D 382 PHE cc_start: 0.8437 (m-80) cc_final: 0.8092 (m-80) REVERT: D 636 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8219 (tp30) REVERT: D 640 GLU cc_start: 0.8085 (pp20) cc_final: 0.7747 (pp20) REVERT: D 807 ASP cc_start: 0.8498 (t70) cc_final: 0.8111 (t0) REVERT: D 810 LEU cc_start: 0.8433 (mt) cc_final: 0.8040 (mt) REVERT: D 957 CYS cc_start: 0.8392 (p) cc_final: 0.7720 (p) REVERT: D 987 MET cc_start: 0.8435 (ppp) cc_final: 0.8173 (mmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1038 time to fit residues: 34.5836 Evaluate side-chains 162 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 6.9990 chunk 186 optimal weight: 0.0020 chunk 139 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.077460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060284 restraints weight = 76670.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.062328 restraints weight = 42269.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.063585 restraints weight = 28523.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.064554 restraints weight = 22172.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.065174 restraints weight = 18749.887| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18064 Z= 0.118 Angle : 0.548 8.153 24390 Z= 0.280 Chirality : 0.039 0.201 2728 Planarity : 0.003 0.034 3076 Dihedral : 10.077 149.899 2474 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.87 % Favored : 94.72 % 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 aren not related in a simple way. whole: 0.33 (0.19), residues: 2176 helix: 0.97 (0.17), residues: 998 sheet: -0.75 (0.33), residues: 262 loop : -0.18 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 294 TYR 0.011 0.001 TYR C 136 PHE 0.041 0.002 PHE C 382 TRP 0.008 0.001 TRP C 243 HIS 0.004 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00253 (18064) covalent geometry : angle 0.54836 (24390) hydrogen bonds : bond 0.03979 ( 769) hydrogen bonds : angle 4.43884 ( 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 208 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.659 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: 0.7643 (tt0) cc_final: 0.7390 (tm-30) REVERT: A 158 MET cc_start: 0.6256 (mmm) cc_final: 0.5827 (mmm) REVERT: A 219 ILE cc_start: 0.9179 (mm) cc_final: 0.8939 (mm) REVERT: A 290 ASP cc_start: 0.8479 (t0) cc_final: 0.8243 (p0) REVERT: B 63 MET cc_start: 0.8157 (ppp) cc_final: 0.7759 (tmm) REVERT: B 65 VAL cc_start: 0.7946 (t) cc_final: 0.7507 (t) REVERT: B 219 ILE cc_start: 0.9198 (mm) cc_final: 0.8914 (mm) REVERT: B 263 TYR cc_start: 0.8485 (m-80) cc_final: 0.8242 (m-80) REVERT: C 230 ILE cc_start: 0.9303 (mm) cc_final: 0.8924 (mt) REVERT: C 636 GLU cc_start: 0.8708 (tp30) cc_final: 0.8370 (tp30) REVERT: C 665 VAL cc_start: 0.9444 (t) cc_final: 0.8930 (p) REVERT: C 669 CYS cc_start: 0.8952 (m) cc_final: 0.8712 (m) REVERT: C 846 ASP cc_start: 0.7979 (t0) cc_final: 0.7501 (t0) REVERT: C 943 LEU cc_start: 0.9175 (tp) cc_final: 0.8896 (tt) REVERT: C 1008 MET cc_start: 0.7611 (mmm) cc_final: 0.7401 (mmm) REVERT: D 230 ILE cc_start: 0.9213 (mm) cc_final: 0.8849 (mt) REVERT: D 301 MET cc_start: 0.8337 (tpp) cc_final: 0.7991 (mmm) REVERT: D 382 PHE cc_start: 0.8332 (m-80) cc_final: 0.8108 (m-80) REVERT: D 636 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8128 (tp30) REVERT: D 640 GLU cc_start: 0.8085 (pp20) cc_final: 0.7763 (pp20) REVERT: D 807 ASP cc_start: 0.8517 (t70) cc_final: 0.8105 (t0) REVERT: D 810 LEU cc_start: 0.8442 (mt) cc_final: 0.8101 (mt) REVERT: D 957 CYS cc_start: 0.8466 (p) cc_final: 0.7643 (p) REVERT: D 987 MET cc_start: 0.8425 (ppp) cc_final: 0.8120 (mmm) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1055 time to fit residues: 34.9827 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 : 0.577 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 217 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 49 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.077491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.060186 restraints weight = 76310.