Starting phenix.real_space_refine on Mon Nov 18 23:34:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/11_2024/8sxn_40855_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/11_2024/8sxn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/11_2024/8sxn_40855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/11_2024/8sxn_40855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/11_2024/8sxn_40855_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/11_2024/8sxn_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 11.50, per 1000 atoms: 0.65 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: 4.94 Conformation dependent library (CDL) restraints added in 2.4 seconds 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 12 sheets defined 49.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 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: 6.23 Time building geometry restraints manager: 5.54 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: 0.00 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: 2.790 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.340 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.560 ------------------------------------------------------------------------------- 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= 0.812 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 *********************** 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 : 2.239 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: 0.3323 time to fit residues: 200.4621 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 : 2.381 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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= 0.215 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 *********************** 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 : 2.271 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: 0.7590 (mt) cc_final: 0.5047 (mt) REVERT: A 110 VAL cc_start: 0.7515 (t) cc_final: 0.7035 (t) REVERT: A 112 GLU cc_start: 0.7914 (tt0) cc_final: 0.7679 (tm-30) REVERT: A 140 LYS cc_start: 0.9269 (tttp) cc_final: 0.9044 (ttpt) REVERT: A 142 PHE cc_start: 0.8704 (t80) cc_final: 0.8459 (t80) REVERT: A 152 MET cc_start: 0.9167 (ttm) cc_final: 0.8935 (ttm) REVERT: A 158 MET cc_start: 0.6777 (mtm) cc_final: 0.6504 (mtm) REVERT: B 26 MET cc_start: 0.7847 (mmm) cc_final: 0.7433 (mpp) REVERT: B 104 ASP cc_start: 0.9252 (m-30) cc_final: 0.8956 (t0) REVERT: B 110 VAL cc_start: 0.8197 (t) cc_final: 0.6792 (p) REVERT: B 152 MET cc_start: 0.9269 (ttm) cc_final: 0.9015 (ttt) REVERT: B 158 MET cc_start: 0.6947 (mpp) cc_final: 0.6584 (mpp) REVERT: B 229 MET cc_start: 0.8990 (mtp) cc_final: 0.8774 (mtp) REVERT: B 263 TYR cc_start: 0.8521 (m-80) cc_final: 0.8213 (m-80) REVERT: C 205 MET cc_start: 0.7380 (ttp) cc_final: 0.6885 (tpp) REVERT: C 230 ILE cc_start: 0.9191 (mm) cc_final: 0.8974 (mt) REVERT: C 521 ILE cc_start: 0.9233 (pt) cc_final: 0.9026 (tp) REVERT: C 591 TYR cc_start: 0.6774 (m-80) cc_final: 0.6512 (m-10) REVERT: C 742 SER cc_start: 0.8174 (m) cc_final: 0.7940 (p) REVERT: C 943 LEU cc_start: 0.9223 (tp) cc_final: 0.8885 (tt) REVERT: C 1025 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8646 (mttp) REVERT: D 205 MET cc_start: 0.7017 (ttp) cc_final: 