Starting phenix.real_space_refine on Mon May 19 02:28:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxn_40855/05_2025/8sxn_40855_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxn_40855/05_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_40855/05_2025/8sxn_40855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxn_40855/05_2025/8sxn_40855.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxn_40855/05_2025/8sxn_40855_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxn_40855/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.98, per 1000 atoms: 0.62 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: 4.18 Conformation dependent library (CDL) restraints added in 2.1 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: 1.90 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: 6.14 Time building geometry restraints manager: 4.93 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.180 Find NCS groups from input model: 0.550 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- 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 : 1.912 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: 0.3128 time to fit residues: 188.8343 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 : 1.963 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.079679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062802 restraints weight = 77714.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064786 restraints weight = 44880.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.066126 restraints weight = 30807.342| |-----------------------------------------------------------------------------| 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 4.94703 ( 2148) covalent geometry : bond 0.00322 (18064) covalent geometry : angle 0.64829 (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 : 2.085 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: 0.8312 (tmm) cc_final: 0.8012 (ppp) REVERT: A 109 ILE cc_start: 0.8829 (mt) cc_final: 0.8130 (mt) REVERT: A 112 GLU cc_start: 0.7678 (tt0) cc_final: 0.7342 (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: 0.7882 (mmm) cc_final: 0.7492 (mpp) REVERT: B 63 MET cc_start: 0.8487 (tmm) cc_final: 0.8148 (ppp) REVERT: B 152 MET cc_start: 0.8983 (ttm) cc_final: 0.8736 (ttt) REVERT: B 158 MET cc_start: 0.7051 (mpp) cc_final: 0.6633 (mpp) REVERT: B 229 MET cc_start: 0.9049 (mtp) cc_final: 0.8799 (mtp) REVERT: B 263 TYR cc_start: 0.8435 (m-80) cc_final: 0.8176 (m-80) REVERT: C 205 MET cc_start: 0.8051 (ttp) cc_final: 0.7494 (tpp) REVERT: C 230 ILE cc_start: 0.9225 (mm) cc_final: 0.8920 (mt) REVERT: C 665 VAL cc_start: 0.9389 (t) cc_final: 0.9066 (p) REVERT: C 742 SER cc_start: 0.8135 (m) cc_final: 0.7904 (p) REVERT: C 943 LEU cc_start: 0.9242 (tp) cc_final: 0.8922 (tt) REVERT: C 1025 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8605 (mttp) REVERT: D 205 MET cc_start: 0.7564 (ttp) cc_final: 0.6848 (tpp) REVERT: D 230 ILE cc_start: 0.9198 (mm) cc_final: 0.8848 (mt) REVERT: D 239 MET cc_start: 0.8761 (ttp) cc_final: 0.8535 (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: 0.8774 (mt) REVERT: D 508 PHE cc_start: 0.8370 (m-80) cc_final: 0.8166 (m-10) REVERT: D 595 LYS cc_start: 0.8297 (tptt) cc_final: 0.8066 (tptp) REVERT: D 636 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8192 (tp30) REVERT: D 640 GLU cc_start: 0.8115 (pp20) cc_final: 0.7898 (pp20) REVERT: D 1025 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8824 (mmtp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2852 time to fit residues: 123.3537 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 : 2.174 ------------------------------------------------------------------------------- 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: 9.9990 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.074993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.058161 restraints weight = 77647.