Starting phenix.real_space_refine on Sat Mar 16 03:50:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgr_32485/03_2024/7wgr_32485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgr_32485/03_2024/7wgr_32485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgr_32485/03_2024/7wgr_32485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgr_32485/03_2024/7wgr_32485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgr_32485/03_2024/7wgr_32485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgr_32485/03_2024/7wgr_32485_updated.pdb" } resolution = 2.92 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= 0.077 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 8624 2.51 5 N 2374 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 959": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B GLU 679": "OE1" <-> "OE2" Residue "B GLU 952": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13614 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6779 Classifications: {'peptide': 850} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 802} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6779 Classifications: {'peptide': 850} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 802} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' CA': 1, ' MG': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' CA': 1, ' MG': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.40, per 1000 atoms: 0.54 Number of scatterers: 13614 At special positions: 0 Unit cell: (107.315, 117.455, 122.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 82 16.00 P 4 15.00 Mg 2 11.99 O 2526 8.00 N 2374 7.00 C 8624 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 - 3.50 Amino acid : False - 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: 5.89 Conformation dependent library (CDL) restraints added in 2.5 seconds 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 10 sheets defined 40.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 130 through 144 removed outlier: 6.433A pdb=" N HIS A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N HIS A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.761A pdb=" N LEU A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 228 through 239 removed outlier: 3.505A pdb=" N PHE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.734A pdb=" N ASP A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 428 removed outlier: 4.474A pdb=" N ASP A 428 " --> pdb=" O PHE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 480 through 497 Processing helix chain 'A' and resid 524 through 532 removed outlier: 4.310A pdb=" N LYS A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 Processing helix chain 'A' and resid 552 through 573 Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 633 through 647 Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.700A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 5.366A pdb=" N CYS A 756 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 760 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 819 through 824 removed outlier: 3.517A pdb=" N ASP A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 847 removed outlier: 3.820A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 890 through 893 No H-bonds generated for 'chain 'A' and resid 890 through 893' Processing helix chain 'A' and resid 895 through 897 No H-bonds generated for 'chain 'A' and resid 895 through 897' Processing helix chain 'A' and resid 907 through 919 Processing helix chain 'A' and resid 940 through 947 Processing helix chain 'A' and resid 966 through 976 Proline residue: A 971 - end of helix Processing helix chain 'A' and resid 999 through 1014 removed outlier: 4.053A pdb=" N LEU A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A1004 " --> pdb=" O LYS A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1022 No H-bonds generated for 'chain 'A' and resid 1020 through 1022' Processing helix chain 'B' and resid 130 through 143 removed outlier: 6.434A pdb=" N HIS B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 removed outlier: 3.758A pdb=" N LEU B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 173 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 284 through 300 removed outlier: 3.567A pdb=" N ILE B 287 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Proline residue: B 288 - end of helix Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.729A pdb=" N ASP B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 463 through 468 removed outlier: 3.603A pdb=" N VAL B 468 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 497 Processing helix chain 'B' and resid 524 through 532 removed outlier: 4.184A pdb=" N LYS B 532 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 Processing helix chain 'B' and resid 552 through 573 Processing helix chain 'B' and resid 611 through 621 Processing helix chain 'B' and resid 633 through 647 Processing helix chain 'B' and resid 653 through 666 Processing helix chain 'B' and resid 702 through 705 Processing helix chain 'B' and resid 724 through 735 removed outlier: 3.914A pdb=" N ALA