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.062256 restraints weight = 41988.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.063628 restraints weight = 28288.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064574 restraints weight = 21881.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065105 restraints weight = 18340.499| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18064 Z= 0.112 Angle : 0.542 7.936 24390 Z= 0.274 Chirality : 0.039 0.185 2728 Planarity : 0.003 0.034 3076 Dihedral : 10.107 150.460 2474 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.96 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.19), residues: 2176 helix: 0.96 (0.17), residues: 1010 sheet: -0.89 (0.33), residues: 270 loop : -0.31 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 294 TYR 0.014 0.001 TYR A 49 PHE 0.044 0.001 PHE C 502 TRP 0.008 0.001 TRP C 478 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00239 (18064) covalent geometry : angle 0.54224 (24390) hydrogen bonds : bond 0.03760 ( 769) hydrogen bonds : angle 4.35944 ( 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 215 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.668 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: 0.7636 (tt0) cc_final: 0.7435 (tm-30) REVERT: A 152 MET cc_start: 0.8835 (ttm) cc_final: 0.8622 (ttt) REVERT: A 158 MET cc_start: 0.6340 (mmm) cc_final: 0.5333 (mmm) REVERT: A 269 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8768 (mp10) REVERT: B 63 MET cc_start: 0.8247 (ppp) cc_final: 0.7796 (tmm) REVERT: B 65 VAL cc_start: 0.7932 (t) cc_final: 0.7350 (t) REVERT: B 158 MET cc_start: 0.6838 (mmm) cc_final: 0.6273 (mmt) REVERT: B 219 ILE cc_start: 0.9157 (mm) cc_final: 0.8885 (mm) REVERT: B 263 TYR cc_start: 0.8498 (m-80) cc_final: 0.8282 (m-80) REVERT: B 290 ASP cc_start: 0.8380 (t0) cc_final: 0.8176 (p0) REVERT: C 230 ILE cc_start: 0.9284 (mm) cc_final: 0.8908 (mt) REVERT: C 622 GLN cc_start: 0.8318 (tt0) cc_final: 0.8030 (tm-30) REVERT: C 636 GLU cc_start: 0.8716 (tp30) cc_final: 0.8420 (tp30) REVERT: C 665 VAL cc_start: 0.9325 (t) cc_final: 0.8937 (p) REVERT: C 669 CYS cc_start: 0.8884 (m) cc_final: 0.8540 (m) REVERT: C 846 ASP cc_start: 0.8040 (t0) cc_final: 0.7549 (t0) REVERT: C 943 LEU cc_start: 0.9190 (tp) cc_final: 0.8981 (tp) REVERT: C 961 LEU cc_start: 0.9361 (mt) cc_final: 0.9076 (mt) REVERT: D 208 LEU cc_start: 0.9247 (mt) cc_final: 0.9033 (mt) REVERT: D 230 ILE cc_start: 0.9199 (mm) cc_final: 0.8834 (mt) REVERT: D 382 PHE cc_start: 0.8380 (m-80) cc_final: 0.8126 (m-80) REVERT: D 532 MET cc_start: 0.9070 (tpp) cc_final: 0.8486 (tpp) REVERT: D 636 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8140 (tp30) REVERT: D 640 GLU cc_start: 0.8023 (pp20) cc_final: 0.7723 (pp20) REVERT: D 669 CYS cc_start: 0.8906 (m) cc_final: 0.8705 (m) REVERT: D 807 ASP cc_start: 0.8519 (t70) cc_final: 0.8073 (t0) REVERT: D 810 LEU cc_start: 0.8510 (mt) cc_final: 0.8180 (mt) REVERT: D 957 CYS cc_start: 0.8591 (p) cc_final: 0.7817 (p) REVERT: D 987 MET cc_start: 0.8472 (ppp) cc_final: 0.8196 (mmm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1007 time to fit residues: 34.9313 Evaluate side-chains 163 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS C 260 HIS C 360 HIS C 883 GLN D 220 HIS ** 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 = 0.3594 r_free = 0.3594 target = 0.074846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.057338 restraints weight = 77932.