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059913 restraints weight = 46997.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060715 restraints weight = 33328.981| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3486 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= 0.258 Angle : 0.709 10.535 24390 Z= 0.358 Chirality : 0.042 0.142 2728 Planarity : 0.004 0.032 3076 Dihedral : 10.248 148.601 2474 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.78 % Favored : 94.76 % Rotamer: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.07 % 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: 0.69 (0.16), residues: 1008 sheet: -0.73 (0.32), residues: 266 loop : -0.25 (0.22), residues: 902 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 0.042 0.002 PHE C 382 TYR 0.013 0.002 TYR D 443 ARG 0.007 0.001 ARG C 779 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 769) hydrogen bonds : angle 5.00035 ( 2148) covalent geometry : bond 0.00556 (18064) covalent geometry : angle 0.70881 (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 205 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 1.970 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: 0.8751 (mt) cc_final: 0.8175 (mt) REVERT: A 112 GLU cc_start: 0.8026 (tt0) cc_final: 0.7424 (tm-30) REVERT: B 63 MET cc_start: 0.7980 (tmm) cc_final: 0.7737 (tmm) REVERT: B 152 MET cc_start: 0.8955 (ttm) cc_final: 0.8690 (ttt) REVERT: B 158 MET cc_start: 0.7085 (mpp) cc_final: 0.6853 (mmm) REVERT: C 230 ILE cc_start: 0.9404 (mm) cc_final: 0.9009 (mt) REVERT: C 665 VAL cc_start: 0.9499 (t) cc_final: 0.9091 (p) REVERT: C 810 LEU cc_start: 0.8628 (mt) cc_final: 0.8166 (mt) REVERT: C 943 LEU cc_start: 0.9234 (tp) cc_final: 0.9018 (tp) REVERT: D 230 ILE cc_start: 0.9359 (mm) cc_final: 0.8991 (mt) REVERT: D 240 MET cc_start: 0.8578 (mmm) cc_final: 0.8374 (tpt) REVERT: D 382 PHE cc_start: 0.8235 (m-80) cc_final: 0.8023 (m-80) REVERT: D 502 PHE cc_start: 0.7914 (m-80) cc_final: 0.7607 (m-80) REVERT: D 595 LYS cc_start: 0.8291 (tptt) cc_final: 0.8071 (tptp) REVERT: D 636 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8239 (tp30) REVERT: D 640 GLU cc_start: 0.8200 (pp20) cc_final: 0.7742 (pp20) REVERT: D 957 CYS cc_start: 0.8648 (p) cc_final: 0.8111 (p) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.2717 time to fit residues: 87.5268 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 : 1.925 ------------------------------------------------------------------------------- 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: 1.9990 chunk 123 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** C 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.057177 restraints weight = 78894.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.058935 restraints weight = 47313.