B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.577A pdb=" N THR B 753 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N CYS B 756 " --> pdb=" O THR B 753 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 760 " --> pdb=" O ILE B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 removed outlier: 3.502A pdb=" N GLN B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 823 Processing helix chain 'B' and resid 835 through 847 removed outlier: 3.800A pdb=" N LEU B 842 " --> pdb=" O PHE B 838 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 846 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 874 No H-bonds generated for 'chain 'B' and resid 872 through 874' Processing helix chain 'B' and resid 890 through 893 No H-bonds generated for 'chain 'B' and resid 890 through 893' Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 907 through 918 removed outlier: 3.525A pdb=" N ASP B 911 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 914 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 945 Processing helix chain 'B' and resid 966 through 976 Proline residue: B 971 - end of helix Processing helix chain 'B' and resid 999 through 1012 removed outlier: 4.037A pdb=" N LEU B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B1004 " --> pdb=" O LYS B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1022 No H-bonds generated for 'chain 'B' and resid 1020 through 1022' Processing sheet with id= A, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.708A pdb=" N LEU A 201 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 218 through 221 removed outlier: 6.882A pdb=" N VAL A 502 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N VAL A 475 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP A 504 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR A 304 " --> pdb=" O MET A 404 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A 406 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 306 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU A 408 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 308 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N GLY A 410 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR A 367 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N MET A 307 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 369 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 713 through 717 removed outlier: 6.770A pdb=" N ILE A 671 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N CYS A 716 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A 673 " --> pdb=" O CYS A 716 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 776 " --> pdb=" O TRP A 743 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA A 745 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU A 778 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 854 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A 779 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 856 " --> pdb=" O LEU A 779 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 954 through 956 removed outlier: 6.852A pdb=" N TRP A 984 " --> pdb=" O TRP A 955 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 899 through 904 removed outlier: 4.111A pdb=" N ALA A 926 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU A 901 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR A 928 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A 903 " --> pdb=" O THR A 928 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= G, first strand: chain 'B' and resid 218 through 221 removed outlier: 6.887A pdb=" N VAL B 502 " --> pdb=" O PHE B 473 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL B 475 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 504 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 304 " --> pdb=" O MET B 404 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 406 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 306 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU B 408 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY B 308 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N GLY B 410 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR B 367 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N MET B 307 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER B 369 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 713 through 715 removed outlier: 6.780A pdb=" N ILE B 671 " --> pdb=" O THR B 714 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 776 " --> pdb=" O TRP B 743 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ALA B 745 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU B 778 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 854 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU B 779 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 856 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 954 through 956 removed outlier: 6.808A pdb=" N TRP B 984 " --> pdb=" O TRP B 955 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 899 through 904 removed outlier: 4.082A pdb=" N ALA B 926 " --> pdb=" O LYS B 899 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU B 901 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR B 928 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 903 " --> pdb=" O THR B 928 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 452 hydrogen bonds defined for protein. 