Starting phenix.real_space_refine on Sun Jun 15 22:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxn_40855/06_2025/8sxn_40855_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxn_40855/06_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_40855/06_2025/8sxn_40855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxn_40855/06_2025/8sxn_40855.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxn_40855/06_2025/8sxn_40855_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxn_40855/06_2025/8sxn_40855_neut.cif" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.83, per 1000 atoms: 0.56 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: 3.91 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.03 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: 5.69 Time building geometry restraints manager: 4.69 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: 0.06 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.930 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.430 ------------------------------------------------------------------------------- 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 : 2.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (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 TRP 0.023 0.004 TRP D 611 HIS 0.006 0.001 HIS C 916 PHE 0.020 0.003 PHE C 502 TYR 0.025 0.004 TYR D 443 ARG 0.004 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.17600 ( 769) hydrogen bonds : angle 6.58618 ( 2148) covalent geometry : bond 0.01250 (18064) covalent geometry : angle 1.26254 (24390) *********************** 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 : 1.971 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: 0.3139 time to fit residues: 189.7546 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 : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 165 ASN C 269 GLN C1001 GLN D 622 GLN ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.079695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062807 restraints weight = 77734.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.064828 restraints weight = 44908.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.066140 restraints weight = 30810.201| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18064 Z= 0.153 Angle : 0.648 9.978 24390 Z= 0.335 Chirality : 0.041 0.213 2728 Planarity : 0.004 0.030 3076 Dihedral : 10.041 147.984 2474 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.00 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2176 helix: 0.77 (0.16), residues: 1016 sheet: -0.29 (0.33), residues: 248 loop : 0.01 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 478 HIS 0.004 0.001 HIS D 784 PHE 0.033 0.002 PHE C 502 TYR 0.023 0.002 TYR C 136 ARG 0.006 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.05517 ( 769) hydrogen bonds : angle 4.94702 ( 2148) covalent geometry : bond 0.00322 (18064) covalent geometry : angle 0.64828 (24390) *********************** 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 : 2.037 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: 0.8314 (tmm) cc_final: 0.8013 (ppp) REVERT: A 109 ILE cc_start: 0.8832 (mt) cc_final: 0.8135 (mt) REVERT: A 112 GLU cc_start: 0.7684 (tt0) cc_final: 0.7343 (tm-30) REVERT: A 140 LYS cc_start: 0.8970 (tttp) cc_final: 0.8755 (ttpt) REVERT: A 142 PHE cc_start: 0.8519 (t80) cc_final: 0.8290 (t80) REVERT: B 26 MET cc_start: 0.7886 (mmm) cc_final: 0.7494 (mpp) REVERT: B 63 MET cc_start: 0.8488 (tmm) cc_final: 0.8147 (ppp) REVERT: B 152 MET cc_start: 0.8982 (ttm) cc_final: 0.8736 (ttt) REVERT: B 158 MET cc_start: 0.7050 (mpp) cc_final: 0.6633 (mpp) REVERT: B 229 MET cc_start: 0.9052 (mtp) cc_final: 0.8801 (mtp) REVERT: B 263 TYR