Starting phenix.real_space_refine on Sun Sep 13 06:39:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ro9_54113/09_2026/9ro9_54113_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ro9_54113/09_2026/9ro9_54113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ro9_54113/09_2026/9ro9_54113_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ro9_54113/09_2026/9ro9_54113_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ro9_54113/09_2026/9ro9_54113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ro9_54113/09_2026/9ro9_54113.map" } resolution = 3.27 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= -0.000 sd= 0.019 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: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 61 5.16 5 Na 3 4.78 5 C 6595 2.51 5 N 1701 2.21 5 O 1937 1.98 5 H 10146 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20447 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 15226 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 942} Chain: "B" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4517 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 258} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 91 Unusual residues: {' MG': 1, ' NA': 3, 'ATP': 1, 'CLR': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.57, per 1000 atoms: 0.17 Number of scatterers: 20447 At special positions: 0 Unit cell: (94.4072, 79.5008, 173.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 61 16.00 P 3 15.00 Mg 1 11.99 Na 3 11.00 O 1937 8.00 N 1701 7.00 C 6595 6.00 H 10146 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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 402 " - " ASN B 265 " " NAG B 403 " - " ASN B 193 " " NAG B 404 " - " ASN B 158 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 673.7 milliseconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 50.1% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.874A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 108 removed outlier: 4.031A pdb=" N GLY A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 154 removed outlier: 3.615A pdb=" N LEU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 272 through 303 Processing helix chain 'A' and resid 306 through 321 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 353 through 359 removed outlier: 3.550A pdb=" N LEU A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 Processing helix chain 'A' and resid 426 through 430 removed outlier: 4.072A pdb=" N ASN A 429 " --> pdb=" O GLY A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 removed outlier: 3.641A pdb=" N LEU A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.754A pdb=" N MET A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.617A pdb=" N ARG A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.914A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 656 through 662 removed outlier: 3.501A pdb=" N ASP A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 675 removed outlier: 3.538A pdb=" N HIS A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.774A pdb=" N GLU A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 744 through 772 removed outlier: 3.532A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 813 removed outlier: 3.879A pdb=" N ALA A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 844 Processing helix chain 'A' and resid 846 through 867 removed outlier: 3.544A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 897 through 928 removed outlier: 3.942A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.510A pdb=" N VAL B 72 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 115 through 119 removed outlier: 4.469A pdb=" N ASP B 119 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.826A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 4.462A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'C' and resid 32 through 57 removed outlier: 3.684A pdb=" N LEU C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 171 removed outlier: 11.659A pdb=" N GLN A 158 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N LYS A 184 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN A 238 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS A 202 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 242 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY A 200 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 