Starting phenix.real_space_refine on Thu Jul 2 15:56:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ty7_26168/07_2026/7ty7_26168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty7_26168/07_2026/7ty7_26168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ty7_26168/07_2026/7ty7_26168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty7_26168/07_2026/7ty7_26168.map" model { file = "/net/cci-nas-00/data/ceres_data/7ty7_26168/07_2026/7ty7_26168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty7_26168/07_2026/7ty7_26168.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ty7_26168/07_2026/7ty7_26168.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ty7_26168/07_2026/7ty7_26168.cif" } resolution = 3.37 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= -0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5757 2.51 5 N 1312 2.21 5 O 1431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8538 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Chain: "B" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 170 Unusual residues: {'BCT': 1, 'CLR': 4, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'BCT': 1, 'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" 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: 1.40, per 1000 atoms: 0.16 Number of scatterers: 8538 At special positions: 0 Unit cell: (121.588, 89.308, 85.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1431 8.00 N 1312 7.00 C 5757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 642 " " NAG D 1 " - " ASN B 642 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 198.9 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 73.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 392 through 400 removed outlier: 3.623A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.692A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.585A pdb=" N GLY A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 508 removed outlier: 3.691A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.706A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.535A pdb=" N LEU A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.561A pdb=" N ARG A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.511A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 666 removed outlier: 4.082A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.562A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 719 removed outlier: 4.016A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 760 through 772 Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.887A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 872 removed outlier: 3.599A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 878 removed outlier: 3.766A pdb=" N LEU A 876 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 removed outlier: 3.519A pdb=" N LEU A 883 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 400 removed outlier: 3.622A pdb=" N ALA B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.694A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.585A pdb=" N GLY B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 508 removed outlier: 3.692A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.706A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.534A pdb=" N LEU B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.560A pdb=" N ARG B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.511A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 666 removed outlier: 4.083A pdb=" N MET B 664 " --> pdb=" O PRO B 660 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.562A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 685 " --> pdb=" O GLU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 719 removed outlier: 4.016A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 739 Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.885A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 