0.6316 (tpp) REVERT: D 230 ILE cc_start: 0.9185 (mm) cc_final: 0.8906 (mt) REVERT: D 239 MET cc_start: 0.8787 (ttp) cc_final: 0.8537 (ttp) REVERT: D 240 MET cc_start: 0.8553 (mmm) cc_final: 0.8134 (mmt) REVERT: D 256 LEU cc_start: 0.9162 (mt) cc_final: 0.8878 (mt) REVERT: D 508 PHE cc_start: 0.8260 (m-80) cc_final: 0.8030 (m-10) REVERT: D 521 ILE cc_start: 0.9330 (pt) cc_final: 0.9113 (tp) REVERT: D 595 LYS cc_start: 0.8589 (tptt) cc_final: 0.8339 (tptp) REVERT: D 636 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8358 (tp30) REVERT: D 640 GLU cc_start: 0.8631 (pp20) cc_final: 0.8423 (pp20) REVERT: D 1025 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8857 (mmtp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3041 time to fit residues: 131.5178 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 : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 164 optimal weight: 0.3980 chunk 134 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 214 optimal weight: 0.0060 chunk 176 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 252 GLN B 108 ASN C 360 HIS C 845 GLN D 824 HIS D1001 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18064 Z= 0.165 Angle : 0.575 9.735 24390 Z= 0.297 Chirality : 0.039 0.146 2728 Planarity : 0.004 0.031 3076 Dihedral : 9.974 148.743 2474 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.27 % Favored : 95.27 % Rotamer: Outliers : 0.05 % Allowed : 1.82 % 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: 0.32 (0.19), residues: 2176 helix: 0.87 (0.17), residues: 1008 sheet: -0.63 (0.32), residues: 266 loop : -0.12 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 243 HIS 0.004 0.001 HIS D 492 PHE 0.041 0.002 PHE C 382 TYR 0.018 0.001 TYR A 49 ARG 0.010 0.000 ARG D 779 *********************** 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 235 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 2.167 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 109 ILE cc_start: 0.6726 (mt) cc_final: 0.6223 (mt) REVERT: A 112 GLU cc_start: 0.7860 (tt0) cc_final: 0.7593 (tm-30) REVERT: A 158 MET cc_start: 0.6876 (mtm) cc_final: 0.6594 (mtm) REVERT: A 203 MET cc_start: 0.7022 (mtp) cc_final: 0.6470 (mtp) REVERT: B 28 TYR cc_start: 0.5858 (m-10) cc_final: 0.5603 (m-10) REVERT: B 65 VAL cc_start: 0.8241 (t) cc_final: 0.5293 (t) REVERT: B 152 MET cc_start: 0.9346 (ttm) cc_final: 0.9084 (ttt) REVERT: B 158 MET cc_start: 0.6905 (mpp) cc_final: 0.6526 (mmm) REVERT: B 179 ASP cc_start: 0.6992 (m-30) cc_final: 0.6752 (m-30) REVERT: B 186 PHE cc_start: 0.8586 (m-80) cc_final: 0.8169 (m-80) REVERT: B 263 TYR cc_start: 0.8482 (m-80) cc_final: 0.8203 (m-80) REVERT: C 230 ILE cc_start: 0.9245 (mm) cc_final: 0.8957 (mt) REVERT: C 521 ILE cc_start: 0.9238 (pt) cc_final: 0.8951 (mm) REVERT: C 600 ILE cc_start: 0.9250 (mm) cc_final: 0.8780 (tp) REVERT: C 943 LEU cc_start: 0.9173 (tp) cc_final: 0.8842 (tt) REVERT: C 961 LEU cc_start: 0.9322 (mt) cc_final: 0.9114 (mt) REVERT: C 1009 TYR cc_start: 0.6400 (t80) cc_final: 0.6163 (t80) REVERT: D 140 TYR cc_start: 0.8215 (t80) cc_final: 0.7989 (t80) REVERT: D 205 MET cc_start: 0.7270 (ttp) cc_final: 0.6402 (tpp) REVERT: D 230 ILE cc_start: 0.9194 (mm) cc_final: 0.8918 (mt) REVERT: D 239 MET cc_start: 0.8823 (ttp) cc_final: 