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.060086 restraints weight = 33394.608| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18064 Z= 0.249 Angle : 0.685 11.409 24390 Z= 0.345 Chirality : 0.042 0.180 2728 Planarity : 0.004 0.039 3076 Dihedral : 10.532 149.555 2474 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.74 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 0.65 (0.16), residues: 1006 sheet: -1.05 (0.33), residues: 254 loop : -0.46 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 478 HIS 0.011 0.001 HIS B 159 PHE 0.029 0.002 PHE C 148 TYR 0.014 0.002 TYR D 632 ARG 0.005 0.001 ARG C 779 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 769) hydrogen bonds : angle 4.92283 ( 2148) covalent geometry : bond 0.00544 (18064) covalent geometry : angle 0.68497 (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 187 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.967 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: 0.8080 (tt0) cc_final: 0.7449 (tm-30) REVERT: A 158 MET cc_start: 0.6606 (mmm) cc_final: 0.5700 (mmm) REVERT: A 263 TYR cc_start: 0.8796 (m-80) cc_final: 0.8570 (m-10) REVERT: B 63 MET cc_start: 0.8272 (tmm) cc_final: 0.7875 (tmm) REVERT: B 152 MET cc_start: 0.9024 (ttm) cc_final: 0.8817 (ttt) REVERT: C 230 ILE cc_start: 0.9376 (mm) cc_final: 0.9070 (mt) REVERT: C 382 PHE cc_start: 0.8297 (m-80) cc_final: 0.8031 (m-80) REVERT: C 665 VAL cc_start: 0.9463 (t) cc_final: 0.9074 (p) REVERT: D 230 ILE cc_start: 0.9342 (mm) cc_final: 0.9020 (mt) REVERT: D 484 PHE cc_start: 0.8668 (m-10) cc_final: 0.8350 (m-10) REVERT: D 502 PHE cc_start: 0.7752 (m-80) cc_final: 0.7515 (m-80) REVERT: D 758 MET cc_start: 0.9341 (tpp) cc_final: 0.9050 (tpp) REVERT: D 807 ASP cc_start: 0.8582 (t70) cc_final: 0.8280 (t0) REVERT: D 864 GLU cc_start: 0.7921 (tp30) cc_final: 0.7615 (tp30) REVERT: D 957 CYS cc_start: 0.8691 (p) cc_final: 0.8112 (p) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2707 time to fit residues: 79.7228 Evaluate side-chains 150 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 233 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.073206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.055772 restraints weight = 78461.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057675 restraints weight = 44762.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058925 restraints weight = 30758.354| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18064 Z= 0.214 Angle : 0.632 8.919 24390 Z= 0.321 Chirality : 0.041 0.151 2728 Planarity : 0.004 0.034 3076 Dihedral : 10.603 150.183 2474 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.84 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -0.23 (0.19), residues: 2176 helix: 0.74 (0.16), residues: 1010 sheet: -1.33 (0.31), residues: 274 loop : -0.69 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 478 HIS 0.006 0.001 HIS B 159 PHE 0.036 0.002 PHE C 502 TYR 0.011 0.002 TYR C 136 ARG 0.005 0.001 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 769) hydrogen bonds : angle 4.78089 ( 2148) covalent geometry : bond 0.00466 (18064) covalent geometry : angle 0.63159 (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 179 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.099 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 112 GLU cc_start: 0.8127 (tt0) cc_final: 0.7470 (tm-30) REVERT: A 158 MET cc_start: 0.6828 (mmm) cc_final: 0.6354 (mmt) REVERT: A 219 ILE cc_start: 0.9371 (mm) cc_final: 0.9104 (mm) REVERT: A 263 TYR cc_start: 0.8815 (m-80) cc_final: 0.8613 (m-10) REVERT: B 63 MET cc_start: 0.8280 (tmm) cc_final: 0.7886 (tmm) REVERT: B 152 MET cc_start: 0.9120 (ttm) cc_final: 0.8835 (ttt) REVERT: B 158 MET cc_start: 0.7114 (mmm) cc_final: 0.6572 (mmm) REVERT: B 263 TYR cc_start: 0.8669 (m-80) cc_final: 0.8456 (m-80) REVERT: C 208 LEU cc_start: 0.9328 (mt) cc_final: 0.9076 (mt) REVERT: C 230 ILE cc_start: 0.9378 (mm) cc_final: 0.9049 (mt) REVERT: C 665 VAL cc_start: 0.9337 (t) cc_final: 