865 through 872 removed outlier: 3.598A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 878 removed outlier: 3.765A pdb=" N LEU B 876 " --> pdb=" O VAL B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 removed outlier: 3.518A pdb=" N LEU B 883 " --> pdb=" O ARG B 879 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463 removed outlier: 4.798A pdb=" N VAL A 461 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 461 through 463 removed outlier: 4.798A pdb=" N VAL B 461 " --> pdb=" O THR B 727 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1488 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: 0.85 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1323 1.32 - 1.45: 2194 1.45 - 1.57: 5154 1.57 - 1.69: 4 1.69 - 1.82: 66 Bond restraints: 8741 Sorted by residual: bond pdb=" N ILE A 783 " pdb=" CA ILE A 783 " ideal model delta sigma weight residual 1.460 1.497 -0.038 7.50e-03 1.78e+04 2.50e+01 bond pdb=" N ILE B 783 " pdb=" CA ILE B 783 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.42e+01 bond pdb=" N HIS B 819 " pdb=" CA HIS B 819 " ideal model delta sigma weight residual 1.453 1.492 -0.038 8.30e-03 1.45e+04 2.14e+01 bond pdb=" N HIS A 819 " pdb=" CA HIS A 819 " ideal model delta sigma weight residual 1.453 1.491 -0.038 8.30e-03 1.45e+04 2.07e+01 bond pdb=" N VAL A 634 " pdb=" CA VAL A 634 " ideal model delta sigma weight residual 1.461 1.496 -0.035 8.70e-03 1.32e+04 1.65e+01 ... (remaining 8736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8031 1.70 - 3.39: 3032 3.39 - 5.09: 745 5.09 - 6.79: 88 6.79 - 8.48: 4 Bond angle restraints: 11900 Sorted by residual: angle pdb=" N LEU B 680 " pdb=" CA LEU B 680 " pdb=" C LEU B 680 " ideal model delta sigma weight residual 111.36 105.56 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" N LEU A 680 " pdb=" CA LEU A 680 " pdb=" C LEU A 680 " ideal model delta sigma weight residual 111.36 105.58 5.78 1.09e+00 8.42e-01 2.81e+01 angle pdb=" C THR A 837 " pdb=" N GLY A 838 " pdb=" CA GLY A 838 " ideal model delta sigma weight residual 119.98 125.81 -5.83 1.11e+00 8.12e-01 2.76e+01 angle pdb=" C THR B 837 " pdb=" N GLY B 838 " pdb=" CA GLY B 838 " ideal model delta sigma weight residual 119.98 125.80 -5.82 1.11e+00 8.12e-01 2.75e+01 angle pdb=" C LEU A 427 " pdb=" N GLY A 428 " pdb=" CA GLY A 428 " ideal model delta sigma weight residual 119.94 125.58 -5.64 1.11e+00 8.12e-01 2.58e+01 ... (remaining 11895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 4556 16.01 - 32.02: 375 32.02 - 48.03: 107 48.03 - 64.04: 28 64.04 - 80.05: 3 Dihedral angle restraints: 5069 sinusoidal: 2093 harmonic: 2976 Sorted by residual: dihedral pdb=" CA GLN A 625 " pdb=" C GLN A 625 " pdb=" N ASP A 626 " pdb=" CA ASP A 626 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLN B 625 " pdb=" C GLN B 625 " pdb=" N ASP B 626 " pdb=" CA ASP B 626 " ideal model delta harmonic sigma weight residual 180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA VAL B 822 " pdb=" C VAL B 822 " pdb=" N PRO B 823 " pdb=" CA PRO B 823 " ideal model delta harmonic sigma weight residual -180.00 -162.83 -17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 602 0.058 - 0.116: 509 0.116 - 0.174: 285 0.174 - 0.231: 28 0.231 - 0.289: 4 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.09e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" CA LEU B 680 " pdb=" N LEU B 680 " pdb=" C LEU B 680 " pdb=" CB LEU B 680 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1425 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.147 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG D 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.337 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG D 2 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.205 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1264 2.82 - 3.34: 9215 3.34 - 3.86: 13300 3.86 - 4.38: 17762 4.38 - 4.90: 28719 Nonbonded