cc_start: 0.8437 (m-80) cc_final: 0.8177 (m-80) REVERT: C 205 MET cc_start: 0.8048 (ttp) cc_final: 0.7494 (tpp) REVERT: C 230 ILE cc_start: 0.9223 (mm) cc_final: 0.8919 (mt) REVERT: C 665 VAL cc_start: 0.9388 (t) cc_final: 0.9066 (p) REVERT: C 742 SER cc_start: 0.8133 (m) cc_final: 0.7903 (p) REVERT: C 943 LEU cc_start: 0.9243 (tp) cc_final: 0.8924 (tt) REVERT: C 1025 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8606 (mttp) REVERT: D 205 MET cc_start: 0.7563 (ttp) cc_final: 0.6848 (tpp) REVERT: D 230 ILE cc_start: 0.9197 (mm) cc_final: 0.8847 (mt) REVERT: D 239 MET cc_start: 0.8762 (ttp) cc_final: 0.8536 (ttp) REVERT: D 240 MET cc_start: 0.8490 (mmm) cc_final: 0.8071 (mmt) REVERT: D 256 LEU cc_start: 0.9046 (mt) cc_final: 0.8773 (mt) REVERT: D 508 PHE cc_start: 0.8372 (m-80) cc_final: 0.8169 (m-10) REVERT: D 595 LYS cc_start: 0.8296 (tptt) cc_final: 0.8066 (tptp) REVERT: D 636 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8191 (tp30) REVERT: D 640 GLU cc_start: 0.8114 (pp20) cc_final: 0.7896 (pp20) REVERT: D 1025 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8823 (mmtp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2865 time to fit residues: 124.1975 Evaluate side-chains 176 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 139 optimal weight: 10.0000 chunk 60 optimal weight: 0.0670 chunk 107 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 108 ASN C 215 HIS C 260 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 845 GLN C 995 GLN D 165 ASN D 215 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN D 824 HIS D 995 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.074998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.058163 restraints weight = 77618.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059932 restraints weight = 46897.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.061098 restraints weight = 33263.999| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18064 Z= 0.259 Angle : 0.702 10.415 24390 Z= 0.356 Chirality : 0.042 0.176 2728 Planarity : 0.004 0.035 3076 Dihedral : 10.250 148.601 2474 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.78 % Favored : 94.76 % Rotamer: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 2176 helix: 0.72 (0.16), residues: 1006 sheet: -0.72 (0.32), residues: 266 loop : -0.26 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 478 HIS 0.005 0.001 HIS D 492 PHE 0.039 0.002 PHE C 382 TYR 0.013 0.002 TYR D 443 ARG 0.010 0.001 ARG C 779 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 769) hydrogen bonds : angle 4.99252 ( 2148) covalent geometry : bond 0.00563 (18064) covalent geometry : angle 0.70220 (24390) *********************** 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 206 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 2.049 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: 0.8758 (mt) cc_final: 0.8182 (mt) REVERT: A 112 GLU cc_start: 0.7998 (tt0) cc_final: 0.7406 (tm-30) REVERT: B 63 MET cc_start: 0.7959 (tmm) cc_final: 0.7713 (tmm) REVERT: B 152 MET cc_start: 0.8966 (ttm) cc_final: 0.8701 (ttt) REVERT: B 158 MET cc_start: 0.7087 (mpp) cc_final: 0.6860 (mmm) REVERT: C 230 ILE cc_start: 0.9401 (mm) cc_final: 0.9003 (mt) REVERT: C 665 VAL cc_start: 0.9497 (t) cc_final: 0.9091 (p) REVERT: C 807 ASP cc_start: 0.8377 (t70) cc_final: 0.8163 (t0) REVERT: C 810 LEU cc_start: 0.8626 (mt) cc_final: 0.8168 (mt) REVERT: C 943 LEU cc_start: 0.9231 (tp) cc_final: 0.9016 (tp) REVERT: D 230 ILE cc_start: 0.9358 (mm) cc_final: 0.8986 (mt) REVERT: D 240 MET cc_start: 0.8574 (mmm) cc_final: 0.8371 (tpt) REVERT: D 382 PHE cc_start: 0.8206 (m-80) cc_final: 0.7973 (m-80) REVERT: D 502 PHE cc_start: 0.7858 (m-80) cc_final: 