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.059298 restraints weight = 43808.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060603 restraints weight = 29913.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061349 restraints weight = 23293.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.061952 restraints weight = 19957.454| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 18064 Z= 0.207 Angle : 0.625 7.827 24390 Z= 0.316 Chirality : 0.041 0.267 2728 Planarity : 0.004 0.046 3076 Dihedral : 10.383 150.301 2474 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.88 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.19), residues: 2176 helix: 0.87 (0.17), residues: 1016 sheet: -1.13 (0.32), residues: 272 loop : -0.39 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 779 TYR 0.013 0.001 TYR A 287 PHE 0.037 0.002 PHE D 502 TRP 0.015 0.001 TRP C 478 HIS 0.006 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00454 (18064) covalent geometry : angle 0.62485 (24390) hydrogen bonds : bond 0.04103 ( 769) hydrogen bonds : angle 4.61845 ( 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 182 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.720 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: 0.7881 (tt0) cc_final: 0.7473 (tm-30) REVERT: A 158 MET cc_start: 0.6404 (mmm) cc_final: 0.5967 (mmt) REVERT: A 263 TYR cc_start: 0.8661 (m-80) cc_final: 0.8445 (m-10) REVERT: B 63 MET cc_start: 0.8244 (ppp) cc_final: 0.7751 (tmm) REVERT: B 158 MET cc_start: 0.6751 (mmm) cc_final: 0.6104 (mmt) REVERT: B 219 ILE cc_start: 0.9257 (mm) cc_final: 0.9006 (mm) REVERT: B 263 TYR cc_start: 0.8639 (m-80) cc_final: 0.8409 (m-80) REVERT: B 290 ASP cc_start: 0.8428 (t0) cc_final: 0.8224 (p0) REVERT: C 230 ILE cc_start: 0.9363 (mm) cc_final: 0.8962 (mt) REVERT: C 405 LEU cc_start: 0.8967 (tp) cc_final: 0.8700 (tt) REVERT: C 409 CYS cc_start: 0.8353 (m) cc_final: 0.8112 (m) REVERT: C 665 VAL cc_start: 0.9371 (t) cc_final: 0.9070 (p) REVERT: C 669 CYS cc_start: 0.9033 (m) cc_final: 0.8764 (m) REVERT: C 987 MET cc_start: 0.8203 (mmt) cc_final: 0.7996 (mmt) REVERT: D 230 ILE cc_start: 0.9285 (mm) cc_final: 0.8916 (mt) REVERT: D 382 PHE cc_start: 0.8367 (m-80) cc_final: 0.8101 (m-80) REVERT: D 405 LEU cc_start: 0.9103 (tp) cc_final: 0.8768 (tt) REVERT: D 409 CYS cc_start: 0.8413 (m) cc_final: 0.8150 (m) REVERT: D 532 MET cc_start: 0.9098 (tpp) cc_final: 0.8591 (tpp) REVERT: D 636 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8195 (tp30) REVERT: D 640 GLU cc_start: 0.8033 (pp20) cc_final: 0.7689 (pp20) REVERT: D 669 CYS cc_start: 0.8920 (m) cc_final: 0.8652 (m) REVERT: D 807 ASP cc_start: 0.8575 (t70) cc_final: 0.8162 (t0) REVERT: D 864 GLU cc_start: 0.7922 (tp30) cc_final: 0.7604 (tp30) REVERT: D 987 MET cc_start: 0.8495 (ppp) cc_final: 0.8181 (mmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1087 time to fit residues: 31.9139 Evaluate side-chains 148 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 2.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 0.0770 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.076535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.059065 restraints weight = 76397.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.061085 restraints weight = 42791.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.062427 restraints weight = 29119.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063328 restraints weight = 22492.