0.9039 (p) REVERT: C 987 MET cc_start: 0.8292 (mmt) cc_final: 0.8029 (mmt) REVERT: D 208 LEU cc_start: 0.9379 (mt) cc_final: 0.9159 (mt) REVERT: D 230 ILE cc_start: 0.9339 (mm) cc_final: 0.8981 (mt) REVERT: D 426 MET cc_start: 0.8602 (mtp) cc_final: 0.8362 (mtm) REVERT: D 484 PHE cc_start: 0.8518 (m-10) cc_final: 0.8189 (m-10) REVERT: D 502 PHE cc_start: 0.7792 (m-80) cc_final: 0.7573 (m-80) REVERT: D 532 MET cc_start: 0.9158 (tpp) cc_final: 0.8610 (tpp) REVERT: D 758 MET cc_start: 0.9388 (tpp) cc_final: 0.9041 (tpp) REVERT: D 807 ASP cc_start: 0.8622 (t70) cc_final: 0.8285 (t0) REVERT: D 864 GLU cc_start: 0.8048 (tp30) cc_final: 0.7730 (tp30) REVERT: D 957 CYS cc_start: 0.8769 (p) cc_final: 0.7677 (p) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2770 time to fit residues: 78.3679 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 : 1.952 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 156 optimal weight: 0.0270 chunk 102 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.074551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056853 restraints weight = 77779.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058820 restraints weight = 43855.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060160 restraints weight = 30020.272| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4599 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= 0.138 Angle : 0.572 9.103 24390 Z= 0.290 Chirality : 0.039 0.148 2728 Planarity : 0.004 0.037 3076 Dihedral : 10.590 150.797 2474 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.65 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -0.13 (0.19), residues: 2176 helix: 0.82 (0.17), residues: 1024 sheet: -1.31 (0.32), residues: 272 loop : -0.65 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 478 HIS 0.005 0.001 HIS C 492 PHE 0.028 0.002 PHE C 581 TYR 0.010 0.001 TYR C 591 ARG 0.010 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 769) hydrogen bonds : angle 4.53663 ( 2148) covalent geometry : bond 0.00302 (18064) covalent geometry : angle 0.57221 (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 187 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8115 (tt0) cc_final: 0.7540 (tm-30) REVERT: A 158 MET cc_start: 0.6818 (mmm) cc_final: 0.6288 (mmt) REVERT: A 219 ILE cc_start: 0.9281 (mm) cc_final: 0.9013 (mm) REVERT: A 269 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8798 (mp10) REVERT: B 63 MET cc_start: 0.8312 (tmm) cc_final: 0.7926 (tmm) REVERT: B 65 VAL cc_start: 0.8015 (t) cc_final: 0.7785 (t) REVERT: B 152 MET cc_start: 0.9135 (ttm) cc_final: 0.8848 (ttt) REVERT: B 158 MET cc_start: 0.7032 (mmm) cc_final: 0.6546 (mmm) REVERT: B 203 MET cc_start: 0.7321 (mtp) cc_final: 0.7114 (mtt) REVERT: B 219 ILE cc_start: 0.9289 (mm) cc_final: 0.9044 (mm) REVERT: B 263 TYR cc_start: 0.8668 (m-80) cc_final: 0.8458 (m-80) REVERT: C 205 MET cc_start: 0.8056 (ttm) cc_final: 0.7545 (tpp) REVERT: C 208 LEU cc_start: 0.9331 (mt) cc_final: 0.9002 (mt) REVERT: C 230 ILE cc_start: 0.9381 (mm) cc_final: 0.9021 (mt) REVERT: C 239 MET cc_start: 0.8972 (ttp) cc_final: 0.8600 (ttp) REVERT: C 636 GLU cc_start: 0.8797 (tp30) cc_final: 0.8591 (tp30) REVERT: C 665 VAL cc_start: 0.9290 (t) cc_final: 0.9003 (p) REVERT: C 669 CYS cc_start: 0.8919 (m) cc_final: 0.8672 (m) REVERT: D 230 ILE cc_start: 0.9320 (mm) cc_final: 0.8956 (mt) REVERT: D 382 PHE cc_start: 0.8429 (m-80) cc_final: 0.8058 (m-80) REVERT: D 484 PHE cc_start: 0.8524 (m-10) cc_final: 0.8141 (m-10) REVERT: D 532 MET cc_start: 0.9150 (tpp) cc_final: 0.8567 (tpp) REVERT: D 640 