0.7575 (m-80) REVERT: D 595 LYS cc_start: 0.8279 (tptt) cc_final: 0.8059 (tptp) REVERT: D 636 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8231 (tp30) REVERT: D 640 GLU cc_start: 0.8188 (pp20) cc_final: 0.7736 (pp20) REVERT: D 957 CYS cc_start: 0.8617 (p) cc_final: 0.8080 (p) REVERT: D 987 MET cc_start: 0.8410 (ppp) cc_final: 0.8132 (mmt) outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.2864 time to fit residues: 93.3947 Evaluate side-chains 149 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 141 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 193 optimal weight: 0.0570 chunk 202 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 HIS ** 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 = 0.3630 r_free = 0.3630 target = 0.076311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.058836 restraints weight = 76211.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060877 restraints weight = 42120.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.062242 restraints weight = 28447.447| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18064 Z= 0.133 Angle : 0.576 10.379 24390 Z= 0.292 Chirality : 0.040 0.302 2728 Planarity : 0.004 0.037 3076 Dihedral : 10.258 149.469 2474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.64 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 2176 helix: 0.85 (0.17), residues: 1014 sheet: -0.70 (0.33), residues: 248 loop : -0.19 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 478 HIS 0.005 0.001 HIS B 159 PHE 0.022 0.002 PHE D 484 TYR 0.012 0.001 TYR A 237 ARG 0.004 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 769) hydrogen bonds : angle 4.58312 ( 2148) covalent geometry : bond 0.00288 (18064) covalent geometry : angle 0.57620 (24390) *********************** 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 206 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7889 (tt0) cc_final: 0.7400 (tm-30) REVERT: A 158 MET cc_start: 0.6062 (mmm) cc_final: 0.5669 (mmm) REVERT: A 219 ILE cc_start: 0.9231 (mm) cc_final: 0.9021 (mm) REVERT: B 63 MET cc_start: 0.8271 (tmm) cc_final: 0.7855 (tmm) REVERT: B 152 MET cc_start: 0.9118 (ttm) cc_final: 0.8809 (ttt) REVERT: B 158 MET cc_start: 0.7086 (mpp) cc_final: 0.6845 (mmm) REVERT: B 263 TYR cc_start: 0.8495 (m-80) cc_final: 0.8271 (m-80) REVERT: C 230 ILE cc_start: 0.9339 (mm) cc_final: 0.9013 (mt) REVERT: C 636 GLU cc_start: 0.8749 (tp30) cc_final: 0.8429 (tp30) REVERT: C 665 VAL cc_start: 0.9413 (t) cc_final: 0.9023 (p) REVERT: C 807 ASP cc_start: 0.8376 (t70) cc_final: 0.8157 (t0) REVERT: C 810 LEU cc_start: 0.8574 (mt) cc_final: 0.8202 (mt) REVERT: C 943 LEU cc_start: 0.9221 (tp) cc_final: 0.9014 (tp) REVERT: D 230 ILE cc_start: 0.9291 (mm) cc_final: 0.8929 (mt) REVERT: D 502 PHE cc_start: 0.7815 (m-80) cc_final: 0.7558 (m-80) REVERT: D 636 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8249 (tp30) REVERT: D 640 GLU cc_start: 0.8257 (pp20) cc_final: 0.7988 (pp20) REVERT: D 758 MET cc_start: 0.9322 (tpp) cc_final: 0.8791 (tpp) REVERT: D 761 LEU cc_start: 0.9542 (tp) cc_final: 0.9302 (tp) REVERT: D 957 CYS cc_start: 0.8743 (p) cc_final: 0.7868 (p) REVERT: D 961 LEU cc_start: 0.9400 (mt) cc_final: 0.8884 (mt) REVERT: D 987 MET cc_start: 0.8516 (ppp) cc_final: 0.8263 (mmt) REVERT: D 1008 MET cc_start: 0.7795 (mmm) cc_final: 0.7548 (mmm) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2638 time to fit residues: 86.1374 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 : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 91 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 153 optimal weight: 0.4980 chunk 167 optimal weight: 9.9990 chunk 18 optimal weight: 0.0040 chunk 1 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 296 HIS ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN C 883 GLN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 GLN D 883 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.072932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056042 restraints weight = 80237.