1206 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: 4.19 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2282 1.30 - 1.43: 3595 1.43 - 1.56: 7921 1.56 - 1.68: 8 1.68 - 1.81: 126 Bond restraints: 13932 Sorted by residual: bond pdb=" C PRO A 937 " pdb=" O PRO A 937 " ideal model delta sigma weight residual 1.235 1.174 0.062 1.30e-02 5.92e+03 2.24e+01 bond pdb=" O1A TPP A1103 " pdb=" PA TPP A1103 " ideal model delta sigma weight residual 1.479 1.522 -0.043 1.00e-02 1.00e+04 1.88e+01 bond pdb=" O1A TPP B1103 " pdb=" PA TPP B1103 " ideal model delta sigma weight residual 1.479 1.522 -0.043 1.00e-02 1.00e+04 1.86e+01 bond pdb=" N CYS B 763 " pdb=" CA CYS B 763 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.63e+01 bond pdb=" N CYS A 763 " pdb=" CA CYS A 763 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.61e+01 ... (remaining 13927 not shown) Histogram of bond angle deviations from ideal: 91.30 - 101.01: 39 101.01 - 110.71: 4345 110.71 - 120.41: 9117 120.41 - 130.12: 5290 130.12 - 139.82: 97 Bond angle restraints: 18888 Sorted by residual: angle pdb=" N GLN A 766 " pdb=" CA GLN A 766 " pdb=" C GLN A 766 " ideal model delta sigma weight residual 114.12 106.29 7.83 1.39e+00 5.18e-01 3.17e+01 angle pdb=" C ASP A 818 " pdb=" CA ASP A 818 " pdb=" CB ASP A 818 " ideal model delta sigma weight residual 110.42 99.61 10.81 1.99e+00 2.53e-01 2.95e+01 angle pdb=" O3A TPP A1103 " pdb=" PB TPP A1103 " pdb=" O3B TPP A1103 " ideal model delta sigma weight residual 104.26 111.41 -7.15 1.33e+00 5.64e-01 2.88e+01 angle pdb=" O3A TPP B1103 " pdb=" PB TPP B1103 " pdb=" O3B TPP B1103 " ideal model delta sigma weight residual 104.26 111.32 -7.06 1.33e+00 5.64e-01 2.81e+01 angle pdb=" C PRO A 937 " pdb=" CA PRO A 937 " pdb=" CB PRO A 937 " ideal model delta sigma weight residual 111.56 103.07 8.49 1.65e+00 3.67e-01 2.64e+01 ... (remaining 18883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7483 17.75 - 35.50: 721 35.50 - 53.25: 131 53.25 - 71.00: 32 71.00 - 88.75: 15 Dihedral angle restraints: 8382 sinusoidal: 3442 harmonic: 4940 Sorted by residual: dihedral pdb=" CA SER A 934 " pdb=" C SER A 934 " pdb=" N PRO A 935 " pdb=" CA PRO A 935 " ideal model delta harmonic sigma weight residual 0.00 -41.59 41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" C ASP A 818 " pdb=" N ASP A 818 " pdb=" CA ASP A 818 " pdb=" CB ASP A 818 " ideal model delta harmonic sigma weight residual -122.60 -107.67 -14.93 0 2.50e+00 1.60e-01 3.57e+01 dihedral pdb=" C PHE B 817 " pdb=" N PHE B 817 " pdb=" CA PHE B 817 " pdb=" CB PHE B 817 " ideal model delta harmonic sigma weight residual -122.60 -134.80 12.20 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 8379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1702 0.073 - 0.146: 285 0.146 - 0.219: 48 0.219 - 0.292: 19 0.292 - 0.365: 2 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA PHE B 817 " pdb=" N PHE B 817 " pdb=" C PHE B 817 " pdb=" CB PHE B 817 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASP A 818 " pdb=" N ASP A 818 " pdb=" C ASP A 818 " pdb=" CB ASP A 818 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA GLN B 772 " pdb=" N GLN B 772 " pdb=" C GLN B 772 " pdb=" CB GLN B 772 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2053 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 706 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C LEU A 706 " 0.089 2.00e-02 2.50e+03 pdb=" O LEU A 706 " -0.033 2.00e-02 2.50e+03 pdb=" N TRP A 707 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 144 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C VAL B 144 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL B 144 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA B 145 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 427 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C SER A 427 " -0.064 2.00e-02 2.50e+03 pdb=" O SER A 427 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 428 " 0.021 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 33 2.48 - 3.09: 9012 3.09 - 3.69: 20046 3.69 - 4.30: 30360 4.30 - 4.90: 51442 Nonbonded interactions: 110893 Sorted by model distance: nonbonded pdb=" OD1 ASN B 444 " pdb="MG MG B1102 " model vdw 1.877 2.170 nonbonded pdb=" OD1 ASN A 444 " pdb="MG MG A1102 " model vdw 1.952 2.170 nonbonded pdb="MG MG B1102 " pdb=" O2A TPP B1103 " model vdw 2.035 2.170 nonbonded pdb="MG MG B1102 " pdb=" O3B TPP B1103 " model vdw 2.035 2.170 nonbonded pdb="MG MG A1102 " pdb=" O2B TPP A1103 " model vdw 2.044 2.170 ... (remaining 110888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 0.740 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: 4.230 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 39.710 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.007 0.062 13932 Z= 0.443 Angle : 0.986 10.812 18888 Z= 0.662 Chirality : 0.061 0.365 2056 Planarity : 0.005 0.051 2468 Dihedral : 14.711 88.752 5186 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.56 % Favored : 95.08 % Rotamer: Outliers : 0.54 % Allowed : 2.49 % Favored : 96.97 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.28 (0.21), residues: 1688 helix: 1.03 (0.21), residues: 710 sheet: -0.08 (0.37), residues: 216 loop : -1.40 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 827 HIS 0.009 0.001 HIS A 960 PHE 0.045 0.002 PHE A 817 TYR 0.024 0.002 TYR B 985 ARG 0.008 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 249 time to evaluate : 1.705 Fit side-chains REVERT: B 628 ASN cc_start: 0.6740 (p0) cc_final: 0.5761 (t160) outliers start: 8 outliers final: 4 residues processed: 254 average time/residue: 1.4302 time to fit residues: 393.6882 Evaluate side-chains 170 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 826 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 0.0020 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 0.0870 overall best weight: 0.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 316 ASN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 HIS B 316 ASN B 751 HIS B 773 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN B 924 GLN B1002 HIS B1007 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13932 Z= 0.153 Angle : 0.499 8.487 18888 Z= 0.256 Chirality : 0.042 0.145 2056 Planarity : 0.004 0.041 2468 Dihedral : 4.929 59.439 1863 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.69 % Allowed : 10.43 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1688 helix: 1.25 (0.21), residues: 698 sheet: -0.13 (0.37), residues: 222 loop : -1.10 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 827 HIS 0.003 0.001 HIS B1002 PHE 0.022 0.001 PHE A 193 TYR 0.012 0.001 TYR B 658 ARG 0.005 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 1.511 Fit side-chains REVERT: A 223 MET cc_start: 0.7411 (tpt) cc_final: 0.6951 (tpt) REVERT: A 270 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7368 (ptt-90) REVERT: A 309 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7356 (ppp) REVERT: A 454 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6809 (mtt) REVERT: A 722 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: A 1006 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8362 (tt) REVERT: B 223 MET cc_start: 0.7388 (mmt) cc_final: 0.7159 (tpt) REVERT: B 500 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: B 722 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: B 723 TYR cc_start: 0.7511 (t80) cc_final: 0.7267 (t80) outliers start: 40 outliers final: 11 residues processed: 211 average time/residue: 1.3667 time to fit residues: 313.8375 Evaluate side-chains 191 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 967 ASP Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A1002 HIS B 316 ASN B 474 HIS ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13932 Z= 0.300 Angle : 0.570 7.987 18888 Z= 0.294 Chirality : 0.046 0.147 2056 Planarity : 0.005 0.040 2468 Dihedral : 4.699 59.312 1856 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.70 % Allowed : 13.19 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.20), residues: 1688 helix: 1.04 (0.21), residues: 700 sheet: -0.20 (0.36), residues: 220 loop : -1.28 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 827 HIS 0.007 0.002 HIS B 840 PHE 0.017 0.002 PHE A 683 TYR 0.024 0.002 TYR A 562 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 1.679 Fit side-chains REVERT: A 223 MET cc_start: 0.7425 (tpt) cc_final: 0.7067 (tpt) REVERT: A 270 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7328 (ptt-90) REVERT: A 309 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7236 (ptm) REVERT: A 323 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6828 (mpt-90) REVERT: A 334 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6288 (m-30) REVERT: A 500 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: A 1006 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8348 (tt) REVERT: B 334 ASP cc_start: 0.6523 (OUTLIER) cc_final: 0.6274 (m-30) REVERT: B 454 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6754 (mtt) REVERT: B 500 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6797 (m-30) outliers start: 55 outliers final: 16 residues processed: 210 average time/residue: 1.3443 time to fit residues: 307.6845 Evaluate side-chains 191 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A1002 HIS B 316 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13932 Z= 0.163 Angle : 0.484 7.363 18888 Z= 0.246 Chirality : 0.042 0.144 2056 Planarity : 0.004 0.043 2468 Dihedral : 4.381 58.912 1856 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.89 % Allowed : 15.61 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.07 (0.21), residues: 1688 helix: 1.15 (0.21), residues: 708 sheet: -0.08 (0.36), residues: 218 loop : -1.19 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 769 HIS 0.004 0.001 HIS B1002 PHE 0.020 0.001 PHE B 817 TYR 0.016 0.001 TYR A 562 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 174 