GLU cc_start: 0.8176 (pp20) cc_final: 0.7968 (pp20) REVERT: D 758 MET cc_start: 0.9355 (tpp) cc_final: 0.9014 (tpp) REVERT: D 807 ASP cc_start: 0.8594 (t70) cc_final: 0.8241 (t0) REVERT: D 864 GLU cc_start: 0.8064 (tp30) cc_final: 0.7735 (tp30) REVERT: D 957 CYS cc_start: 0.8848 (p) cc_final: 0.8103 (p) REVERT: D 1008 MET cc_start: 0.7659 (mmm) cc_final: 0.7338 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2711 time to fit residues: 81.4740 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 : 2.264 ------------------------------------------------------------------------------- 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: 0.9980 chunk 157 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056066 restraints weight = 78660.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057999 restraints weight = 44698.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059281 restraints weight = 30793.083| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18064 Z= 0.189 Angle : 0.615 9.835 24390 Z= 0.310 Chirality : 0.040 0.153 2728 Planarity : 0.004 0.031 3076 Dihedral : 10.656 152.325 2474 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.25 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -0.25 (0.19), residues: 2176 helix: 0.77 (0.17), residues: 1028 sheet: -1.45 (0.31), residues: 274 loop : -0.74 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.011 0.001 HIS C 364 PHE 0.038 0.002 PHE C 502 TYR 0.026 0.001 TYR C 632 ARG 0.005 0.000 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 769) hydrogen bonds : angle 4.66948 ( 2148) covalent geometry : bond 0.00412 (18064) covalent geometry : angle 0.61494 (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 179 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.951 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 219 ILE cc_start: 0.9313 (mm) cc_final: 0.9034 (mm) REVERT: B 63 MET cc_start: 0.8267 (tmm) cc_final: 0.7845 (tmm) REVERT: B 152 MET cc_start: 0.9138 (ttm) cc_final: 0.8890 (ttt) REVERT: B 158 MET cc_start: 0.6916 (mmm) cc_final: 0.6155 (mmm) REVERT: B 219 ILE cc_start: 0.9299 (mm) cc_final: 0.9042 (mm) REVERT: B 263 TYR cc_start: 0.8712 (m-80) cc_final: 0.8503 (m-80) REVERT: C 208 LEU cc_start: 0.9348 (mt) cc_final: 0.9130 (mt) REVERT: C 230 ILE cc_start: 0.9387 (mm) cc_final: 0.9058 (mt) REVERT: C 484 PHE cc_start: 0.8490 (m-10) cc_final: 0.8259 (m-10) REVERT: C 665 VAL cc_start: 0.9377 (t) cc_final: 0.9076 (p) REVERT: C 669 CYS cc_start: 0.9032 (m) cc_final: 0.8819 (m) REVERT: C 1008 MET cc_start: 0.6970 (mmm) cc_final: 0.6708 (mmm) REVERT: D 230 ILE cc_start: 0.9338 (mm) cc_final: 0.8984 (mt) REVERT: D 382 PHE cc_start: 0.8380 (m-80) cc_final: 0.7979 (m-80) REVERT: D 484 PHE cc_start: 0.8535 (m-10) cc_final: 0.8167 (m-10) REVERT: D 502 PHE cc_start: 0.7786 (m-80) cc_final: 0.7542 (m-80) REVERT: D 505 MET cc_start: 0.8151 (pmm) cc_final: 0.7855 (pmm) REVERT: D 532 MET cc_start: 0.9130 (tpp) cc_final: 0.8560 (tpp) REVERT: D 669 CYS cc_start: 0.8901 (m) cc_final: 0.8673 (m) REVERT: D 758 MET cc_start: 0.9367 (tpp) cc_final: 0.9045 (tpp) REVERT: D 807 ASP cc_start: 0.8579 (t70) cc_final: 0.8231 (t0) REVERT: D 864 GLU cc_start: 0.8072 (tp30) cc_final: 0.7822 (tp30) REVERT: D 1008 MET cc_start: 0.7805 (mmm) cc_final: 0.7594 (mmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2810 time to fit residues: 79.6964 Evaluate side-chains 141 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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: 7.