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057746 restraints weight = 48633.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058817 restraints weight = 34651.934| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18064 Z= 0.291 Angle : 0.727 9.363 24390 Z= 0.363 Chirality : 0.042 0.160 2728 Planarity : 0.005 0.040 3076 Dihedral : 10.623 149.426 2474 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.43 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 2176 helix: 0.61 (0.16), residues: 1006 sheet: -1.31 (0.31), residues: 274 loop : -0.63 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 478 HIS 0.009 0.001 HIS B 159 PHE 0.037 0.003 PHE D 382 TYR 0.014 0.002 TYR B 201 ARG 0.011 0.001 ARG C 779 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 769) hydrogen bonds : angle 4.98938 ( 2148) covalent geometry : bond 0.00631 (18064) covalent geometry : angle 0.72686 (24390) *********************** 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 174 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.097 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: 0.8136 (tt0) cc_final: 0.7487 (tm-30) REVERT: A 142 PHE cc_start: 0.8648 (t80) cc_final: 0.8414 (t80) REVERT: A 158 MET cc_start: 0.6629 (mmm) cc_final: 0.5774 (mmt) REVERT: A 219 ILE cc_start: 0.9403 (mm) cc_final: 0.9165 (mm) REVERT: B 63 MET cc_start: 0.8268 (tmm) cc_final: 0.7826 (tmm) REVERT: B 152 MET cc_start: 0.9040 (ttm) cc_final: 0.8830 (ttt) REVERT: B 158 MET cc_start: 0.7117 (mpp) cc_final: 0.6835 (mmm) REVERT: B 263 TYR cc_start: 0.8719 (m-80) cc_final: 0.8502 (m-80) REVERT: B 295 MET cc_start: 0.8660 (mmm) cc_final: 0.8379 (mmp) REVERT: C 208 LEU cc_start: 0.9313 (mt) cc_final: 0.9094 (mt) REVERT: C 230 ILE cc_start: 0.9407 (mm) cc_final: 0.9078 (mt) REVERT: C 636 GLU cc_start: 0.8650 (tp30) cc_final: 0.8402 (tp30) REVERT: C 665 VAL cc_start: 0.9415 (t) cc_final: 0.9140 (p) REVERT: D 208 LEU cc_start: 0.9372 (mt) cc_final: 0.9167 (mt) REVERT: D 230 ILE cc_start: 0.9357 (mm) cc_final: 0.8987 (mt) REVERT: D 502 PHE cc_start: 0.7883 (m-80) cc_final: 0.7670 (m-80) REVERT: D 640 GLU cc_start: 0.8121 (pp20) cc_final: 0.7719 (pp20) REVERT: D 758 MET cc_start: 0.9384 (tpp) cc_final: 0.9047 (tpp) REVERT: D 987 MET cc_start: 0.8478 (ppp) cc_final: 0.8182 (mmt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2738 time to fit residues: 76.0802 Evaluate side-chains 142 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 130 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 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 = 0.3607 r_free = 0.3607 target = 0.075196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057669 restraints weight = 77053.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059633 restraints weight = 43571.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.060949 restraints weight = 29860.787| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18064 Z= 0.123 Angle : 0.565 8.791 24390 Z= 0.287 Chirality : 0.039 0.151 2728 Planarity : 0.004 0.039 3076 Dihedral : 10.550 150.777 2474 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.06 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 2176 helix: 0.79 (0.17), residues: 1024 sheet: -1.27 (0.32), residues: 272 loop : -0.56 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 478 HIS 0.005 0.001 HIS A 151 PHE 0.021 0.002 PHE C 581 TYR 0.012 0.001 