Starting phenix.real_space_refine on Wed Sep 17 15:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsg_51547/09_2025/9gsg_51547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsg_51547/09_2025/9gsg_51547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gsg_51547/09_2025/9gsg_51547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsg_51547/09_2025/9gsg_51547.map" model { file = "/net/cci-nas-00/data/ceres_data/9gsg_51547/09_2025/9gsg_51547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsg_51547/09_2025/9gsg_51547.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.123 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 Al 1 5.89 5 Mg 1 5.21 5 S 54 5.16 5 C 5800 2.51 5 N 1527 2.21 5 O 1706 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9093 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 939, 7290 Classifications: {'peptide': 939} Link IDs: {'PTRANS': 45, 'TRANS': 893} Chain breaks: 4 Chain: "B" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1703 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 2.18, per 1000 atoms: 0.24 Number of scatterers: 9093 At special positions: 0 Unit cell: (87.36, 98.28, 179.27, 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) S 54 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1706 8.00 N 1527 7.00 C 5800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 315 " distance=2.03 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 Links applied NAG-ASN " NAG B 501 " - " ASN B 283 " " NAG B 502 " - " ASN B 316 " " NAG B 503 " - " ASN B 295 " " NAG B 504 " - " ASN B 170 " " NAG B 505 " - " ASN B 228 " " NAG B 506 " - " ASN B 196 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 352.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 45.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.541A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.796A pdb=" N GLN A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 removed outlier: 3.515A pdb=" N LEU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 removed outlier: 3.507A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 339 through 379 Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.995A pdb=" N GLU A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 444 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N MET A 445 " --> pdb=" O CYS A 442 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 448 " --> pdb=" O MET A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 502 removed outlier: 3.684A pdb=" N ALA A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.732A pdb=" N LEU A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.588A pdb=" N ARG A 543 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 615 through 622 Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 729 through 737 removed outlier: 3.519A pdb=" N ILE A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 761 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 786 Processing helix chain 'A' and resid 797 through 804 removed outlier: 3.808A pdb=" N LYS A 801 " --> pdb=" O THR A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 854 removed outlier: 3.951A pdb=" N VAL A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 839 " --> pdb=" O GLN A 835 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 881 removed outlier: 3.600A pdb=" N VAL A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 removed outlier: 3.604A pdb=" N LEU A 891 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 892 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 932 removed outlier: 3.937A pdb=" N TYR A 916 " --> pdb=" O GLY A 912 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS A 930 " --> pdb=" O PHE A 926 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 968 removed outlier: 4.314A pdb=" N ILE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 967 " --> pdb=" O PHE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1005 removed outlier: 3.613A pdb=" N CYS A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1028 removed outlier: 3.532A pdb=" N TRP A1019 " --> pdb=" O GLN A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'B' and resid 338 through 360 removed outlier: 3.770A pdb=" N PHE B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.861A pdb=" N VAL A 264 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 236 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 266 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 234 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 230 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 272 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE A 228 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR A 274 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY A 226 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 234 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.861A pdb=" N VAL A 264 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 236 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 266 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 234 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 230 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 272 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE A 228 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR A 274 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY A 226 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 434 through 436 removed outlier: 6.227A pdb=" N GLY A 789 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A 808 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 791 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 770 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N PHE A 790 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 772 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N MET A 792 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY A 774 " --> pdb=" O MET A 792 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 741 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU A 710 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU A 743 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 712 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.677A pdb=" N VAL A 471 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 659 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA A 469 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 657 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 471 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N ILE A 655 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N LEU A 652 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ASP A 633 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N CYS A 654 " --> pdb=" O TYR A 631 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR A 631 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 656 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 565 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 555 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.677A pdb=" N VAL A 471 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 659 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA A 469 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 657 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 471 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N ILE A 655 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 654 " --> pdb=" O CYS A 591 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 593 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N CYS A 656 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 508 removed outlier: 3.534A pdb=" N ARG A 518 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.425A pdb=" N ARG B 149 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.568A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ALA B 236 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.568A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ALA B 236 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 263 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 261 " --> pdb=" O PRO B 237 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE B 239 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS B 259 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 241 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR B 257 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 245 through 249 removed outlier: 4.865A pdb=" N GLU B 312 " --> pdb=" O LYS B 273 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1311 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: 1.73 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2914 1.34 - 1.46: 1636 1.46 - 1.58: 4612 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 9251 Sorted by residual: bond pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.781 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" F4 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.686 1.778 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.774 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.684 1.772 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" N LEU A 901 " pdb=" CA LEU A 901 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 ... (remaining 9246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.93: 12539 13.93 - 27.87: 