interactions: 70260 Sorted by model distance: nonbonded pdb=" O PRO A 561 " pdb=" CG LYS A 562 " model vdw 2.304 3.440 nonbonded pdb=" O PRO B 561 " pdb=" CG LYS B 562 " model vdw 2.305 3.440 nonbonded pdb=" O LEU A 577 " pdb=" OG1 THR A 581 " model vdw 2.412 3.040 nonbonded pdb=" O LEU B 577 " pdb=" OG1 THR B 581 " model vdw 2.412 3.040 nonbonded pdb=" NH2 ARG B 832 " pdb=" OE1 GLU B 882 " model vdw 2.457 3.120 ... (remaining 70255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 369 through 2103) selection = (chain 'B' and resid 369 through 2103) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.200 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.470 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.013 0.081 8745 Z= 1.013 Angle : 1.815 8.482 11912 Z= 1.379 Chirality : 0.088 0.289 1428 Planarity : 0.014 0.301 1402 Dihedral : 13.658 80.047 3149 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.45 % Allowed : 4.57 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.03 (0.21), residues: 1024 helix: -1.79 (0.16), residues: 678 sheet: None (None), residues: 0 loop : -2.14 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 827 TYR 0.017 0.002 TYR B 824 PHE 0.014 0.002 PHE A 471 TRP 0.010 0.002 TRP B 492 HIS 0.006 0.002 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.01318 / 1.01 ( 8741) covalent geometry : angle 1.81443 / 1.38 (11900) hydrogen bonds : bond 0.25099 / 16.78 ( 508) hydrogen bonds : angle 8.53976 / 6.13 ( 1488) link_BETA1-4 : bond 0.00389 / 0.19 ( 2) link_BETA1-4 : angle 1.73622 / 0.90 ( 6) link_NAG-ASN : bond 0.00151 / 0.08 ( 2) link_NAG-ASN : angle 2.05971 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.297 Fit side-chains REVERT: A 479 CYS cc_start: 0.8762 (m) cc_final: 0.8481 (m) REVERT: A 626 ASP cc_start: 0.8246 (m-30) cc_final: 0.7950 (m-30) REVERT: A 821 ASP cc_start: 0.8875 (t0) cc_final: 0.8625 (t0) REVERT: B 479 CYS cc_start: 0.8730 (m) cc_final: 0.8473 (m) REVERT: B 626 ASP cc_start: 0.8182 (m-30) cc_final: 0.7895 (m-30) REVERT: B 821 ASP cc_start: 0.8901 (t0) cc_final: 0.8643 (t0) outliers start: 4 outliers final: 0 residues processed: 139 average time/residue: 0.0436 time to fit residues: 9.7464 Evaluate side-chains 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.045889 restraints weight = 37128.222| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.67 r_work: 0.2656 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8745 Z= 0.151 Angle : 0.656 11.029 11912 Z= 0.318 Chirality : 0.043 0.299 1428 Planarity : 0.005 0.040 1402 Dihedral : 8.481 62.300 1243 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.67 % Allowed : 10.02 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.25), residues: 1024 helix: 0.84 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 490 TYR 0.014 0.001 TYR A 824 PHE 0.020 0.002 PHE B 411 TRP 0.009 0.002 TRP A 831 HIS 0.005 0.001 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8741) covalent geometry : angle 0.65466 / 0.32 (11900) hydrogen bonds : bond 0.05112 / 3.48 ( 508) hydrogen bonds : angle 4.52585 / 3.23 ( 1488) link_BETA1-4 : bond 0.00806 / 0.42 ( 2) link_BETA1-4 : angle 1.03640 / 0.57 ( 6) link_NAG-ASN : bond 0.00352 / 0.17 ( 2) link_NAG-ASN : angle 1.87874 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.338 Fit side-chains REVERT: A 479 CYS cc_start: 0.9232 (m) cc_final: 0.9010 (m) REVERT: A 617 MET cc_start: 0.9474 (mmm) cc_final: 0.9255 (mmm) REVERT: A 626 ASP cc_start: 0.8474 (m-30) cc_final: 0.8158 (m-30) REVERT: A 776 MET cc_start: 0.9440 (ptp) cc_final: 0.9113 (ptp) REVERT: A 805 LEU cc_start: 0.9356 (tp) cc_final: 0.9111 (tp) REVERT: A 821 ASP cc_start: 0.9197 (t0) cc_final: 0.8928 (t0) REVERT: A 880 ASN cc_start: 0.9439 (p0) cc_final: 0.9007 (t0) REVERT: B 479 CYS cc_start: 0.9284 (m) cc_final: 0.9064 (m) REVERT: B 617 MET cc_start: 0.9460 (mmm) cc_final: 0.9247 (mmm) REVERT: B 626 ASP cc_start: 0.8458 (m-30) cc_final: 