TYR D 572 ARG 0.007 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 769) hydrogen bonds : angle 4.50172 ( 2148) covalent geometry : bond 0.00267 (18064) covalent geometry : angle 0.56485 (24390) *********************** 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 188 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 2.114 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: A 112 GLU cc_start: 0.8001 (tt0) cc_final: 0.7545 (tm-30) REVERT: A 158 MET cc_start: 0.6866 (mmm) cc_final: 0.6411 (mmm) REVERT: A 219 ILE cc_start: 0.9324 (mm) cc_final: 0.9041 (mm) REVERT: B 63 MET cc_start: 0.8329 (tmm) cc_final: 0.7891 (tmm) REVERT: B 152 MET cc_start: 0.9120 (ttm) cc_final: 0.8894 (ttt) REVERT: B 158 MET cc_start: 0.7077 (mpp) cc_final: 0.6815 (mmm) REVERT: B 263 TYR cc_start: 0.8616 (m-80) cc_final: 0.8390 (m-80) REVERT: C 230 ILE cc_start: 0.9370 (mm) cc_final: 0.9075 (mt) REVERT: C 382 PHE cc_start: 0.8263 (m-80) cc_final: 0.7737 (m-80) REVERT: C 636 GLU cc_start: 0.8684 (tp30) cc_final: 0.8457 (tp30) REVERT: C 665 VAL cc_start: 0.9339 (t) cc_final: 0.8986 (p) REVERT: C 669 CYS cc_start: 0.8901 (m) cc_final: 0.8636 (m) REVERT: D 230 ILE cc_start: 0.9286 (mm) cc_final: 0.8928 (mt) REVERT: D 277 MET cc_start: 0.8202 (mpp) cc_final: 0.7801 (ttp) REVERT: D 484 PHE cc_start: 0.8693 (m-80) cc_final: 0.8336 (m-10) REVERT: D 636 GLU cc_start: 0.8694 (tp30) cc_final: 0.8417 (tp30) REVERT: D 758 MET cc_start: 0.9319 (tpp) cc_final: 0.8980 (tpp) REVERT: D 987 MET cc_start: 0.8514 (ppp) cc_final: 0.8302 (mmt) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2745 time to fit residues: 81.8560 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 : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 176 optimal weight: 3.9990 chunk 157 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 215 optimal weight: 0.0030 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 chunk 197 optimal weight: 6.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** 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 = 0.3616 r_free = 0.3616 target = 0.075566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.057996 restraints weight = 77175.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059995 restraints weight = 43271.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.061321 restraints weight = 29410.866| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18064 Z= 0.120 Angle : 0.574 10.757 24390 Z= 0.289 Chirality : 0.039 0.193 2728 Planarity : 0.004 0.030 3076 Dihedral : 10.531 151.222 2474 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.47 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 2176 helix: 0.83 (0.17), residues: 1024 sheet: -1.33 (0.31), residues: 272 loop : -0.57 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 243 HIS 0.005 0.001 HIS C 492 PHE 0.042 0.001 PHE C 502 TYR 0.019 0.001 TYR A 202 ARG 0.007 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 769) hydrogen bonds : angle 4.47319 ( 2148) covalent geometry : bond 0.00260 (18064) covalent geometry : angle 0.57374 (24390) *********************** 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 186 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.337 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 63 MET cc_start: 0.8015 (ppp) cc_final: 0.7692 (ppp) REVERT: A 112 GLU cc_start: 0.8008 (tt0) cc_final: 0.7588 (tm-30) REVERT: A 158 MET cc_start: 0.6818 (mmm) cc_final: 0.6356 (mmt) REVERT: A 219 ILE cc_start: 0.9282 (mm) cc_final: 0.8987 (mm) REVERT: B 63 MET cc_start: 0.8328 (tmm) cc_final: 0.7914 (tmm) REVERT: B 152 MET cc_start: 0.9156 (ttm) cc_final: 0.8903 (ttt) REVERT: B 158 MET cc_start: 0.7098 (mpp) cc_final: 0.6817 (mmm) REVERT: B 219 ILE cc_start: 0.9230 (mm) cc_final: 0.8986 (mm) REVERT: B 263 TYR cc_start: 0.8639 (m-80) cc_final: 0.8425 (m-80) REVERT: B 269 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8661 (mp10) REVERT: C 230 ILE cc_start: 0.9345 (mm) cc_final: 0.9021 (mt) REVERT: C 669 CYS cc_start: 0.9018 (m) cc_final: 0.8785 (m) REVERT: D 230 ILE cc_start: 0.9282 (mm) cc_final: 0.8903 (mt) REVERT: D 484 PHE cc_start: 0.8603 (m-80) cc_final: 0.8360 (m-10) REVERT: D 505 MET cc_start: 0.8046 (pmm) cc_final: 0.7757 (pmm) REVERT: D 532 MET cc_start: 0.9097 (tpp) cc_final: 0.8566 (tpp) REVERT: D 636 GLU cc_start: 0.8726 (tp30) cc_final: 0.8451 (tp30) REVERT: D 669 CYS cc_start: 0.8852 (m) cc_final: 0.8626 (m) REVERT: D 758 MET cc_start: 0.9344 (tpp) cc_final: 0.9007 (tpp) REVERT: D 807 ASP cc_start: 0.8589 (t70) cc_final: 0.8314 (t0) REVERT: D 987 MET cc_start: 0.8451 (ppp) cc_final: 0.8236 (mmt) REVERT: D 1008 MET cc_start: 0.7661 (mmm) cc_final: 0.7431 (mmm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2788 time to fit residues: 82.3677 Evaluate side-chains 145 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 153 optimal weight: 0.0980 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** 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 = 0.3624 r_free = 0.3624 target = 0.075905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058365 restraints weight = 78101.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060367 restraints weight = 43837.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061701 restraints weight = 29979.178| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18064 Z= 0.114 Angle : 0.572 10.070 24390 Z= 0.287 Chirality : 0.039 0.180 2728 Planarity : 0.003 0.032 3076 Dihedral : 10.473 151.396 2474 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.51 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 2176 helix: 0.82 (0.17), residues: 1028 sheet: -1.38 (0.32), residues: 270 loop : -0.52 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 478 HIS 0.005 0.001 HIS C 492 PHE 0.021 0.001 PHE C 484 TYR 0.015 0.001 TYR A 202 ARG 0.007 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 769) hydrogen bonds : angle 4.42974 ( 2148) covalent geometry : bond 0.00245 (18064) covalent geometry : angle 0.57220 (24390) *********************** 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 186 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.053 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: A 63 MET cc_start: 0.8046 (ppp) cc_final: 0.7725 (ppp) REVERT: A 112 GLU cc_start: 0.8019 (tt0) cc_final: 0.7615 (tm-30) REVERT: A 158 MET cc_start: 0.6770 (mmm) cc_final: 0.6314 (mmt) REVERT: A 219 ILE cc_start: 0.9236 (mm) cc_final: 0.8964 (mm) REVERT: B 63 MET cc_start: 0.8320 (tmm) cc_final: 0.7917 (tmm) REVERT: B 152 MET cc_start: 0.9170 (ttm) cc_final: 0.8945 (ttt) REVERT: B 219 ILE cc_start: 0.9201 (mm) cc_final: 0.8984 (mm) REVERT: B 233 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 263 TYR cc_start: 0.8657 (m-80) cc_final: 0.8431 (m-80) REVERT: C 230 ILE cc_start: 0.9360 (mm) cc_final: 0.9023 (mt) REVERT: C 239 MET cc_start: 0.8954 (ttp) cc_final: 0.8516 (ttp) REVERT: C 669 CYS cc_start: 0.8802 (m) cc_final: 0.8412 (m) REVERT: C 1008 MET cc_start: 0.7039 (mmm) cc_final: 0.6559 (mmt) REVERT: D 230 ILE cc_start: 0.9274 (mm) cc_final: 0.8905 (mt) REVERT: D 239 MET cc_start: 0.8964 (ttp) cc_final: 0.8707 (ttp) REVERT: D 505 MET cc_start: 0.8035 (pmm) cc_final: 0.7773 (pmm) REVERT: D 532 MET cc_start: 0.9094 (tpp) cc_final: 0.8607 (tpp) REVERT: D 636 GLU cc_start: 0.8694 (tp30) cc_final: 0.8467 (tp30) REVERT: D 669 CYS cc_start: 0.8719 (m) cc_final: 0.8515 (m) REVERT: D 758 MET cc_start: 