4 27.87 - 41.80: 0 41.80 - 55.74: 0 55.74 - 69.67: 2 Bond angle restraints: 12545 Sorted by residual: angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F2 ALF A1301 " ideal model delta sigma weight residual 108.68 178.35 -69.67 3.00e+00 1.11e-01 5.39e+02 angle pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.63 177.79 -68.16 3.00e+00 1.11e-01 5.16e+02 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.69 89.51 20.18 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.02 89.05 19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.59 90.33 19.26 3.00e+00 1.11e-01 4.12e+01 ... (remaining 12540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 5121 15.31 - 30.61: 460 30.61 - 45.92: 76 45.92 - 61.22: 26 61.22 - 76.53: 9 Dihedral angle restraints: 5692 sinusoidal: 2362 harmonic: 3330 Sorted by residual: dihedral pdb=" CA THR A 797 " pdb=" C THR A 797 " pdb=" N ASP A 798 " pdb=" CA ASP A 798 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ALA A 881 " pdb=" C ALA A 881 " pdb=" N THR A 882 " pdb=" CA THR A 882 " ideal model delta harmonic sigma weight residual 180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ALA B 229 " pdb=" C ALA B 229 " pdb=" N THR B 230 " pdb=" CA THR B 230 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1174 0.056 - 0.113: 268 0.113 - 0.169: 42 0.169 - 0.225: 3 0.225 - 0.281: 2 Chirality restraints: 1489 Sorted by residual: chirality pdb=" C1 NAG B 505 " pdb=" ND2 ASN B 228 " pdb=" C2 NAG B 505 " pdb=" O5 NAG B 505 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 316 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 170 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1486 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 68 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 69 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 516 " 0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO A 517 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 353 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C VAL B 353 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL B 353 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL B 354 " -0.013 2.00e-02 2.50e+03 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 49 2.56 - 3.15: 7394 3.15 - 3.73: 13284 3.73 - 4.32: 18971 4.32 - 4.90: 31751 Nonbonded interactions: 71449 Sorted by model distance: nonbonded pdb=" F2 ALF A1301 " pdb="MG MG A1302 " model vdw 1.976 2.120 nonbonded pdb=" OD1 ASP A 454 " pdb=" F3 ALF A1301 " model vdw 2.026 2.990 nonbonded pdb=" O THR A 456 " pdb="MG MG A1302 " model vdw 2.208 2.170 nonbonded pdb=" N GLY A 687 " pdb=" F1 ALF A1301 " model vdw 2.287 3.070 nonbonded pdb=" OG SER A 574 " pdb=" OD1 ASP A 633 " model vdw 2.290 3.040 ... (remaining 71444 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.410 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.006 0.096 9259 Z= 0.258 Angle : 1.217 69.673 12567 Z= 0.546 Chirality : 0.049 0.281 1489 Planarity : 0.007 0.102 1580 Dihedral : 12.451 76.527 3532 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.24), residues: 1141 helix: -0.46 (0.24), residues: 479 sheet: 1.04 (0.39), residues: 168 loop : -1.47 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 608 TYR 0.018 0.002 TYR A 470 PHE 0.020 0.002 PHE A1024 TRP 0.021 0.002 TRP A 867 HIS 0.004 0.001 HIS A 913 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 9251) covalent geometry : angle 1.21601 (12545) SS BOND : bond 0.00196 ( 2) SS BOND : angle 0.77375 ( 4) hydrogen bonds : bond 0.17059 ( 446) hydrogen bonds : angle 7.40808 ( 1311) link_NAG-ASN : bond 0.00533 ( 6) link_NAG-ASN : angle 1.96475 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.369 Fit side-chains REVERT: A 84 GLN cc_start: 0.7467 (pt0) cc_final: 0.7118 (pt0) REVERT: A 220 ASP cc_start: 0.7261 (m-30) cc_final: 0.6552 (m-30) REVERT: A 477 LYS cc_start: 0.7775 (mmtp) cc_final: 0.7511 (mmmm) REVERT: A 564 MET cc_start: 0.7215 (tmm) cc_final: 0.6886 (tmm) REVERT: A 729 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7931 (mt-10) REVERT: A 983 ARG cc_start: 0.6896 (ttp-170) cc_final: 0.6080 (tmm-80) REVERT: B 200 MET cc_start: 0.2046 (ptt) cc_final: 0.0517 (mpp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.5898 time to fit residues: 72.0523 Evaluate side-chains 85 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 100 optimal weight: 20.0000 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 ASN B 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.211068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127245 restraints weight = 9539.668| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.46 r_work: 0.3147 