244 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA A 198 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY A 246 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 196 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.377A pdb=" N THR A 237 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN A 238 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS A 202 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 242 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY A 200 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 244 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA A 198 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY A 246 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 196 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.212A pdb=" N GLY A 721 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU A 740 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 723 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 720 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A 724 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.257A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.257A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY A 577 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.249A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 515 hydrogen bonds defined for protein. 1458 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: 4.81 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10122 1.03 - 1.23: 147 1.23 - 1.43: 4150 1.43 - 1.62: 6153 1.62 - 1.82: 90 Bond restraints: 20662 Sorted by residual: bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" CB ARG C 58 " pdb=" CG ARG C 58 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" C5 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C1 NAG B 404 " pdb=" O5 NAG B 404 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C1 NAG B 403 " pdb=" O5 NAG B 403 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.38e+00 ... (remaining 20657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 37126 1.92 - 3.85: 244 3.85 - 5.77: 15 5.77 - 7.69: 6 7.69 - 9.62: 1 Bond angle restraints: 37392 Sorted by residual: angle pdb=" CA ARG C 58 " pdb=" CB ARG C 58 " pdb=" CG ARG C 58 " ideal model delta sigma weight residual 114.10 120.92 -6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CB MET A 31 " pdb=" CG MET A 31 " pdb=" SD MET A 31 " ideal model delta sigma weight residual 112.70 122.32 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CB ARG C 58 " pdb=" CG ARG C 58 " pdb=" CD ARG C 58 " ideal model delta sigma weight residual 111.30 118.62 -7.32 2.30e+00 1.89e-01 1.01e+01 angle pdb=" C3' ATP A1101 " pdb=" C4' ATP A1101 " pdb=" O4' ATP A1101 " ideal model delta sigma weight residual 105.22 101.58 3.64 1.30e+00 5.94e-01 7.86e+00 angle pdb=" C1' ATP A1101 " pdb=" C2' ATP A1101 " pdb=" O2' ATP A1101 " ideal model delta sigma weight residual 110.58 103.72 6.86 2.79e+00 1.28e-01 6.03e+00 ... (remaining 37387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 9137 23.71 - 47.42: 564 47.42 - 71.12: 173 71.12 - 94.83: 35 94.83 - 118.54: 19 Dihedral angle restraints: 9928 sinusoidal: 5585 harmonic: 4343 Sorted by residual: dihedral pdb=" CA ASN A 473 " pdb=" C ASN A 473 " pdb=" N SER A 474 " pdb=" CA SER A 474 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA PHE A 472 " pdb=" C PHE A 472 " pdb=" N ASN A 473 " pdb=" CA ASN A 473 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 53.86 39.14 1 1.00e+01 1.00e-02 2.15e+01 ... (remaining 9925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1430 0.060 - 0.120: 190 0.120 - 0.181: 8 0.181 - 0.241: 1 0.241 - 0.301: 2 Chirality restraints: 1631 Sorted by residual: chirality pdb=" C2' ATP A1101 " pdb=" C1' ATP A1101 " pdb=" C3' ATP A1101 " pdb=" O2' ATP A1101 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C4' ATP A1101 " pdb=" C3' ATP A1101 " pdb=" C5' ATP A1101 " pdb=" O4' ATP A1101 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 265 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1628 not shown) Planarity restraints: 3051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 470 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 471 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 471 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 471 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 