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.063831 restraints weight = 18955.068| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18064 Z= 0.120 Angle : 0.559 8.126 24390 Z= 0.282 Chirality : 0.039 0.232 2728 Planarity : 0.004 0.036 3076 Dihedral : 10.340 150.776 2474 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.28 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.19), residues: 2176 helix: 0.98 (0.17), residues: 1014 sheet: -1.20 (0.32), residues: 270 loop : -0.33 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 294 TYR 0.019 0.001 TYR A 202 PHE 0.034 0.002 PHE D 484 TRP 0.008 0.001 TRP C 478 HIS 0.004 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00261 (18064) covalent geometry : angle 0.55906 (24390) hydrogen bonds : bond 0.03720 ( 769) hydrogen bonds : angle 4.43430 ( 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 194 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.506 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: 0.8138 (ppp) cc_final: 0.7812 (ppp) REVERT: A 112 GLU cc_start: 0.7877 (tt0) cc_final: 0.7565 (tm-30) REVERT: A 158 MET cc_start: 0.6366 (mmm) cc_final: 0.5419 (mmt) REVERT: A 219 ILE cc_start: 0.9201 (mm) cc_final: 0.8973 (mm) REVERT: A 263 TYR cc_start: 0.8599 (m-80) cc_final: 0.8398 (m-80) REVERT: A 295 MET cc_start: 0.8839 (mmm) cc_final: 0.8604 (mmp) REVERT: B 63 MET cc_start: 0.8271 (ppp) cc_final: 0.7778 (ppp) REVERT: B 152 MET cc_start: 0.8956 (ttm) cc_final: 0.8708 (ttt) REVERT: B 158 MET cc_start: 0.6846 (mmm) cc_final: 0.5685 (mmt) REVERT: B 219 ILE cc_start: 0.9204 (mm) cc_final: 0.8972 (mm) REVERT: B 263 TYR cc_start: 0.8582 (m-80) cc_final: 0.8362 (m-80) REVERT: C 205 MET cc_start: 0.7746 (ttm) cc_final: 0.7470 (tpp) REVERT: C 230 ILE cc_start: 0.9326 (mm) cc_final: 0.8962 (mt) REVERT: C 239 MET cc_start: 0.8879 (ttp) cc_final: 0.8580 (ttp) REVERT: C 405 LEU cc_start: 0.9071 (tp) cc_final: 0.8748 (tt) REVERT: C 669 CYS cc_start: 0.8865 (m) cc_final: 0.8650 (m) REVERT: C 846 ASP cc_start: 0.8190 (t0) cc_final: 0.7636 (t0) REVERT: D 208 LEU cc_start: 0.9382 (mt) cc_final: 0.9180 (mt) REVERT: D 230 ILE cc_start: 0.9231 (mm) cc_final: 0.8862 (mt) REVERT: D 256 LEU cc_start: 0.9194 (mt) cc_final: 0.8849 (mt) REVERT: D 382 PHE cc_start: 0.8455 (m-80) cc_final: 0.8044 (m-80) REVERT: D 405 LEU cc_start: 0.9072 (tp) cc_final: 0.8720 (tt) REVERT: D 409 CYS cc_start: 0.8362 (m) cc_final: 0.8109 (m) REVERT: D 640 GLU cc_start: 0.7994 (pp20) cc_final: 0.7696 (pp20) REVERT: D 669 CYS cc_start: 0.8817 (m) cc_final: 0.8565 (m) REVERT: D 807 ASP cc_start: 0.8545 (t70) cc_final: 0.8115 (t0) REVERT: D 810 LEU cc_start: 0.8641 (mt) cc_final: 0.8239 (mt) REVERT: D 864 GLU cc_start: 0.7914 (tp30) cc_final: 0.7606 (tp30) REVERT: D 957 CYS cc_start: 0.8632 (p) cc_final: 0.7834 (p) REVERT: D 987 MET cc_start: 0.8465 (ppp) cc_final: 0.8188 (mmm) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0985 time to fit residues: 31.0588 Evaluate side-chains 156 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 10.0000 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3618 r_free = 0.3618 target = 0.075656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.058213 restraints weight = 77122.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060198 restraints weight = 43712.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061323 restraints weight = 30019.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062316 restraints weight = 23774.