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9259 Z= 0.196 Angle : 0.666 8.523 12567 Z= 0.355 Chirality : 0.047 0.233 1489 Planarity : 0.006 0.070 1580 Dihedral : 5.281 25.323 1356 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.10 % Allowed : 6.59 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.25), residues: 1141 helix: 0.64 (0.24), residues: 486 sheet: 0.88 (0.40), residues: 160 loop : -1.11 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 975 TYR 0.017 0.002 TYR B 180 PHE 0.018 0.002 PHE A 833 TRP 0.017 0.002 TRP A 737 HIS 0.003 0.001 HIS A 913 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9251) covalent geometry : angle 0.66246 (12545) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.68035 ( 4) hydrogen bonds : bond 0.07466 ( 446) hydrogen bonds : angle 4.92832 ( 1311) link_NAG-ASN : bond 0.00489 ( 6) link_NAG-ASN : angle 1.88576 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.295 Fit side-chains REVERT: A 220 ASP cc_start: 0.7581 (m-30) cc_final: 0.6971 (m-30) REVERT: A 266 GLU cc_start: 0.7992 (tt0) cc_final: 0.7665 (tt0) REVERT: A 477 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7679 (mmmm) REVERT: A 564 MET cc_start: 0.6873 (tmm) cc_final: 0.6570 (tmm) REVERT: A 729 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 983 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.6791 (tmm-80) REVERT: B 200 MET cc_start: 0.2692 (ptt) cc_final: 0.0527 (mpp) outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 0.5818 time to fit residues: 60.7482 Evaluate side-chains 94 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN A 475 HIS ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.206300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120027 restraints weight = 9599.952| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.99 r_work: 0.3136 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.083 9259 Z= 0.411 Angle : 0.830 7.395 12567 Z= 0.443 Chirality : 0.057 0.252 1489 Planarity : 0.007 0.063 1580 Dihedral : 5.733 29.533 1356 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.20 % Allowed : 9.78 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.24), residues: 1141 helix: 0.30 (0.23), residues: 485 sheet: 0.68 (0.39), residues: 160 loop : -1.31 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 969 TYR 0.018 0.002 TYR B 180 PHE 0.020 0.003 PHE A 717 TRP 0.021 0.003 TRP A 867 HIS 0.008 0.002 HIS A 913 Details of bonding type rmsd covalent geometry : bond 0.01066 ( 9251) covalent geometry : angle 0.82508 (12545) SS BOND : bond 0.00329 ( 2) SS BOND : angle 0.64547 ( 4) hydrogen bonds : bond 0.10129 ( 446) hydrogen bonds : angle 5.15808 ( 1311) link_NAG-ASN : bond 0.00508 ( 6) link_NAG-ASN : angle 2.44930 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 220 ASP cc_start: 0.7718 (m-30) cc_final: 0.7476 (m-30) REVERT: A 266 GLU cc_start: 0.8077 (tt0) cc_final: 0.7768 (tt0) REVERT: A 477 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7692 (mmmm) REVERT: A 564 MET cc_start: 0.7181 (tmm) cc_final: 0.6861 (tmm) REVERT: A 577 MET cc_start: 0.4996 (OUTLIER) cc_final: 0.4664 (ttm) REVERT: A 729 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7614 (mt-10) REVERT: A 983 ARG cc_start: 0.7584 (ttp-170) cc_final: 0.6918 (tmm-80) REVERT: B 210 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6846 (tm-30) outliers start: 22 outliers final: 13 residues processed: 101 average time/residue: 0.5859 time to fit residues: 62.9360 Evaluate side-chains 97 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 0.0060 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.214267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129110 restraints weight = 9700.596| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.06 r_work: 0.3255 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9259 Z= 0.121 Angle : 0.564 6.747 12567 Z= 0.300 Chirality : 0.044 0.208 1489 Planarity : 0.005 0.052 1580 Dihedral : 4.884 24.835 1356 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.00 % Allowed : 11.98 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.25), residues: 1141 helix: 1.22 (0.24), residues: 491 sheet: 0.82 (0.39), residues: 162 loop : -0.99 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.017 0.001 TYR B 180 PHE 0.016 0.001 PHE B 221 TRP 0.013 0.001 TRP A 737 HIS 0.003 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9251) covalent geometry : angle 0.56044 (12545) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.75778 ( 4) hydrogen bonds : bond 0.05363 ( 446) hydrogen bonds : angle 4.46378 ( 1311) link_NAG-ASN : bond 0.00496 ( 6) link_NAG-ASN : angle 1.80507 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 220 ASP