174 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C GLU A 174 " -0.025 2.00e-02 2.50e+03 pdb=" O GLU A 174 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 175 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 500 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 501 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 501 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 501 " 0.016 5.00e-02 4.00e+02 ... (remaining 3048 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1338 2.19 - 2.79: 42453 2.79 - 3.39: 59114 3.39 - 4.00: 75749 4.00 - 4.60: 116149 Nonbonded interactions: 294803 Sorted by model distance: nonbonded pdb=" O PHE A 234 " pdb=" HG1 THR A 237 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASN A 473 " pdb=" H THR A 475 " model vdw 1.597 2.450 nonbonded pdb=" OE1 GLN A 846 " pdb=" HH TYR A 991 " model vdw 1.600 2.450 nonbonded pdb=" OE1 GLU A 324 " pdb=" H GLU A 324 " model vdw 1.602 2.450 nonbonded pdb=" O VAL A1007 " pdb=" HG1 THR A1011 " model vdw 1.605 2.450 ... (remaining 294798 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=0.00 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.110 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.003 0.040 10523 Z= 0.130 Angle : 0.538 9.618 14296 Z= 0.264 Chirality : 0.041 0.301 1631 Planarity : 0.003 0.050 1817 Dihedral : 18.201 118.538 4127 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.19 % Favored : 94.58 % Rotamer: Outliers : 0.09 % Allowed : 17.27 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.40 (0.24), residues: 1291 helix: 1.84 (0.23), residues: 561 sheet: -1.05 (0.43), residues: 157 loop : -0.94 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 58 TYR 0.011 0.001 TYR A 984 PHE 0.013 0.001 PHE A 472 TRP 0.004 0.001 TRP B 32 HIS 0.002 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10516) covalent geometry : angle 0.53786 / 0.26 (14279) SS BOND : bond 0.00190 / 0.07 ( 4) SS BOND : angle 0.82713 / 0.54 ( 8) hydrogen bonds : bond 0.16596 / 11.13 ( 504) hydrogen bonds : angle 6.50800 / 4.76 ( 1458) link_NAG-ASN : bond 0.00163 / 0.07 ( 3) link_NAG-ASN : angle 0.97310 / 0.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.2424 time to fit residues: 31.8993 Evaluate side-chains 88 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.119448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079289 restraints weight = 69510.889| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.23 r_work: 0.3025 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10523 Z= 0.165 Angle : 0.571 8.676 14296 Z= 0.292 Chirality : 0.042 0.284 1631 Planarity : 0.004 0.047 1817 Dihedral : 11.975 114.078 1690 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.73 % Favored : 94.04 % Rotamer: Outliers : 2.07 % Allowed : 15.74 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.24 (0.24), residues: 1291 helix: 1.56 (0.22), residues: 589 sheet: -1.05 (0.42), residues: 156 loop : -1.02 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 217 TYR 0.018 0.001 TYR A 859 PHE 0.019 0.001 PHE A 82 TRP 0.004 0.001 TRP A 921 HIS 0.002 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (10516) covalent geometry : angle 0.57080 / 0.29 (14279) SS BOND : bond 0.00276 / 0.11 ( 4) SS BOND : angle 0.75266 / 0.49 ( 8) hydrogen bonds : bond 0.04243 / 2.86 ( 504) hydrogen bonds : angle 4.82595 / 3.47 ( 1458) link_NAG-ASN : bond 0.00337 / 0.11 ( 3) link_NAG-ASN : angle 0.90366 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8389 (m-30) outliers start: 23 outliers final: 14 residues processed: 104 average time/residue: 0.2339 time to fit residues: 35.1689 Evaluate side-chains 98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 0.0010 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.120105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079643 restraints weight = 69499.391| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.25 r_work: 0.3034 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10523 Z= 0.134 Angle : 0.525 6.229 14296 Z= 0.270 Chirality : 0.040 0.253 1631 Planarity : 0.004 0.047 1817 Dihedral : 9.823 109.959 1690 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 1.71 % Allowed : 16.19 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.23 (0.24), residues: 1291 helix: 1.57 (0.22), residues: 590 sheet: -1.09 (0.41), residues: 156 loop : -1.05 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.016 0.001 TYR A 859 PHE 0.016 0.001 PHE A 82 TRP 0.003 0.001 TRP A 921 HIS 0.002 0.000 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10516) covalent geometry : angle 0.52384 / 0.27 (14279) SS BOND : bond 0.00250 / 0.10 ( 4) SS BOND : angle 1.01782 / 0.53 ( 8) hydrogen bonds : bond 0.03947 / 2.67 ( 504) hydrogen bonds : angle 4.57266 / 3.29 ( 1458) link_NAG-ASN : bond 0.00488 / 0.15 ( 3) link_NAG-ASN : angle 0.90436 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7502 (t0) outliers start: 19 outliers final: 14 residues processed: 101 average time/residue: 0.2344 time to fit residues: 34.2303 Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.118612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077648 restraints weight = 69276.411| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.25 r_work: 0.3014 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10523 Z= 0.180 Angle : 0.532 6.189 14296 Z= 0.277 Chirality : 0.040 0.218 1631 Planarity : 0.004 0.046 1817 Dihedral : 9.581 106.382 1690 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.12 % Favored : 93.57 % Rotamer: Outliers : 2.16 % Allowed : 15.83 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.16 (0.24), residues: 1291 helix: 1.54 (0.22), residues: 590 sheet: -1.18 (0.41), residues: 156 loop : -1.09 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 217 TYR 0.021 0.001 TYR A 859 PHE 0.017 0.001 PHE A 82 TRP 0.004 0.001 TRP A 95 HIS 0.002 0.000 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (10516) covalent geometry : angle 0.53098 / 0.28 (14279) SS BOND : bond 0.00352 / 0.15 ( 4) SS BOND : angle 1.21088 / 0.75 ( 8) hydrogen bonds : bond 0.03789 / 2.58 ( 504) hydrogen bonds : angle 4.53104 / 3.26 ( 1458) link_NAG-ASN : bond 0.00175 / 0.06 ( 3) link_NAG-ASN : angle 1.14379 / 0.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 ILE cc_start: 0.8956 (tp) cc_final: 0.8726 (tp) REVERT: A 842 MET cc_start: 0.9000 (tpp) cc_final: 0.8584 (tpp) outliers start: 24 outliers final: 19 residues processed: 102 average time/residue: 0.2259 time to fit residues: 33.7329 Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.118014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.076983 restraints weight = 69960.909| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.26 r_work: 0.3001 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10523 Z= 0.194 Angle : 0.542 6.210 14296 Z= 0.282 Chirality : 0.041 0.220 1631 Planarity : 0.004 0.045 1817 Dihedral : 9.369 104.077 1690 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.04 % Favored : 93.65 % Rotamer: Outliers : 2.43 % Allowed : 16.10 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.15 (0.24), residues: 1291 helix: 1.52 (0.22), residues: 588 sheet: -1.27 (0.41), residues: 156 loop : -1.04 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 217 TYR 0.023 0.001 TYR A 859 PHE 0.016 0.001 PHE A 82 TRP 0.004 0.001 TRP A 307 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (10516) covalent geometry : angle 0.54024 / 0.28 (14279) SS BOND : bond 0.00377 / 0.16 ( 4) SS BOND : angle 1.56168 / 1.02 ( 8) hydrogen bonds : bond 0.03793 / 2.60 ( 504) hydrogen bonds : angle 4.47797 / 3.22 ( 1458) link_NAG-ASN : bond 0.00143 / 0.04 ( 3) link_NAG-ASN : angle 1.24451 / 0.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 ILE cc_start: 0.8993 (tp) cc_final: 0.8741 (tp) REVERT: A 842 MET cc_start: 0.8964 (tpp) cc_final: 0.8572 (tpp) outliers start: 27 outliers final: 24 residues processed: 107 average time/residue: 0.2207 time to fit residues: 34.6210 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 16 optimal weight: 0.0570 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.119776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078884 restraints weight = 69102.353| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.26 r_work: 0.3038 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10523 Z= 0.102 Angle : 0.509 6.042 14296 Z= 0.260 Chirality : 0.040 0.195 1631 Planarity : 0.004 0.045 1817 Dihedral : 9.086 102.128 1690 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.19 % Favored : 94.50 % Rotamer: Outliers : 2.25 % Allowed : 16.37 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.30 (0.24), residues: 1291 helix: 1.68 (0.22), residues: 590 sheet: -1.20 (0.41), residues: 