0.8528 (ttp) REVERT: D 240 MET cc_start: 0.8603 (mmm) cc_final: 0.8198 (mmt) REVERT: D 502 PHE cc_start: 0.7738 (m-80) cc_final: 0.7342 (m-80) REVERT: D 508 PHE cc_start: 0.8232 (m-80) cc_final: 0.8021 (m-10) REVERT: D 595 LYS cc_start: 0.8589 (tptt) cc_final: 0.8385 (tptp) REVERT: D 636 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8227 (tp30) REVERT: D 807 ASP cc_start: 0.8528 (t70) cc_final: 0.8246 (t0) REVERT: D 957 CYS cc_start: 0.8493 (p) cc_final: 0.7839 (p) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.2859 time to fit residues: 106.8545 Evaluate side-chains 172 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 6.9990 chunk 149 optimal weight: 0.0370 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 133 optimal weight: 0.0040 chunk 199 optimal weight: 0.8980 chunk 210 optimal weight: 0.0030 chunk 103 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 674 HIS D 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18064 Z= 0.152 Angle : 0.555 9.405 24390 Z= 0.282 Chirality : 0.039 0.354 2728 Planarity : 0.004 0.035 3076 Dihedral : 9.960 149.270 2474 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.37 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.19), residues: 2176 helix: 0.89 (0.17), residues: 1004 sheet: -0.49 (0.34), residues: 246 loop : -0.11 (0.22), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 220 HIS 0.004 0.001 HIS D 367 PHE 0.036 0.001 PHE C 502 TYR 0.010 0.001 TYR C 381 ARG 0.005 0.000 ARG B 294 *********************** 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 227 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 2.249 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 109 ILE cc_start: 0.6698 (mt) cc_final: 0.6242 (mt) REVERT: A 112 GLU cc_start: 0.7841 (tt0) cc_final: 0.7632 (tm-30) REVERT: A 158 MET cc_start: 0.6758 (mtm) cc_final: 0.6432 (mtt) REVERT: A 203 MET cc_start: 0.6867 (mtp) cc_final: 0.6319 (mtp) REVERT: A 263 TYR cc_start: 0.8744 (m-80) cc_final: 0.8466 (m-80) REVERT: B 110 VAL cc_start: 0.8240 (t) cc_final: 0.7043 (t) REVERT: B 219 ILE cc_start: 0.9373 (mm) cc_final: 0.9085 (mm) REVERT: B 263 TYR cc_start: 0.8494 (m-80) cc_final: 0.8224 (m-80) REVERT: C 230 ILE cc_start: 0.9202 (mm) cc_final: 0.8959 (mt) REVERT: C 521 ILE cc_start: 0.9215 (pt) cc_final: 0.8941 (mm) REVERT: C 600 ILE cc_start: 0.9238 (mm) cc_final: 0.8768 (tp) REVERT: C 636 GLU cc_start: 0.8668 (tp30) cc_final: 0.8379 (tp30) REVERT: C 669 CYS cc_start: 0.9560 (m) cc_final: 0.9331 (m) REVERT: C 943 LEU cc_start: 0.9156 (tp) cc_final: 0.8811 (tt) REVERT: C 961 LEU cc_start: 0.9348 (mt) cc_final: 0.9133 (mt) REVERT: D 140 TYR cc_start: 0.8270 (t80) cc_final: 0.8050 (t80) REVERT: D 205 MET cc_start: 0.7362 (ttp) cc_final: 0.6488 (tpp) REVERT: D 230 ILE cc_start: 0.9162 (mm) cc_final: 0.8913 (mt) REVERT: D 239 MET cc_start: 0.8789 (ttp) cc_final: 0.8470 (ttp) REVERT: D 240 MET cc_start: 0.8572 (mmm) cc_final: 0.8129 (mmt) REVERT: D 382 PHE cc_start: 0.8652 (m-80) cc_final: 0.8291 (m-80) REVERT: D 502 PHE cc_start: 0.7675 (m-80) cc_final: 0.7336 (m-80) REVERT: D 595 LYS cc_start: 0.8538 (tptt) cc_final: 0.8318 (tptp) REVERT: D 636 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8251 (tp30) REVERT: D 807 ASP cc_start: 0.8578 (t70) cc_final: 0.8233 (t0) REVERT: D 957 CYS cc_start: 0.8479 (p) cc_final: 0.7817 (p) REVERT: D 961 LEU cc_start: 0.9433 (mt) cc_final: 0.9061 (mt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2805 time to fit residues: 100.7061 Evaluate side-chains 169 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 5.9990 chunk 119 optimal weight: 0.0770 chunk 3 optimal weight: 20.0000 chunk 156 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 HIS D 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18064 Z= 0.228 Angle : 0.582 10.362 24390 Z= 0.296 Chirality : 0.040 0.223 2728 Planarity : 0.004 0.035 3076 Dihedral : 10.051 149.606 2474 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.83 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.17), residues: 1006 sheet: -0.54 (0.34), residues: 248 loop : -0.26 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 478 HIS 0.007 0.001 HIS B 159 PHE 0.041 0.002 PHE C 382 TYR 0.013 0.001 TYR A 287 ARG 0.004 0.000 ARG D 605 *********************** 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 203 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6365 (mt) cc_final: 0.5279 (mt) REVERT: A 112 GLU cc_start: 0.7800 (tt0) cc_final: 0.7562 (tm-30) REVERT: A 152 MET cc_start: 0.9040 (ttm) cc_final: 0.8817 (ttt) REVERT: A 158 MET cc_start: 0.6827 (mtm) cc_final: 0.6506 (mtm) REVERT: A 186 PHE cc_start: 0.8303 (m-80) cc_final: 0.8016 (m-80) REVERT: A 203 MET cc_start: 0.6876 (mtp) cc_final: 0.6322 (mtp) REVERT: A 219 ILE cc_start: 0.9410 (mm) cc_final: 0.9193 (mm) REVERT: B 65 VAL cc_start: 0.8385 (t) cc_final: 0.6217 (t) REVERT: B 158 MET cc_start: 0.6524 (mmm) cc_final: 0.6075 (mmm) REVERT: B 186 PHE cc_start: 0.8400 (m-80) cc_final: 0.7913 (m-80) REVERT: B 219 ILE cc_start: 0.9407 (mm) cc_final: 0.9088 (mm) REVERT: B 263 TYR cc_start: 0.8602 (m-80) cc_final: 0.8332 (m-80) REVERT: C 230 ILE cc_start: 0.9269 (mm) cc_final: 0.8996 (mt) REVERT: C 521 ILE cc_start: 0.9249 (pt) cc_final: 0.8950 (mm) REVERT: C 669 CYS cc_start: 0.9524 (m) cc_final: 0.9303 (m) REVERT: C 943 LEU cc_start: 0.9171 (tp) cc_final: 0.8963 (tp) REVERT: C 961 LEU cc_start: 0.9364 (mt) cc_final: 0.9139 (mt) REVERT: D 230 ILE cc_start: 0.9232 (mm) cc_final: 0.8965 (mt) REVERT: D 382 PHE cc_start: 0.8562 (m-80) cc_final: 0.8300 (m-80) REVERT: D 502 PHE cc_start: 0.7673 (m-80) cc_final: 0.7423 (m-80) REVERT: D 807 ASP cc_start: 0.8635 (t70) cc_final: 0.8254 (t0) REVERT: D 810 LEU cc_start: 0.8596 (mt) cc_final: 0.8184 (mt) REVERT: D 957 CYS cc_start: 0.8616 (p) cc_final: 0.8038 (p) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2898 time to fit residues: 93.4821 Evaluate side-chains 157 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4084 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= 0.214 Angle : 0.563 7.902 24390 Z= 0.287 Chirality : 0.040 0.193 2728 Planarity : 0.004 0.063 3076 Dihedral : 10.189 150.033 2474 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.24 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 0.87 (0.17), residues: 1020 sheet: -0.52 (0.34), residues: 246 loop : -0.34 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 478 HIS 0.005 0.001 HIS B 159 PHE 0.041 0.002 PHE C 502 TYR 0.011 0.001 TYR C 136 ARG 0.004 0.000 ARG A 294 *********************** 