cc_start: 0.7528 (m-30) cc_final: 0.6915 (m-30) REVERT: A 266 GLU cc_start: 0.8020 (tt0) cc_final: 0.7731 (tt0) REVERT: A 270 ARG cc_start: 0.8102 (ptp-170) cc_final: 0.7714 (ptp90) REVERT: A 477 LYS cc_start: 0.7643 (mmtp) cc_final: 0.7189 (mmtp) REVERT: A 564 MET cc_start: 0.6993 (tmm) cc_final: 0.6709 (tmm) REVERT: A 729 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7456 (mt-10) REVERT: A 983 ARG cc_start: 0.7577 (ttp-170) cc_final: 0.6870 (tmm-80) REVERT: B 210 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 280 GLU cc_start: 0.8216 (mp0) cc_final: 0.7905 (mt-10) REVERT: B 287 ARG cc_start: 0.6112 (mtm110) cc_final: 0.5879 (mtm110) outliers start: 10 outliers final: 1 residues processed: 104 average time/residue: 0.5424 time to fit residues: 60.5853 Evaluate side-chains 93 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 0.0070 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.214235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128713 restraints weight = 9598.348| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.10 r_work: 0.3253 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9259 Z= 0.121 Angle : 0.549 6.363 12567 Z= 0.290 Chirality : 0.044 0.221 1489 Planarity : 0.005 0.048 1580 Dihedral : 4.558 22.631 1356 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.80 % Allowed : 12.97 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1141 helix: 1.56 (0.24), residues: 490 sheet: 1.04 (0.38), residues: 169 loop : -0.97 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.018 0.001 TYR B 180 PHE 0.016 0.001 PHE B 221 TRP 0.012 0.001 TRP A 737 HIS 0.002 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9251) covalent geometry : angle 0.54586 (12545) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.66129 ( 4) hydrogen bonds : bond 0.05328 ( 446) hydrogen bonds : angle 4.24678 ( 1311) link_NAG-ASN : bond 0.00451 ( 6) link_NAG-ASN : angle 1.61235 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 180 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7294 (ttp-170) REVERT: A 220 ASP cc_start: 0.7611 (m-30) cc_final: 0.7045 (m-30) REVERT: A 227 LEU cc_start: 0.8547 (mt) cc_final: 0.8279 (mm) REVERT: A 266 GLU cc_start: 0.8087 (tt0) cc_final: 0.7722 (tt0) REVERT: A 270 ARG cc_start: 0.8021 (ptp-170) cc_final: 0.7550 (ptp-110) REVERT: A 477 LYS cc_start: 0.7538 (mmtp) cc_final: 0.7066 (mmtp) REVERT: A 564 MET cc_start: 0.6973 (tmm) cc_final: 0.6660 (tmm) REVERT: A 729 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 821 MET cc_start: 0.8334 (ttm) cc_final: 0.7990 (ttp) REVERT: A 983 ARG cc_start: 0.7675 (ttp-170) cc_final: 0.6900 (tmm-80) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.5976 time to fit residues: 65.7616 Evaluate side-chains 101 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 525 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN B 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.213972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128356 restraints weight = 9585.611| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.05 r_work: 0.3242 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9259 Z= 0.131 Angle : 0.561 6.384 12567 Z= 0.296 Chirality : 0.044 0.218 1489 Planarity : 0.005 0.048 1580 Dihedral : 4.551 21.972 1356 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.30 % Allowed : 12.97 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.25), residues: 1141 helix: 1.56 (0.24), residues: 490 sheet: 1.02 (0.38), residues: 169 loop : -0.95 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 625 TYR 0.019 0.001 TYR B 180 PHE 0.015 0.001 PHE A 833 TRP 0.010 0.001 TRP A 737 HIS 0.002 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9251) covalent geometry : angle 0.55831 (12545) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.68204 ( 4) hydrogen bonds : bond 0.05550 ( 446) hydrogen bonds : angle 4.24472 ( 1311) link_NAG-ASN : bond 0.00441 ( 6) link_NAG-ASN : angle 1.56740 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 220 ASP cc_start: 0.7621 (m-30) cc_final: 0.7054 (m-30) REVERT: A 227 LEU cc_start: 0.8501 (mt) cc_final: 0.8225 (mm) REVERT: A 266 GLU cc_start: 0.8090 (tt0) cc_final: 0.7738 (tt0) REVERT: A 270 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.7633 (ptp90) REVERT: A 477 LYS cc_start: 0.7545 (mmtp) cc_final: 0.7196 (mmtp) REVERT: A 564 MET cc_start: 0.6952 (tmm) cc_final: 0.6543 (tmt) REVERT: A 729 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7355 (mt-10) REVERT: A 802 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: A 983 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.6938 (tmm-80) REVERT: B 280 GLU cc_start: 0.8244 (mp0) cc_final: 