154 loop : -1.02 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 294 TYR 0.015 0.001 TYR A 859 PHE 0.014 0.001 PHE A 82 TRP 0.008 0.001 TRP A 95 HIS 0.001 0.000 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (10516) covalent geometry : angle 0.50714 / 0.26 (14279) SS BOND : bond 0.00227 / 0.09 ( 4) SS BOND : angle 1.12864 / 0.74 ( 8) hydrogen bonds : bond 0.03479 / 2.38 ( 504) hydrogen bonds : angle 4.27213 / 3.07 ( 1458) link_NAG-ASN : bond 0.00195 / 0.07 ( 3) link_NAG-ASN : angle 1.29875 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 ILE cc_start: 0.8946 (tp) cc_final: 0.8647 (tp) REVERT: A 992 ASP cc_start: 0.8900 (t70) cc_final: 0.8657 (t0) outliers start: 25 outliers final: 20 residues processed: 111 average time/residue: 0.2315 time to fit residues: 37.2307 Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 39 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078285 restraints weight = 69317.756| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.25 r_work: 0.3026 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10523 Z= 0.133 Angle : 0.513 6.135 14296 Z= 0.263 Chirality : 0.040 0.203 1631 Planarity : 0.004 0.048 1817 Dihedral : 8.953 101.364 1690 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.27 % Favored : 94.42 % Rotamer: Outliers : 2.25 % Allowed : 16.19 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.34 (0.24), residues: 1291 helix: 1.70 (0.22), residues: 590 sheet: -1.20 (0.41), residues: 160 loop : -0.97 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 217 TYR 0.016 0.001 TYR A 859 PHE 0.014 0.001 PHE A 82 TRP 0.007 0.001 TRP A 95 HIS 0.001 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10516) covalent geometry : angle 0.51146 / 0.26 (14279) SS BOND : bond 0.00258 / 0.10 ( 4) SS BOND : angle 0.99253 / 0.65 ( 8) hydrogen bonds : bond 0.03468 / 2.37 ( 504) hydrogen bonds : angle 4.26617 / 3.06 ( 1458) link_NAG-ASN : bond 0.00142 / 0.05 ( 3) link_NAG-ASN : angle 1.32196 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 ILE cc_start: 0.8916 (tp) cc_final: 0.8629 (tp) REVERT: A 842 MET cc_start: 0.9030 (tpp) cc_final: 0.8643 (tpp) REVERT: A 992 ASP cc_start: 0.8915 (t70) cc_final: 0.8644 (t0) REVERT: B 217 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8683 (mtp-110) outliers start: 25 outliers final: 23 residues processed: 107 average time/residue: 0.2303 time to fit residues: 35.6766 Evaluate side-chains 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 10.0000 chunk 116 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.118052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077114 restraints weight = 69515.190| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.24 r_work: 0.3003 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10523 Z= 0.188 Angle : 0.536 6.245 14296 Z= 0.278 Chirality : 0.041 0.219 1631 Planarity : 0.004 0.044 1817 Dihedral : 8.884 101.660 1690 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.65 % Favored : 94.04 % Rotamer: Outliers : 2.34 % Allowed : 16.55 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.27 (0.24), residues: 1291 helix: 1.63 (0.22), residues: 590 sheet: -1.19 (0.41), residues: 160 loop : -1.01 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 217 TYR 0.020 0.001 TYR A 859 PHE 0.015 0.001 PHE A 82 TRP 0.008 0.001 TRP A 95 HIS 0.001 0.000 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (10516) covalent geometry : angle 0.53484 / 0.28 (14279) SS BOND : bond 0.00330 / 0.12 ( 4) SS BOND : angle 0.97223 / 0.63 ( 8) hydrogen bonds : bond 0.03630 / 2.49 ( 504) hydrogen bonds : angle 4.34161 / 3.13 ( 1458) link_NAG-ASN : bond 0.00087 / 0.03 ( 3) link_NAG-ASN : angle 1.32687 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7559 (t0) REVERT: A 810 ILE cc_start: 0.9047 (tp) cc_final: 0.8754 (tp) REVERT: A 842 MET cc_start: 0.9000 (tpp) cc_final: 0.8587 (tpp) REVERT: A 992 ASP cc_start: 0.8976 (t70) cc_final: 0.8695 (t0) outliers start: 26 outliers final: 24 residues processed: 107 average time/residue: 0.2383 time to fit residues: 36.8231 Evaluate side-chains 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 34 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.119011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078152 restraints weight = 68961.172| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.23 r_work: 0.3026 