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.074392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056816 restraints weight = 77798.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.058739 restraints weight = 43817.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060100 restraints weight = 29895.936| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18064 Z= 0.138 Angle : 0.579 10.485 24390 Z= 0.292 Chirality : 0.039 0.173 2728 Planarity : 0.004 0.033 3076 Dihedral : 10.604 151.312 2474 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.07 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.15 (0.19), residues: 2176 helix: 0.86 (0.17), residues: 1026 sheet: -1.46 (0.31), residues: 272 loop : -0.68 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.005 0.001 HIS A 151 PHE 0.033 0.002 PHE D 502 TYR 0.017 0.001 TYR A 202 ARG 0.006 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 769) hydrogen bonds : angle 4.54820 ( 2148) covalent geometry : bond 0.00303 (18064) covalent geometry : angle 0.57867 (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 182 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 2.415 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 86 LEU cc_start: 0.9284 (mp) cc_final: 0.8846 (mt) REVERT: A 219 ILE cc_start: 0.9242 (mm) cc_final: 0.8968 (mm) REVERT: B 63 MET cc_start: 0.8270 (tmm) cc_final: 0.7844 (tmm) REVERT: B 152 MET cc_start: 0.9143 (ttm) cc_final: 0.8904 (ttt) REVERT: B 158 MET cc_start: 0.6929 (mmm) cc_final: 0.6438 (mmm) REVERT: B 186 PHE cc_start: 0.7382 (m-10) cc_final: 0.7160 (m-10) REVERT: B 219 ILE cc_start: 0.9252 (mm) cc_final: 0.8998 (mm) REVERT: B 263 TYR cc_start: 0.8701 (m-80) cc_final: 0.8491 (m-80) REVERT: B 269 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8724 (mp10) REVERT: C 208 LEU cc_start: 0.9347 (mt) cc_final: 0.9145 (mt) REVERT: C 230 ILE cc_start: 0.9383 (mm) cc_final: 0.9070 (mt) REVERT: C 484 PHE cc_start: 0.8374 (m-10) cc_final: 0.8143 (m-10) REVERT: C 665 VAL cc_start: 0.9405 (t) cc_final: 0.9121 (p) REVERT: C 987 MET cc_start: 0.8002 (tmm) cc_final: 0.7800 (mmt) REVERT: D 230 ILE cc_start: 0.9312 (mm) cc_final: 0.8979 (mt) REVERT: D 484 PHE cc_start: 0.8420 (m-10) cc_final: 0.8084 (m-10) REVERT: D 502 PHE cc_start: 0.7710 (m-80) cc_final: 0.7479 (m-80) REVERT: D 505 MET cc_start: 0.8110 (pmm) cc_final: 0.7838 (pmm) REVERT: D 532 MET cc_start: 0.9045 (tpp) cc_final: 0.8603 (tpp) REVERT: D 669 CYS cc_start: 0.8930 (m) cc_final: 0.8697 (m) REVERT: D 758 MET cc_start: 0.9352 (tpp) cc_final: 0.9007 (tpp) REVERT: D 807 ASP cc_start: 0.8577 (t70) cc_final: 0.8226 (t0) REVERT: D 864 GLU cc_start: 0.8071 (tp30) cc_final: 0.7789 (tp30) REVERT: D 975 SER cc_start: 0.9139 (t) cc_final: 0.8923 (t) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2705 time to fit residues: 78.6993 Evaluate side-chains 143 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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: 0.8980 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 269 GLN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054177 restraints weight = 78231.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.056045 restraints weight = 44524.