0.9298 (tpp) cc_final: 0.8943 (tpp) REVERT: D 807 ASP cc_start: 0.8578 (t70) cc_final: 0.8274 (t0) REVERT: D 987 MET cc_start: 0.8508 (ppp) cc_final: 0.8272 (mmt) REVERT: D 1008 MET cc_start: 0.7726 (mmm) cc_final: 0.7431 (mmm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2631 time to fit residues: 79.7705 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 : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 148 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** 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 = 0.3616 r_free = 0.3616 target = 0.075664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.058393 restraints weight = 78186.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.060375 restraints weight = 44413.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.061445 restraints weight = 30428.627| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5045 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= 0.126 Angle : 0.579 9.968 24390 Z= 0.290 Chirality : 0.040 0.163 2728 Planarity : 0.004 0.031 3076 Dihedral : 10.460 151.541 2474 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.65 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 2176 helix: 0.83 (0.17), residues: 1030 sheet: -1.42 (0.31), residues: 270 loop : -0.49 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 243 HIS 0.004 0.001 HIS A 151 PHE 0.044 0.002 PHE C 382 TYR 0.017 0.001 TYR D 140 ARG 0.006 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 769) hydrogen bonds : angle 4.45303 ( 2148) covalent geometry : bond 0.00277 (18064) covalent geometry : angle 0.57902 (24390) *********************** 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 178 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.072 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 63 MET cc_start: 0.8075 (ppp) cc_final: 0.7743 (ppp) REVERT: A 112 GLU cc_start: 0.8049 (tt0) cc_final: 0.7675 (tm-30) REVERT: A 158 MET cc_start: 0.6789 (mmm) cc_final: 0.6395 (mmt) REVERT: A 219 ILE cc_start: 0.9257 (mm) cc_final: 0.9000 (mm) REVERT: B 63 MET cc_start: 0.8287 (tmm) cc_final: 0.7907 (tmm) REVERT: B 219 ILE cc_start: 0.9224 (mm) cc_final: 0.9001 (mm) REVERT: B 233 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7363 (tm-30) REVERT: B 263 TYR cc_start: 0.8700 (m-80) cc_final: 0.8442 (m-80) REVERT: C 230 ILE cc_start: 0.9349 (mm) cc_final: 0.9023 (mt) REVERT: C 669 CYS cc_start: 0.8917 (m) cc_final: 0.8586 (m) REVERT: C 987 MET cc_start: 0.8128 (tmm) cc_final: 0.7796 (mmt) REVERT: C 1008 MET cc_start: 0.7028 (mmm) cc_final: 0.6732 (mmt) REVERT: D 205 MET cc_start: 0.8364 (tpp) cc_final: 0.7857 (tpp) REVERT: D 230 ILE cc_start: 0.9301 (mm) cc_final: 0.8933 (mt) REVERT: D 505 MET cc_start: 0.8056 (pmm) cc_final: 0.7789 (pmm) REVERT: D 532 MET cc_start: 0.9063 (tpp) cc_final: 0.8604 (tpp) REVERT: D 636 GLU cc_start: 0.8679 (tp30) cc_final: 0.8461 (tp30) REVERT: D 669 CYS cc_start: 0.8828 (m) cc_final: 0.8554 (m) REVERT: D 758 MET cc_start: 0.9309 (tpp) cc_final: 0.8929 (tpp) REVERT: D 807 ASP cc_start: 0.8518 (t70) cc_final: 0.8224 (t0) REVERT: D 987 MET cc_start: 0.8519 (ppp) cc_final: 0.8302 (mmt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2659 time to fit residues: 77.7860 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 : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 113 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** 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 = 0.3631 r_free = 0.3631 target = 0.076387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059151 restraints weight = 77440.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.061150 restraints weight = 43602.