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10523 Z= 0.124 Angle : 0.514 6.079 14296 Z= 0.263 Chirality : 0.040 0.205 1631 Planarity : 0.004 0.049 1817 Dihedral : 8.699 100.694 1690 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.27 % Favored : 94.42 % Rotamer: Outliers : 2.43 % Allowed : 16.37 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.38 (0.24), residues: 1291 helix: 1.71 (0.22), residues: 591 sheet: -1.12 (0.42), residues: 160 loop : -0.93 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 217 TYR 0.016 0.001 TYR A 859 PHE 0.014 0.001 PHE A 82 TRP 0.023 0.001 TRP A 95 HIS 0.001 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10516) covalent geometry : angle 0.51322 / 0.26 (14279) SS BOND : bond 0.00233 / 0.08 ( 4) SS BOND : angle 0.92997 / 0.61 ( 8) hydrogen bonds : bond 0.03438 / 2.37 ( 504) hydrogen bonds : angle 4.21566 / 3.03 ( 1458) link_NAG-ASN : bond 0.00150 / 0.06 ( 3) link_NAG-ASN : angle 1.32953 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 ILE cc_start: 0.9014 (tp) cc_final: 0.8724 (tp) REVERT: A 842 MET cc_start: 0.9012 (tpp) cc_final: 0.8613 (tpp) REVERT: A 992 ASP cc_start: 0.8937 (t70) cc_final: 0.8649 (t0) REVERT: B 217 ARG cc_start: 0.9082 (mmm-85) cc_final: 0.8726 (mtp-110) outliers start: 27 outliers final: 24 residues processed: 111 average time/residue: 0.2419 time to fit residues: 38.2150 Evaluate side-chains 112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.120032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079625 restraints weight = 68954.745| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.23 r_work: 0.3036 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10523 Z= 0.115 Angle : 0.512 6.881 14296 Z= 0.261 Chirality : 0.040 0.202 1631 Planarity : 0.004 0.046 1817 Dihedral : 8.610 99.598 1690 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.19 % Favored : 94.50 % Rotamer: Outliers : 2.07 % Allowed : 16.46 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.46 (0.25), residues: 1291 helix: 1.77 (0.22), residues: 591 sheet: -1.08 (0.42), residues: 160 loop : -0.89 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 217 TYR 0.015 0.001 TYR A 859 PHE 0.012 0.001 PHE A 82 TRP 0.019 0.001 TRP A 95 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10516) covalent geometry : angle 0.51101 / 0.26 (14279) SS BOND : bond 0.00221 / 0.08 ( 4) SS BOND : angle 0.94076 / 0.62 ( 8) hydrogen bonds : bond 0.03345 / 2.30 ( 504) hydrogen bonds : angle 4.14742 / 2.98 ( 1458) link_NAG-ASN : bond 0.00155 / 0.06 ( 3) link_NAG-ASN : angle 1.35822 / 0.83 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue TYR 68 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 ILE cc_start: 0.9031 (tp) cc_final: 0.8720 (tp) REVERT: A 842 MET cc_start: 0.9052 (tpp) cc_final: 0.8685 (tpp) REVERT: A 992 ASP cc_start: 0.8925 (t70) cc_final: 0.8631 (t0) outliers start: 23 outliers final: 22 residues processed: 109 average time/residue: 0.2177 time to fit residues: 34.4940 Evaluate side-chains 114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 54 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.119868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079368 restraints weight = 69745.999| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.24 r_work: 0.3032 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10523 Z= 0.123 Angle : 0.510 6.637 14296 Z= 0.260 Chirality : 0.040 0.206 1631 Planarity : 0.004 0.046 1817 Dihedral : 8.476 98.941 1690 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.88 % Favored : 94.81 % Rotamer: Outliers : 2.16 % Allowed : 16.64 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.49 (0.25), residues: 1291 helix: 1.79 (0.22), residues: 593 sheet: -1.06 (0.42), residues: 160 loop : -0.89 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 217 TYR 0.016 0.001 TYR A 859 PHE 0.011 0.001 PHE A 472 TRP 0.006 0.001 TRP A 95 HIS 0.001 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10516) covalent geometry : angle 0.50858 / 0.26 (14279) SS BOND : bond 0.00226 / 0.08 ( 4) SS BOND : angle 0.93219 / 0.61 ( 8) hydrogen bonds : bond 0.03307 / 2.28 ( 504) hydrogen bonds : angle 4.11968 / 2.96 ( 1458) link_NAG-ASN : bond 0.00144 / 0.05 ( 3) link_NAG-ASN : angle 1.36490 / 0.83 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4923.72 seconds wall clock time: 84 minutes 30.54 seconds (5070.54 seconds total)