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.062847 restraints weight = 19969.221| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18064 Z= 0.145 Angle : 0.583 8.004 24390 Z= 0.292 Chirality : 0.040 0.197 2728 Planarity : 0.004 0.034 3076 Dihedral : 10.374 151.012 2474 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.74 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.19), residues: 2176 helix: 0.99 (0.17), residues: 1016 sheet: -1.28 (0.32), residues: 270 loop : -0.35 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 294 TYR 0.016 0.001 TYR A 202 PHE 0.039 0.002 PHE C 382 TRP 0.010 0.001 TRP C 478 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00320 (18064) covalent geometry : angle 0.58336 (24390) hydrogen bonds : bond 0.03767 ( 769) hydrogen bonds : angle 4.48016 ( 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 : 0.467 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: 0.8065 (ppp) cc_final: 0.7736 (ppp) REVERT: A 112 GLU cc_start: 0.7936 (tt0) cc_final: 0.7606 (tm-30) REVERT: A 158 MET cc_start: 0.6709 (mmm) cc_final: 0.6273 (mmm) REVERT: A 219 ILE cc_start: 0.9211 (mm) cc_final: 0.9008 (mm) REVERT: B 63 MET cc_start: 0.8252 (ppp) cc_final: 0.7718 (tmm) REVERT: B 152 MET cc_start: 0.8953 (ttm) cc_final: 0.8697 (ttt) REVERT: B 158 MET cc_start: 0.6832 (mmm) cc_final: 0.5640 (mmt) REVERT: B 219 ILE cc_start: 0.9230 (mm) cc_final: 0.8982 (mm) REVERT: B 263 TYR cc_start: 0.8582 (m-80) cc_final: 0.8341 (m-80) REVERT: C 230 ILE cc_start: 0.9337 (mm) cc_final: 0.8971 (mt) REVERT: C 239 MET cc_start: 0.8901 (ttp) cc_final: 0.8691 (ttp) REVERT: C 405 LEU cc_start: 0.9090 (tp) cc_final: 0.8771 (tt) REVERT: C 409 CYS cc_start: 0.8366 (m) cc_final: 0.8158 (m) REVERT: C 626 SER cc_start: 0.8528 (p) cc_final: 0.8024 (t) REVERT: C 669 CYS cc_start: 0.8738 (m) cc_final: 0.8394 (m) REVERT: C 807 ASP cc_start: 0.8584 (t70) cc_final: 0.8358 (t0) REVERT: C 987 MET cc_start: 0.8138 (tmm) cc_final: 0.7762 (mmt) REVERT: C 1008 MET cc_start: 0.6774 (mmm) cc_final: 0.6533 (mmm) REVERT: D 208 LEU cc_start: 0.9376 (mt) cc_final: 0.9171 (mt) REVERT: D 230 ILE cc_start: 0.9249 (mm) cc_final: 0.8834 (mt) REVERT: D 382 PHE cc_start: 0.8319 (m-80) cc_final: 0.8055 (m-80) REVERT: D 405 LEU cc_start: 0.9074 (tp) cc_final: 0.8727 (tt) REVERT: D 409 CYS cc_start: 0.8360 (m) cc_final: 0.8116 (m) REVERT: D 484 PHE cc_start: 0.8330 (m-10) cc_final: 0.8116 (m-10) REVERT: D 636 GLU cc_start: 0.8738 (tp30) cc_final: 0.8301 (tp30) REVERT: D 640 GLU cc_start: 0.7997 (pp20) cc_final: 0.7712 (pp20) REVERT: D 669 CYS cc_start: 0.8749 (m) cc_final: 0.8533 (m) REVERT: D 807 ASP cc_start: 0.8538 (t70) cc_final: 0.8109 (t0) REVERT: D 810 LEU cc_start: 0.8669 (mt) cc_final: 0.8305 (mt) REVERT: D 864 GLU cc_start: 0.7915 (tp30) cc_final: 0.7628 (tp30) REVERT: D 987 MET cc_start: 0.8502 (ppp) cc_final: 0.8251 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1120 time to fit residues: 33.4469 Evaluate side-chains 157 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 174 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 194 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3645 r_free = 0.3645 target = 0.077216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.059785 restraints weight = 76500.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.061822 restraints weight = 43318.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.063197 restraints weight = 29600.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.064081 restraints weight = 22786.