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062443 restraints weight = 29727.373| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18064 Z= 0.112 Angle : 0.585 9.601 24390 Z= 0.289 Chirality : 0.040 0.168 2728 Planarity : 0.003 0.033 3076 Dihedral : 10.377 151.679 2474 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.51 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 2176 helix: 0.87 (0.17), residues: 1030 sheet: -1.42 (0.31), residues: 270 loop : -0.47 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 139 HIS 0.009 0.001 HIS B 153 PHE 0.021 0.001 PHE D 410 TYR 0.013 0.001 TYR A 202 ARG 0.005 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 769) hydrogen bonds : angle 4.39725 ( 2148) covalent geometry : bond 0.00240 (18064) covalent geometry : angle 0.58490 (24390) ********************** 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 196 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.926 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: 0.8088 (ppp) cc_final: 0.7725 (ppp) REVERT: A 112 GLU cc_start: 0.8097 (tt0) cc_final: 0.7759 (tm-30) REVERT: A 158 MET cc_start: 0.6853 (mmm) cc_final: 0.6291 (mmt) REVERT: A 219 ILE cc_start: 0.9202 (mm) cc_final: 0.8954 (mm) REVERT: B 63 MET cc_start: 0.8308 (tmm) cc_final: 0.7935 (tmm) REVERT: B 219 ILE cc_start: 0.9164 (mm) cc_final: 0.8949 (mm) REVERT: B 233 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 263 TYR cc_start: 0.8692 (m-80) cc_final: 0.8450 (m-80) REVERT: C 230 ILE cc_start: 0.9340 (mm) cc_final: 0.9011 (mt) REVERT: C 669 CYS cc_start: 0.8915 (m) cc_final: 0.8636 (m) REVERT: D 205 MET cc_start: 0.8255 (tpp) cc_final: 0.7733 (tpp) REVERT: D 230 ILE cc_start: 0.9273 (mm) cc_final: 0.8871 (mt) REVERT: D 505 MET cc_start: 0.8023 (pmm) cc_final: 0.7775 (pmm) REVERT: D 532 MET cc_start: 0.9084 (tpp) cc_final: 0.8604 (tpp) REVERT: D 636 GLU cc_start: 0.8685 (tp30) cc_final: 0.8412 (tp30) REVERT: D 758 MET cc_start: 0.9288 (tpp) cc_final: 0.8928 (tpp) REVERT: D 807 ASP cc_start: 0.8485 (t70) cc_final: 0.8183 (t0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2525 time to fit residues: 79.3397 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 : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 92 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 113 optimal weight: 7.9990 chunk 171 optimal weight: 0.2980 chunk 172 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- 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 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 GLN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3620 r_free = 0.3620 target = 0.075759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.058471 restraints weight = 77723.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060431 restraints weight = 43906.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061757 restraints weight = 30033.377| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18064 Z= 0.128 Angle : 0.595 9.550 24390 Z= 0.295 Chirality : 0.040 0.145 2728 Planarity : 0.004 0.036 3076 Dihedral : 10.388 151.571 2474 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.93 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 2176 helix: 0.89 (0.17), residues: 1028 sheet: -1.38 (0.31), residues: 270 loop : -0.48 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 243 HIS 0.005 0.001 HIS C 492 PHE 0.040 0.002 PHE C 382 TYR 0.012 0.001 TYR D 140 ARG 0.005 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 769) hydrogen bonds : angle 4.44183 ( 2148) covalent geometry : bond 0.00285 (18064) covalent geometry : angle 0.59539 (24390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5334.20 seconds wall clock time: 93 minutes 50.26 seconds (5630.26 seconds total)