0.7952 (mm-30) outliers start: 13 outliers final: 5 residues processed: 100 average time/residue: 0.5984 time to fit residues: 63.8007 Evaluate side-chains 98 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 802 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.205975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112923 restraints weight = 9494.908| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.08 r_work: 0.3097 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9259 Z= 0.116 Angle : 0.543 7.699 12567 Z= 0.286 Chirality : 0.043 0.215 1489 Planarity : 0.004 0.045 1580 Dihedral : 4.408 21.109 1356 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.60 % Allowed : 12.97 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1141 helix: 1.78 (0.24), residues: 484 sheet: 1.10 (0.38), residues: 168 loop : -0.90 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 625 TYR 0.020 0.001 TYR A 50 PHE 0.015 0.001 PHE A 833 TRP 0.011 0.001 TRP A 737 HIS 0.002 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9251) covalent geometry : angle 0.54062 (12545) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.69438 ( 4) hydrogen bonds : bond 0.05000 ( 446) hydrogen bonds : angle 4.13014 ( 1311) link_NAG-ASN : bond 0.00436 ( 6) link_NAG-ASN : angle 1.51719 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 220 ASP cc_start: 0.7408 (m-30) cc_final: 0.6785 (m-30) REVERT: A 227 LEU cc_start: 0.8227 (mt) cc_final: 0.7963 (mm) REVERT: A 266 GLU cc_start: 0.8015 (tt0) cc_final: 0.7641 (tt0) REVERT: A 270 ARG cc_start: 0.7797 (ptp-170) cc_final: 0.7401 (ptm160) REVERT: A 477 LYS cc_start: 0.7317 (mmtp) cc_final: 0.6979 (mmtp) REVERT: A 564 MET cc_start: 0.6921 (tmm) cc_final: 0.6517 (tmt) REVERT: A 983 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.6668 (tmm-80) REVERT: B 280 GLU cc_start: 0.8191 (mp0) cc_final: 0.7938 (mt-10) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.5047 time to fit residues: 57.4466 Evaluate side-chains 106 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN B 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.204763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111306 restraints weight = 9335.674| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.05 r_work: 0.3122 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9259 Z= 0.131 Angle : 0.561 8.691 12567 Z= 0.295 Chirality : 0.044 0.218 1489 Planarity : 0.005 0.064 1580 Dihedral : 4.453 21.175 1356 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.60 % Allowed : 13.57 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1141 helix: 1.73 (0.24), residues: 484 sheet: 1.07 (0.38), residues: 168 loop : -0.89 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 632 TYR 0.018 0.001 TYR B 180 PHE 0.015 0.001 PHE A 833 TRP 0.010 0.001 TRP A 737 HIS 0.002 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9251) covalent geometry : angle 0.55844 (12545) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.70883 ( 4) hydrogen bonds : bond 0.05564 ( 446) hydrogen bonds : angle 4.19665 ( 1311) link_NAG-ASN : bond 0.00426 ( 6) link_NAG-ASN : angle 1.50743 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 220 ASP cc_start: 0.7451 (m-30) cc_final: 0.6807 (m-30) REVERT: A 227 LEU cc_start: 0.8300 (mt) cc_final: 0.8019 (mm) REVERT: A 266 GLU cc_start: 0.8079 (tt0) cc_final: 0.7701 (tt0) REVERT: A 270 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7477 (ptp90) REVERT: A 431 LYS cc_start: 0.7525 (mttt) cc_final: 0.7247 (mttp) REVERT: A 477 LYS cc_start: 0.7415 (mmtp) cc_final: 0.7086 (mmtp) REVERT: A 564 MET cc_start: 0.6872 (tmm) cc_final: 0.6375 (tmt) REVERT: A 611 MET cc_start: 0.4669 (ppp) cc_final: 0.4434 (ppp) REVERT: A 729 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7209 (mt-10) REVERT: A 983 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.6617 (tmm-80) REVERT: B 280 GLU cc_start: 0.8191 (mp0) cc_final: 0.7917 (mm-30) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.5836 time to fit residues: 61.7838 Evaluate side-chains 104 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 overall best weight: 0.6776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.206143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114621 restraints weight = 9362.165| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.41 r_work: 0.3100 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9259 Z= 0.115 Angle : 0.539 7.646 12567 Z= 0.283 Chirality : 0.043 0.215 1489 Planarity : 0.005 0.062 1580 Dihedral : 4.322 20.467 1356 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.40 % Allowed : 13.77 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.26), residues: 