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 207 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6365 (mt) cc_final: 0.5427 (mt) REVERT: A 158 MET cc_start: 0.6769 (mtm) cc_final: 0.6477 (mtt) REVERT: A 186 PHE cc_start: 0.8307 (m-80) cc_final: 0.8038 (m-80) REVERT: A 203 MET cc_start: 0.6824 (mtp) cc_final: 0.6304 (mtp) REVERT: A 219 ILE cc_start: 0.9387 (mm) cc_final: 0.9149 (mm) REVERT: B 110 VAL cc_start: 0.8305 (t) cc_final: 0.7061 (t) REVERT: B 158 MET cc_start: 0.6490 (mmm) cc_final: 0.6029 (mmm) REVERT: B 219 ILE cc_start: 0.9405 (mm) cc_final: 0.9108 (mm) REVERT: B 263 TYR cc_start: 0.8628 (m-80) cc_final: 0.8350 (m-80) REVERT: C 230 ILE cc_start: 0.9265 (mm) cc_final: 0.9022 (mt) REVERT: C 287 ILE cc_start: 0.9474 (mp) cc_final: 0.9185 (pt) REVERT: C 484 PHE cc_start: 0.8590 (m-80) cc_final: 0.8389 (m-10) REVERT: C 521 ILE cc_start: 0.9250 (pt) cc_final: 0.8956 (mm) REVERT: C 669 CYS cc_start: 0.9465 (m) cc_final: 0.9125 (m) REVERT: C 810 LEU cc_start: 0.8743 (mt) cc_final: 0.8315 (mt) REVERT: C 961 LEU cc_start: 0.9374 (mt) cc_final: 0.9148 (mt) REVERT: D 230 ILE cc_start: 0.9238 (mm) cc_final: 0.8962 (mt) REVERT: D 382 PHE cc_start: 0.8556 (m-80) cc_final: 0.8284 (m-80) REVERT: D 502 PHE cc_start: 0.7689 (m-80) cc_final: 0.7442 (m-80) REVERT: D 532 MET cc_start: 0.9023 (tpp) cc_final: 0.8638 (tpp) REVERT: D 807 ASP cc_start: 0.8642 (t70) cc_final: 0.8270 (t0) REVERT: D 810 LEU cc_start: 0.8672 (mt) cc_final: 0.8289 (mt) REVERT: D 957 CYS cc_start: 0.8675 (p) cc_final: 0.7958 (p) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2695 time to fit residues: 89.9147 Evaluate side-chains 159 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18064 Z= 0.216 Angle : 0.574 8.019 24390 Z= 0.293 Chirality : 0.040 0.172 2728 Planarity : 0.004 0.051 3076 Dihedral : 10.267 150.198 2474 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.47 % Favored : 94.12 % 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: 0.32 (0.19), residues: 2176 helix: 1.01 (0.17), residues: 1008 sheet: -0.83 (0.33), residues: 254 loop : -0.24 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.005 0.001 HIS D 492 PHE 0.025 0.001 PHE D 484 TYR 0.012 0.001 TYR D 258 ARG 0.004 0.000 ARG A 294 *********************** 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 198 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6413 (mt) cc_final: 0.5754 (mt) REVERT: A 186 PHE cc_start: 0.8397 (m-80) cc_final: 0.8145 (m-80) REVERT: A 203 MET cc_start: 0.6659 (mtp) cc_final: 0.6226 (mtp) REVERT: A 219 ILE cc_start: 0.9413 (mm) cc_final: 0.9176 (mm) REVERT: B 65 VAL cc_start: 0.8661 (t) cc_final: 0.6722 (t) REVERT: B 158 MET cc_start: 0.6401 (mmm) cc_final: 0.6022 (mmm) REVERT: B 186 PHE cc_start: 0.8195 (m-80) cc_final: 0.7680 (m-80) REVERT: B 219 ILE cc_start: 0.9449 (mm) cc_final: 0.9151 (mm) REVERT: B 263 TYR cc_start: 0.8618 (m-80) cc_final: 0.8348 (m-80) REVERT: C 230 ILE cc_start: 0.9286 (mm) cc_final: 0.9026 (mt) REVERT: C 287 ILE cc_start: 0.9462 (mp) cc_final: 0.9201 (pt) REVERT: C 521 ILE cc_start: 0.9241 (pt) cc_final: 0.8927 (mm) REVERT: C 961 LEU cc_start: 0.9396 (mt) cc_final: 0.9174 (mt) REVERT: C 1008 MET cc_start: 0.7663 (mmm) cc_final: 0.7403 (mmm) REVERT: D 230 ILE cc_start: 0.9243 (mm) cc_final: 0.8959 (mt) REVERT: D 256 LEU cc_start: 0.9277 (mt) cc_final: 0.8884 (mt) REVERT: D 382 PHE cc_start: 0.8617 (m-80) cc_final: 0.8219 (m-80) REVERT: D 484 PHE cc_start: 0.8259 (m-10) cc_final: 0.8020 (m-10) REVERT: D 502 PHE cc_start: 0.7677 (m-80) cc_final: 0.7440 (m-80) REVERT: D 532 MET cc_start: 0.8990 (tpp) cc_final: 0.8611 (tpp) REVERT: D 807 ASP cc_start: 0.8611 (t70) cc_final: 0.8251 (t0) REVERT: D 810 LEU cc_start: 0.8718 (mt) cc_final: 0.8341 (mt) REVERT: D 864 GLU cc_start: 0.8077 (tp30) cc_final: 0.7792 (tp30) REVERT: D 957 CYS cc_start: 0.8715 (p) cc_final: 0.8106 (p) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2893 time to fit residues: 91.2820 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 : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 9.9990 chunk 83 optimal weight: 0.0970 chunk 125 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18064 Z= 0.155 Angle : 0.555 12.020 24390 Z= 0.280 Chirality : 0.039 0.193 2728 Planarity : 0.004 0.037 3076 Dihedral : 10.221 150.840 2474 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.15 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.19), residues: 2176 helix: 0.99 (0.17), residues: 1012 sheet: -0.92 (0.33), residues: 254 loop : -0.24 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 478 HIS 0.003 0.001 HIS B 151 PHE 0.041 0.001 PHE C 502 TYR 0.023 0.001 TYR D 140 ARG 0.004 0.000 ARG A 294 *********************** 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 207 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 2.406 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 62 LEU cc_start: 0.6187 (mt) cc_final: 0.5783 (mt) REVERT: A 109 ILE cc_start: 0.6466 (mt) cc_final: 0.6151 (mp) REVERT: A 158 MET cc_start: 0.6380 (mtp) cc_final: 0.6131 (mmm) REVERT: A 186 PHE cc_start: 0.8486 (m-80) cc_final: 0.8218 (m-80) REVERT: A 203 MET cc_start: 0.6591 (mtp) cc_final: 0.6129 (mtp) REVERT: B 26 MET cc_start: 0.7552 (mmp) cc_final: 0.6994 (mtt) REVERT: B 62 LEU cc_start: 0.6026 (mt) cc_final: 0.5025 (mt) REVERT: B 158 MET cc_start: 0.6484 (mmm) cc_final: 0.6064 (mmm) REVERT: B 263 TYR cc_start: 0.8598 (m-80) cc_final: 0.8351 (m-80) REVERT: C 230 ILE cc_start: 0.9239 (mm) cc_final: 0.9012 (mt) REVERT: C 287 ILE cc_start: 0.9455 (mp) cc_final: 0.9206 (pt) REVERT: C 405 LEU cc_start: 0.9065 (tp) cc_final: 0.8847 (tt) REVERT: C 521 ILE cc_start: 0.9212 (pt) cc_final: 0.8917 (mm) REVERT: C 669 CYS cc_start: 0.9321 (m) cc_final: 0.9047 (m) REVERT: C 810 LEU cc_start: 0.8788 (mp) cc_final: 0.8568 (mt) REVERT: C 961 LEU cc_start: 0.9394 (mt) cc_final: 0.9177 (mt) REVERT: C 1008 MET cc_start: 0.7616 (mmm) cc_final: 0.7114 (mmm) REVERT: C 1009 TYR cc_start: 0.6173 (t80) cc_final: 0.5937 (t80) REVERT: D 230 ILE cc_start: 0.9202 (mm) cc_final: 0.8924 (mt) REVERT: D 256 LEU cc_start: 0.9417 (mt) cc_final: 0.9179 (mt) REVERT: D 484 PHE cc_start: 0.8209 (m-10) cc_final: 0.7968 (m-10) REVERT: D 502 PHE cc_start: 0.7645 (m-80) cc_final: 0.7412 (m-80) REVERT: D 532 MET cc_start: 0.8993 (tpp) cc_final: 0.8614 (tpp) REVERT: D 807 ASP cc_start: 0.8598 (t70) cc_final: 0.8230 (t0) REVERT: D 810 LEU cc_start: 0.8728 (mt) cc_final: 0.8330 (mt) REVERT: D 864 GLU cc_start: 0.8032 (tp30) cc_final: 0.7794 (tp30) REVERT: D 957 CYS cc_start: 0.8703 (p) cc_final: 0.8061 (p) REVERT: D 1008 MET cc_start: 0.7699 (mmm) cc_final: 0.7479 (mmt) REVERT: D 1023 GLU cc_start: 0.9303 (mt-10) cc_final: 0.9059 (pp20) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2747 time to fit residues: 91.0184 Evaluate side-chains 155 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 195 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN C 360 HIS D 627 GLN D 656 ASN D 845 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18064 Z= 0.155 Angle : 0.568 8.200 24390 Z= 0.286 Chirality : 0.040 0.189 2728 Planarity : 0.004 0.036 3076 Dihedral : 10.187 151.261 2474 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.19 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 2176 helix: 0.97 (0.17), residues: 1012 sheet: -0.99 (0.33), residues: 254 loop : -0.25 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 243 HIS 0.003 0.001 HIS B 151 PHE 0.046 0.002 PHE C 382 TYR 0.009 0.001 TYR C 136 ARG 0.005 0.000 ARG C 779 *********************** 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 201 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.290 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: 0.6459 (mtp) cc_final: 0.5765 (mmm) REVERT: A 186 PHE cc_start: 0.8484 (m-80) cc_final: 0.8147 (m-80) REVERT: A 203 MET cc_start: 0.6558 (mtp) cc_final: 0.6120 (mtp) REVERT: B 26 MET cc_start: 0.7385 (mmp) cc_final: 0.6828 (mtt) REVERT: B 158 MET cc_start: 0.6413 (mmm) cc_final: 0.5997 (mmm) REVERT: B 186 PHE cc_start: 0.8117 (m-10) cc_final: 0.7664 (m-10) REVERT: B 263 TYR cc_start: 0.8522 (m-80) cc_final: 0.8279 (m-80) REVERT: C 230 ILE cc_start: 0.9253 (mm) cc_final: 0.9013 (mt) REVERT: C 287 ILE cc_start: 0.9462 (mp) cc_final: 0.9226 (pt) REVERT: C 405 LEU cc_start: 0.9198 (tp) cc_final: 0.8924 (tt) REVERT: C 521 ILE cc_start: 0.9219 (pt) cc_final: 0.8915 (mm) REVERT: C 669 CYS cc_start: 0.9367 (m) cc_final: 0.9133 (m) REVERT: C 846 ASP cc_start: 0.8162 (t0) cc_final: 0.7712 (t0) REVERT: C 961 LEU cc_start: 0.9378 (mt) cc_final: 0.9159 (mt) REVERT: C 1008 MET cc_start: 0.7594 (mmm) cc_final: 0.7135 (mmm) REVERT: D 208 LEU cc_start: 0.9406 (mt) cc_final: 0.9197 (mt) REVERT: D 230 ILE cc_start: 0.9194 (mm) cc_final: 0.8955 (mt) REVERT: D 277 MET cc_start: 0.8422 (mpp) cc_final: 0.8201 (mpp) REVERT: D 484 PHE cc_start: 0.8170 (m-10) cc_final: 0.7911 (m-10) REVERT: D 502 PHE cc_start: 0.7622 (m-80) cc_final: 0.7395 (m-80) REVERT: D 532 MET cc_start: 0.8999 (tpp) cc_final: 0.8643 (tpp) REVERT: D 807 ASP cc_start: 0.8574 (t70) cc_final: 0.8195 (t0) REVERT: D 810 LEU cc_start: 0.8677 (mt) cc_final: 0.8350 (mt) REVERT: D 864 GLU cc_start: 0.8016 (tp30) cc_final: 0.7813 (tp30) REVERT: D 1023 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9050 (pp20) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2789 time to fit residues: 89.3906 Evaluate side-chains 155 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS C 360 HIS C 883 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 18064 Z= 0.269 Angle : 0.624 10.375 24390 Z= 0.312 Chirality : 0.041 0.181 2728 Planarity : 0.004 0.043 3076 Dihedral : 10.326 151.031 2474 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.39 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.19), residues: 2176 helix: 0.99 (0.17), residues: 1012 sheet: -1.12 (0.33), residues: 254 loop : -0.32 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 478 HIS 0.006 0.001 HIS B 159 PHE 0.022 0.002 PHE C 484 TYR 0.012 0.001 TYR A 287 ARG 0.005 0.000 ARG C 779 ********************** 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 179 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.290 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 186 PHE cc_start: 0.8408 (m-80) cc_final: 0.8120 (m-80) REVERT: A 203 MET cc_start: 0.6741 (mtp) cc_final: 0.6295 (mtp) REVERT: B 158 MET cc_start: 0.6468 (mmm) cc_final: 0.6028 (mmt) REVERT: B 186 PHE cc_start: 0.7863 (m-10) cc_final: 0.7622 (m-10) REVERT: B 219 ILE cc_start: 0.9434 (mm) cc_final: 0.9230 (mm) REVERT: B 263 TYR cc_start: 0.8667 (m-80) cc_final: 0.8420 (m-80) REVERT: C 230 ILE cc_start: 0.9308 (mm) cc_final: 0.9040 (mt) REVERT: C 287 ILE cc_start: 0.9478 (mp) cc_final: 0.9246 (pt) REVERT: C 405 LEU cc_start: 0.9260 (tp) cc_final: 0.8947 (tt) REVERT: C 521 ILE cc_start: 0.9229 (pt) cc_final: 0.8918 (mm) REVERT: C 637 MET cc_start: 0.8978 (ttp) cc_final: 0.8300 (tmm) REVERT: C 669 CYS cc_start: 0.9421 (m) cc_final: 0.9191 (m) REVERT: C 961 LEU cc_start: 0.9393 (mt) cc_final: 0.9188 (mt) REVERT: C 1008 MET cc_start: 0.7616 (mmm) cc_final: 0.7142 (mmm) REVERT: D 208 LEU cc_start: 0.9420 (mt) cc_final: 0.9183 (mt) REVERT: D 230 ILE cc_start: 0.9262 (mm) cc_final: 0.9013 (mt) REVERT: D 277 MET cc_start: 0.8496 (mpp) cc_final: 0.8264 (mpp) REVERT: D 382 PHE cc_start: 0.8481 (m-80) cc_final: 0.8205 (m-80) REVERT: D 484 PHE cc_start: 0.8206 (m-10) cc_final: 0.7968 (m-10) REVERT: D 502 PHE cc_start: 0.7772 (m-80) cc_final: 0.7548 (m-80) REVERT: D 532 MET cc_start: 0.9028 (tpp) cc_final: 0.8650 (tpp) REVERT: D 807 ASP cc_start: 0.8618 (t70) cc_final: 0.8279 (t0) REVERT: D 864 GLU cc_start: 0.8111 (tp30) cc_final: 0.7871 (tp30) REVERT: D 1008 MET cc_start: 0.7477 (mmt) cc_final: 0.7001 (mmm) REVERT: D 1023 GLU cc_start: 0.9316 (mt-10) cc_final: 0.9045 (pp20) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2905 time to fit residues: 81.9719 Evaluate side-chains 142 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 72 optimal weight: 0.0470 chunk 177 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 HIS C 602 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.076704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.059394 restraints weight = 77159.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.061391 restraints weight = 43353.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062732 restraints weight = 29617.943| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18064 Z= 0.169 Angle : 0.578 8.280 24390 Z= 0.288 Chirality : 0.040 0.188 2728 Planarity : 0.004 0.034 3076 Dihedral : 10.281 151.000 2474 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.56 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.19), residues: 2176 helix: 1.00 (0.17), residues: 1012 sheet: -1.21 (0.32), residues: 254 loop : -0.30 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 243 HIS 0.006 0.001 HIS A 151 PHE 0.020 0.001 PHE D 446 TYR 0.010 0.001 TYR D 572 ARG 0.004 0.000 ARG A 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.51 seconds wall clock time: 64 minutes 7.28 seconds (3847.28 seconds total)