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6441 (mtt) REVERT: A 309 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7180 (ptm) REVERT: A 500 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6528 (m-30) REVERT: A 722 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: A 1006 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8355 (tt) REVERT: B 500 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6589 (m-30) outliers start: 43 outliers final: 15 residues processed: 201 average time/residue: 1.4049 time to fit residues: 306.3918 Evaluate side-chains 184 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 316 ASN B 766 GLN ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13932 Z= 0.257 Angle : 0.535 7.170 18888 Z= 0.273 Chirality : 0.044 0.142 2056 Planarity : 0.004 0.039 2468 Dihedral : 4.541 59.225 1856 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.43 % Allowed : 16.82 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.20), residues: 1688 helix: 0.98 (0.20), residues: 712 sheet: -0.10 (0.36), residues: 218 loop : -1.28 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 769 HIS 0.004 0.001 HIS B 840 PHE 0.043 0.001 PHE B 817 TYR 0.021 0.002 TYR B 562 ARG 0.008 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7118 (ptm) REVERT: A 500 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6600 (m-30) REVERT: A 1006 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8372 (tt) REVERT: B 334 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6289 (m-30) REVERT: B 500 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6743 (m-30) outliers start: 51 outliers final: 24 residues processed: 195 average time/residue: 1.3677 time to fit residues: 290.1621 Evaluate side-chains 189 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 316 ASN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13932 Z= 0.178 Angle : 0.492 7.356 18888 Z= 0.250 Chirality : 0.042 0.140 2056 Planarity : 0.004 0.041 2468 Dihedral : 4.369 59.118 1856 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.36 % Allowed : 17.23 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1688 helix: 1.06 (0.21), residues: 712 sheet: 0.02 (0.36), residues: 218 loop : -1.18 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 769 HIS 0.004 0.001 HIS B1002 PHE 0.021 0.001 PHE B 817 TYR 0.018 0.001 TYR B 562 ARG 0.009 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6415 (mtt) REVERT: A 309 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7130 (ptm) REVERT: A 500 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6541 (m-30) REVERT: A 694 ASN cc_start: 0.6343 (OUTLIER) cc_final: 0.5673 (p0) REVERT: A 722 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 1006 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8365 (tt) REVERT: B 223 MET cc_start: 0.7427 (tpt) cc_final: 0.6913 (tpt) REVERT: B 500 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6608 (m-30) REVERT: B 722 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6965 (mp0) outliers start: 50 outliers final: 25 residues processed: 192 average time/residue: 1.3773 time to fit residues: 287.8886 Evaluate side-chains 193 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 316 ASN B 365 ASN B 425 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13932 Z= 0.352 Angle : 0.604 7.563 18888 Z= 0.310 Chirality : 0.047 0.141 2056 Planarity : 0.005 0.044 2468 Dihedral : 4.827 59.147 1854 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 3.84 % Allowed : 18.10 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.44 (0.20), residues: 1688 helix: 0.81 (0.20), residues: 702 sheet: -0.17 (0.36), residues: 218 loop : -1.36 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 769 HIS 0.007 0.002 HIS B 376 PHE 0.022 0.002 PHE B 683 TYR 0.028 0.002 TYR B 562 ARG 0.009 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 173 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.7468 (tpt) cc_final: 0.7132 (tpt) REVERT: A 309 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7211 (ptm) REVERT: A 334 ASP cc_start: 0.6614 (OUTLIER) cc_final: 0.6390 (m-30) REVERT: A 500 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: A 694 ASN cc_start: 0.6495 (OUTLIER) cc_final: 0.5836 (p0) REVERT: A 722 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 1006 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 154 ASP cc_start: 0.6345 (OUTLIER) cc_final: 0.5901 (t0) REVERT: B 223 MET cc_start: 0.7438 (tpt) cc_final: 0.6941 (tpt) REVERT: B 334 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6276 (m-30) REVERT: B 500 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: B 722 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6981 (mp0) outliers start: 57 outliers final: 30 residues processed: 210 average time/residue: 1.3307 time to fit residues: 305.3140 Evaluate side-chains 205 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1015 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 316 ASN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 248 ASN B 316 ASN B 365 ASN B 425 HIS B 831 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13932 Z= 0.163 Angle : 0.508 8.277 18888 Z= 0.258 Chirality : 0.042 0.139 2056 Planarity : 0.004 0.041 2468 Dihedral : 4.367 57.779 1854 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.98 % Rotamer: Outliers : 2.89 % Allowed : 19.78 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.05 (0.21), residues: 1688 helix: 1.13 (0.21), residues: 698 sheet: -0.04 (0.36), residues: 218 loop : -1.12 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 769 HIS 0.003 0.001 HIS B1002 PHE 0.022 0.001 PHE A 817 TYR 0.025 0.001 TYR B 562 ARG 0.011 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 1.717 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7800 (mmp-170) REVERT: A 309 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7172 (ptm) REVERT: A 500 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: A 694 ASN cc_start: 0.6450 (OUTLIER) cc_final: 0.5774 (p0) REVERT: A 1006 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8356 (tt) REVERT: B 500 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6555 (m-30) outliers start: 43 outliers final: 21 residues processed: 196 average time/residue: 1.3116 time to fit residues: 280.8226 Evaluate side-chains 185 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 152 optimal weight: 0.0470 chunk 91 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 316 ASN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 248 ASN B 316 ASN B 365 ASN ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13932 Z= 0.163 Angle : 0.510 7.748 18888 Z= 0.260 Chirality : 0.042 0.186 2056 Planarity : 0.004 0.052 2468 Dihedral : 4.274 58.066 1854 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 2.36 % Allowed : 20.66 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.05 (0.21), residues: 1688 helix: 1.17 (0.21), residues: 700 sheet: -0.07 (0.36), residues: 218 loop : -0.99 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 769 HIS 0.004 0.001 HIS B1002 PHE 0.027 0.001 PHE A 683 TYR 0.026 0.001 TYR B 562 ARG 0.011 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7318 (mmm160) cc_final: 0.6836 (mtm110) REVERT: A 309 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7145 (ptm) REVERT: A 694 ASN cc_start: 0.6458 (OUTLIER) cc_final: 0.5785 (p0) REVERT: A 1006 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8348 (tt) REVERT: B 500 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6555 (m-30) outliers start: 35 outliers final: 20 residues processed: 191 average time/residue: 1.3275 time to fit residues: 277.4481 Evaluate side-chains 181 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 316 ASN B 365 ASN ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13932 Z= 0.174 Angle : 0.512 7.796 18888 Z= 0.261 Chirality : 0.042 0.136 2056 Planarity : 0.004 0.054 2468 Dihedral : 4.221 58.389 1854 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 2.02 % Allowed : 20.93 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1688 helix: 1.20 (0.21), residues: 700 sheet: -0.05 (0.36), residues: 218 loop : -0.97 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 769 HIS 0.004 0.001 HIS B1002 PHE 0.020 0.001 PHE A 817 TYR 0.027 0.001 TYR B 562 ARG 0.012 0.000 ARG B 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.768 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6887 (mtm110) REVERT: A 211 GLU cc_start: 0.5452 (tp30) cc_final: 0.5094 (tm-30) REVERT: A 244 MET cc_start: 0.6912 (mtt) cc_final: 0.6676 (mtt) REVERT: A 309 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7119 (ptm) REVERT: A 694 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.5767 (p0) REVERT: A 1006 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8347 (tt) REVERT: B 500 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6563 (m-30) outliers start: 30 outliers final: 19 residues processed: 183 average time/residue: 1.3192 time to fit residues: 264.7974 Evaluate side-chains 181 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 0.0020 chunk 135 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 316 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 316 ASN B 365 ASN B 425 HIS ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 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 = 0.3939 r_free = 0.3939 target = 0.158058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131876 restraints weight = 16522.235| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.89 r_work: 0.3506 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13932 Z= 0.287 Angle : 0.574 7.973 18888 Z= 0.293 Chirality : 0.045 0.139 2056 Planarity : 0.005 0.054 2468 Dihedral : 4.494 58.899 1854 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 2.36 % Allowed : 20.93 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.16 (0.21), residues: 1688 helix: 1.01 (0.21), residues: 700 sheet: -0.10 (0.36), residues: 218 loop : -1.14 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 769 HIS 0.005 0.001 HIS B 376 PHE 0.024 0.001 PHE B 683 TYR 0.030 0.002 TYR A 562 ARG 0.011 0.000 ARG B 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5217.73 seconds wall clock time: 92 minutes 54.99 seconds (5574.99 seconds total)