1141 helix: 1.84 (0.24), residues: 484 sheet: 1.10 (0.38), residues: 168 loop : -0.83 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.021 0.001 TYR A 50 PHE 0.015 0.001 PHE A 833 TRP 0.010 0.001 TRP A 737 HIS 0.002 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9251) covalent geometry : angle 0.53671 (12545) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.71922 ( 4) hydrogen bonds : bond 0.04970 ( 446) hydrogen bonds : angle 4.10158 ( 1311) link_NAG-ASN : bond 0.00433 ( 6) link_NAG-ASN : angle 1.47765 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 220 ASP cc_start: 0.7411 (m-30) cc_final: 0.6755 (m-30) REVERT: A 227 LEU cc_start: 0.8212 (mt) cc_final: 0.7947 (mm) REVERT: A 266 GLU cc_start: 0.8102 (tt0) cc_final: 0.7739 (tt0) REVERT: A 270 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7393 (ptm160) REVERT: A 477 LYS cc_start: 0.7301 (mmtp) cc_final: 0.6971 (mmtp) REVERT: A 564 MET cc_start: 0.6795 (tmm) cc_final: 0.6284 (tmt) REVERT: A 983 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.6591 (tmm-80) REVERT: B 280 GLU cc_start: 0.8220 (mp0) cc_final: 0.7952 (mm-30) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.6112 time to fit residues: 63.9101 Evaluate side-chains 101 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN B 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.205208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112668 restraints weight = 9427.176| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.31 r_work: 0.3064 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9259 Z= 0.127 Angle : 0.560 10.373 12567 Z= 0.292 Chirality : 0.043 0.217 1489 Planarity : 0.005 0.073 1580 Dihedral : 4.380 20.520 1356 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.30 % Allowed : 13.67 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.26), residues: 1141 helix: 1.78 (0.24), residues: 484 sheet: 1.09 (0.38), residues: 168 loop : -0.85 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 632 TYR 0.016 0.001 TYR B 180 PHE 0.015 0.001 PHE A 833 TRP 0.009 0.001 TRP A 737 HIS 0.002 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9251) covalent geometry : angle 0.55744 (12545) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.70789 ( 4) hydrogen bonds : bond 0.05424 ( 446) hydrogen bonds : angle 4.16072 ( 1311) link_NAG-ASN : bond 0.00415 ( 6) link_NAG-ASN : angle 1.46567 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 124 TYR cc_start: 0.6282 (t80) cc_final: 0.5499 (t80) REVERT: A 220 ASP cc_start: 0.7479 (m-30) cc_final: 0.6815 (m-30) REVERT: A 227 LEU cc_start: 0.8257 (mt) cc_final: 0.7984 (mm) REVERT: A 266 GLU cc_start: 0.8098 (tt0) cc_final: 0.7744 (tt0) REVERT: A 270 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7466 (ptp90) REVERT: A 477 LYS cc_start: 0.7399 (mmtp) cc_final: 0.6954 (mmtp) REVERT: A 564 MET cc_start: 0.6857 (tmm) cc_final: 0.6567 (tmm) REVERT: A 729 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7220 (mt-10) REVERT: A 983 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.6628 (tmm-80) REVERT: B 157 ILE cc_start: 0.6415 (pt) cc_final: 0.6165 (pp) REVERT: B 280 GLU cc_start: 0.8229 (mp0) cc_final: 0.7903 (mm-30) outliers start: 13 outliers final: 10 residues processed: 99 average time/residue: 0.6055 time to fit residues: 64.0026 Evaluate side-chains 103 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 30.0000 chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 215 GLN B 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.201829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108936 restraints weight = 9271.619| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.42 r_work: 0.3038 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9259 Z= 0.198 Angle : 0.626 8.333 12567 Z= 0.329 Chirality : 0.046 0.226 1489 Planarity : 0.005 0.090 1580 Dihedral : 4.708 22.086 1356 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.50 % Allowed : 13.67 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.25), residues: 1141 helix: 1.43 (0.24), residues: 483 sheet: 1.00 (0.38), residues: 168 loop : -0.96 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 969 TYR 0.022 0.001 TYR A 218 PHE 0.015 0.002 PHE A 717 TRP 0.011 0.001 TRP A 867 HIS 0.004 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 9251) covalent geometry : angle 0.62346 (12545) SS BOND : bond 0.00181 ( 2) SS BOND : angle 0.70970 ( 4) hydrogen bonds : bond 0.07068 ( 446) hydrogen bonds : angle 4.41247 ( 1311) link_NAG-ASN : bond 0.00406 ( 6) link_NAG-ASN : angle 1.61465 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4107.76 seconds wall clock time: 70 minutes 28.44 seconds (4228.44 seconds total)