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.064572 restraints weight = 19229.414| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18064 Z= 0.111 Angle : 0.579 8.129 24390 Z= 0.288 Chirality : 0.040 0.174 2728 Planarity : 0.003 0.035 3076 Dihedral : 10.308 151.180 2474 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.10 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 2176 helix: 1.00 (0.17), residues: 1018 sheet: -1.29 (0.32), residues: 270 loop : -0.30 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 294 TYR 0.015 0.001 TYR A 202 PHE 0.025 0.002 PHE D 581 TRP 0.006 0.001 TRP B 220 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00237 (18064) covalent geometry : angle 0.57881 (24390) hydrogen bonds : bond 0.03580 ( 769) hydrogen bonds : angle 4.35785 ( 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 204 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.565 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 63 MET cc_start: 0.8094 (ppp) cc_final: 0.7485 (tmm) REVERT: A 112 GLU cc_start: 0.7935 (tt0) cc_final: 0.7665 (tm-30) REVERT: A 158 MET cc_start: 0.6729 (mmm) cc_final: 0.6200 (mmt) REVERT: B 63 MET cc_start: 0.8249 (ppp) cc_final: 0.7936 (ppp) REVERT: B 152 MET cc_start: 0.8977 (ttm) cc_final: 0.8714 (ttt) REVERT: B 158 MET cc_start: 0.6855 (mmm) cc_final: 0.5711 (mmt) REVERT: B 219 ILE cc_start: 0.9187 (mm) cc_final: 0.8971 (mm) REVERT: B 263 TYR cc_start: 0.8560 (m-80) cc_final: 0.8328 (m-80) REVERT: C 205 MET cc_start: 0.8353 (tpp) cc_final: 0.7573 (tpp) REVERT: C 230 ILE cc_start: 0.9327 (mm) cc_final: 0.8973 (mt) REVERT: C 405 LEU cc_start: 0.9069 (tp) cc_final: 0.8770 (tt) REVERT: C 626 SER cc_start: 0.8388 (p) cc_final: 0.7887 (t) REVERT: C 669 CYS cc_start: 0.8873 (m) cc_final: 0.8631 (m) REVERT: C 1008 MET cc_start: 0.6669 (mmm) cc_final: 0.6365 (mmm) REVERT: D 230 ILE cc_start: 0.9213 (mm) cc_final: 0.8803 (mt) REVERT: D 405 LEU cc_start: 0.9070 (tp) cc_final: 0.8706 (tt) REVERT: D 409 CYS cc_start: 0.8364 (m) cc_final: 0.8130 (m) REVERT: D 532 MET cc_start: 0.9042 (tpp) cc_final: 0.8502 (tpp) REVERT: D 640 GLU cc_start: 0.7994 (pp20) cc_final: 0.7723 (pp20) REVERT: D 807 ASP cc_start: 0.8493 (t70) cc_final: 0.8099 (t0) REVERT: D 810 LEU cc_start: 0.8648 (mt) cc_final: 0.8303 (mt) REVERT: D 864 GLU cc_start: 0.7882 (tp30) cc_final: 0.7627 (tp30) REVERT: D 987 MET cc_start: 0.8479 (ppp) cc_final: 0.8271 (mmm) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1147 time to fit residues: 37.7391 Evaluate side-chains 159 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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: 6.9990 chunk 91 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 17 optimal weight: 0.0370 chunk 46 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3639 r_free = 0.3639 target = 0.076972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059580 restraints weight = 77923.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061594 restraints weight = 44210.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.062924 restraints weight = 30285.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.063831 restraints weight = 23519.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.064236 restraints weight = 19797.039| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18064 Z= 0.114 Angle : 0.572 11.231 24390 Z= 0.284 Chirality : 0.040 0.366 2728 Planarity : 0.003 0.032 3076 Dihedral : 10.268 151.087 2474 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.38 % Favored : 94.21 % 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 aren not related in a simple way. whole: 0.19 (0.19), residues: 2176 helix: 1.00 (0.17), residues: 1018 sheet: -1.28 (0.32), residues: 270 loop : -0.30 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 23 TYR 0.014 0.001 TYR A 202 PHE 0.022 0.001 PHE D 484 TRP 0.012 0.001 TRP D 478 HIS 0.006 0.001 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00246 (18064) covalent geometry : angle 0.57239 (24390) hydrogen bonds : bond 0.03502 ( 769) hydrogen bonds : angle 4.32704 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.46 seconds wall clock time: 46 minutes 46.32 seconds (2806.32 seconds total)