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.057311 restraints weight = 30570.840| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18064 Z= 0.217 Angle : 0.654 9.132 24390 Z= 0.329 Chirality : 0.041 0.188 2728 Planarity : 0.004 0.030 3076 Dihedral : 10.652 150.910 2474 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.94 % Favored : 92.69 % 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: -0.31 (0.19), residues: 2176 helix: 0.78 (0.17), residues: 1024 sheet: -1.64 (0.30), residues: 274 loop : -0.79 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 478 HIS 0.007 0.001 HIS C 360 PHE 0.035 0.002 PHE D 382 TYR 0.020 0.002 TYR A 202 ARG 0.004 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 769) hydrogen bonds : angle 4.77568 ( 2148) covalent geometry : bond 0.00477 (18064) covalent geometry : angle 0.65443 (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 170 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.861 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 158 MET cc_start: 0.6830 (mmm) cc_final: 0.6181 (mmt) REVERT: A 219 ILE cc_start: 0.9280 (mm) cc_final: 0.9027 (mm) REVERT: B 63 MET cc_start: 0.8282 (tmm) cc_final: 0.7861 (tmm) REVERT: B 158 MET cc_start: 0.6962 (mmm) cc_final: 0.6510 (mmm) REVERT: B 186 PHE cc_start: 0.7398 (m-10) cc_final: 0.7150 (m-10) REVERT: B 203 MET cc_start: 0.7146 (mtp) cc_final: 0.6853 (mtt) REVERT: B 219 ILE cc_start: 0.9270 (mm) cc_final: 0.8991 (mm) REVERT: C 205 MET cc_start: 0.8543 (tpp) cc_final: 0.7719 (tpp) REVERT: C 208 LEU cc_start: 0.9359 (mt) cc_final: 0.9126 (mt) REVERT: C 230 ILE cc_start: 0.9393 (mm) cc_final: 0.9034 (mt) REVERT: C 239 MET cc_start: 0.9188 (ttp) cc_final: 0.8945 (ttp) REVERT: C 484 PHE cc_start: 0.8498 (m-10) cc_final: 0.8193 (m-10) REVERT: C 665 VAL cc_start: 0.9337 (t) cc_final: 0.9091 (p) REVERT: C 669 CYS cc_start: 0.8810 (m) cc_final: 0.8360 (m) REVERT: D 230 ILE cc_start: 0.9335 (mm) cc_final: 0.8944 (mt) REVERT: D 382 PHE cc_start: 0.8504 (m-80) cc_final: 0.8265 (m-80) REVERT: D 484 PHE cc_start: 0.8461 (m-10) cc_final: 0.8121 (m-10) REVERT: D 505 MET cc_start: 0.8271 (pmm) cc_final: 0.7994 (pmm) REVERT: D 532 MET cc_start: 0.9202 (tpp) cc_final: 0.8603 (tpp) REVERT: D 669 CYS cc_start: 0.8818 (m) cc_final: 0.8548 (m) REVERT: D 758 MET cc_start: 0.9406 (tpp) cc_final: 0.8831 (tpp) REVERT: D 807 ASP cc_start: 0.8643 (t70) cc_final: 0.8283 (t0) REVERT: D 864 GLU cc_start: 0.8160 (tp30) cc_final: 0.7864 (tp30) REVERT: D 975 SER cc_start: 0.9144 (t) cc_final: 0.8911 (t) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2778 time to fit residues: 76.0203 Evaluate side-chains 136 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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: 0.6980 chunk 58 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 169 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** C 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.072980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056153 restraints weight = 75507.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058075 restraints weight = 41806.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059322 restraints weight = 28178.350| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5264 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= 0.131 Angle : 0.590 9.321 24390 Z= 0.297 Chirality : 0.040 0.171 2728 Planarity : 0.004 0.037 3076 Dihedral : 10.613 151.820 2474 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.79 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -0.24 (0.19), residues: 2176 helix: 0.82 (0.17), residues: 1026 sheet: -1.59 (0.31), residues: 272 loop : -0.74 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 478 HIS 0.005 0.001 HIS C 492 PHE 0.035 0.002 PHE D 502 TYR 0.032 0.001 TYR C 632 ARG 0.005 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 769) hydrogen bonds : angle 4.54765 ( 2148) covalent geometry : bond 0.00288 (18064) covalent geometry : angle 0.58968 (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 178 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.818 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 158 MET cc_start: 0.6687 (mmm) cc_final: 0.6059 (mmm) REVERT: A 219 ILE cc_start: 0.9229 (mm) cc_final: 0.8952 (mm) REVERT: B 63 MET cc_start: 0.8296 (tmm) cc_final: 0.7846 (tmm) REVERT: B 152 MET cc_start: 0.9050 (ttm) cc_final: 0.8807 (ttt) REVERT: B 158 MET cc_start: 0.6911 (mmm) cc_final: 0.6295 (mmm) REVERT: B 186 PHE cc_start: 0.7462 (m-10) cc_final: 0.7224 (m-10) REVERT: B 203 MET cc_start: 0.7030 (mtp) cc_final: 0.6796 (mtp) REVERT: B 219 ILE cc_start: 0.9223 (mm) cc_final: 0.8950 (mm) REVERT: B 263 TYR cc_start: 0.8713 (m-80) cc_final: 0.8466 (m-80) REVERT: C 205 MET cc_start: 0.8486 (tpp) cc_final: 0.7966 (tpp) REVERT: C 208 LEU cc_start: 0.9368 (mt) cc_final: 0.9109 (mt) REVERT: C 230 ILE cc_start: 0.9381 (mm) cc_final: 0.9054 (mt) REVERT: C 382 PHE cc_start: 0.8515 (m-80) cc_final: 0.8238 (m-80) REVERT: C 647 MET cc_start: 0.8234 (ttm) cc_final: 0.7805 (ttm) REVERT: C 654 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7115 (mm-30) REVERT: C 669 CYS cc_start: 0.8890 (m) cc_final: 0.8428 (m) REVERT: C 987 MET cc_start: 0.8232 (mmt) cc_final: 0.7972 (tmm) REVERT: D 205 MET cc_start: 0.8624 (tpp) cc_final: 0.8144 (tpp) REVERT: D 230 ILE cc_start: 0.9321 (mm) cc_final: 0.8940 (mt) REVERT: D 484 PHE cc_start: 0.8501 (m-10) cc_final: 0.8157 (m-10) REVERT: D 505 MET cc_start: 0.8193 (pmm) cc_final: 0.7942 (pmm) REVERT: D 532 MET cc_start: 0.9185 (tpp) cc_final: 0.8567 (tpp) REVERT: D 636 GLU cc_start: 0.8826 (tp30) cc_final: 0.8608 (tp30) REVERT: D 669 CYS cc_start: 0.8654 (m) cc_final: 0.8229 (m) REVERT: D 758 MET cc_start: 0.9354 (tpp) cc_final: 0.9011 (tpp) REVERT: D 807 ASP cc_start: 0.8588 (t70) cc_final: 0.8230 (t0) REVERT: D 864 GLU cc_start: 0.8139 (tp30) cc_final: 0.7821 (tp30) REVERT: D 975 SER cc_start: 0.8881 (t) cc_final: 0.8480 (t) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2585 time to fit residues: 73.9930 Evaluate side-chains 141 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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: 0.0020 chunk 113 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 172 optimal weight: 0.0020 chunk 130 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS D 685 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.074523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057602 restraints weight = 75760.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.059534 restraints weight = 42086.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060856 restraints weight = 28294.093| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18064 Z= 0.107 Angle : 0.561 9.258 24390 Z= 0.282 Chirality : 0.039 0.181 2728 Planarity : 0.003 0.035 3076 Dihedral : 10.477 152.100 2474 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.70 % Favored : 93.98 % 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: -0.03 (0.19), residues: 2176 helix: 0.99 (0.17), residues: 1016 sheet: -1.50 (0.31), residues: 270 loop : -0.62 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 243 HIS 0.006 0.001 HIS D 360 PHE 0.018 0.001 PHE D 382 TYR 0.014 0.001 TYR A 202 ARG 0.006 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 769) hydrogen bonds : angle 4.33568 ( 2148) covalent geometry : bond 0.00225 (18064) covalent geometry : angle 0.56078 (24390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5153.51 seconds wall clock time: 91 minutes 41.46 seconds (5501.46 seconds total)