0.8162 (m-30) REVERT: B 696 MET cc_start: 0.8957 (mmm) cc_final: 0.8667 (mmm) REVERT: B 805 LEU cc_start: 0.9376 (tp) cc_final: 0.9133 (tp) REVERT: B 821 ASP cc_start: 0.9238 (t0) cc_final: 0.8956 (t0) REVERT: B 880 ASN cc_start: 0.9407 (p0) cc_final: 0.8942 (t0) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 0.0601 time to fit residues: 8.7784 Evaluate side-chains 69 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 765 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.045029 restraints weight = 37257.117| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.69 r_work: 0.2634 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8745 Z= 0.151 Angle : 0.606 9.455 11912 Z= 0.285 Chirality : 0.041 0.209 1428 Planarity : 0.005 0.040 1402 Dihedral : 8.041 59.763 1243 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.00 % Allowed : 10.69 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.27), residues: 1024 helix: 1.71 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.91 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 490 TYR 0.015 0.001 TYR B 824 PHE 0.016 0.001 PHE B 411 TRP 0.011 0.001 TRP A 492 HIS 0.004 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8741) covalent geometry : angle 0.60512 / 0.29 (11900) hydrogen bonds : bond 0.04150 / 2.83 ( 508) hydrogen bonds : angle 4.15985 / 2.96 ( 1488) link_BETA1-4 : bond 0.00894 / 0.46 ( 2) link_BETA1-4 : angle 1.16099 / 0.67 ( 6) link_NAG-ASN : bond 0.00190 / 0.10 ( 2) link_NAG-ASN : angle 1.18587 / 0.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.389 Fit side-chains REVERT: A 559 MET cc_start: 0.9289 (mpp) cc_final: 0.8965 (mmp) REVERT: A 586 MET cc_start: 0.9237 (mmm) cc_final: 0.9018 (mmm) REVERT: A 617 MET cc_start: 0.9496 (mmm) cc_final: 0.9205 (mmm) REVERT: A 626 ASP cc_start: 0.8492 (m-30) cc_final: 0.8223 (m-30) REVERT: A 805 LEU cc_start: 0.9435 (tp) cc_final: 0.9218 (tp) REVERT: A 821 ASP cc_start: 0.9183 (t0) cc_final: 0.8937 (t0) REVERT: A 833 MET cc_start: 0.9257 (ppp) cc_final: 0.8954 (tmm) REVERT: B 559 MET cc_start: 0.9244 (mpp) cc_final: 0.8946 (mmp) REVERT: B 586 MET cc_start: 0.9225 (mmm) cc_final: 0.9007 (mmm) REVERT: B 626 ASP cc_start: 0.8422 (m-30) cc_final: 0.8143 (m-30) REVERT: B 696 MET cc_start: 0.9053 (mmm) cc_final: 0.8798 (mmm) REVERT: B 805 LEU cc_start: 0.9446 (tp) cc_final: 0.9221 (tp) REVERT: B 821 ASP cc_start: 0.9248 (t0) cc_final: 0.8993 (t0) REVERT: B 833 MET cc_start: 0.9242 (ppp) cc_final: 0.8917 (tmm) REVERT: B 880 ASN cc_start: 0.9394 (p0) cc_final: 0.8862 (t0) outliers start: 18 outliers final: 9 residues processed: 76 average time/residue: 0.0552 time to fit residues: 6.9881 Evaluate side-chains 68 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 GLN A 683 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.043855 restraints weight = 39227.624| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.84 r_work: 0.2605 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 8745 Z= 0.175 Angle : 0.585 9.237 11912 Z= 0.277 Chirality : 0.040 0.217 1428 Planarity : 0.005 0.041 1402 Dihedral : 7.928 59.715 1243 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.45 % Allowed : 10.13 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.27), residues: 1024 helix: 1.90 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.014 0.001 TYR A 824 PHE 0.015 0.001 PHE A 471 TRP 0.010 0.001 TRP B 492 HIS 0.003 0.001 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 8741) covalent geometry : angle 0.58400 / 0.28 (11900) hydrogen bonds : bond 0.03867 / 2.66 ( 508) hydrogen bonds : angle 4.02298 / 2.86 ( 1488) link_BETA1-4 : bond 0.00700 / 0.37 ( 2) link_BETA1-4 : angle 1.02817 / 0.60 ( 6) link_NAG-ASN : bond 0.00133 / 0.07 ( 2) link_NAG-ASN : angle 1.24630 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.325 Fit side-chains REVERT: A 559 MET cc_start: 0.9340 (mpp) cc_final: 0.8796 (mmt) REVERT: A 626 ASP cc_start: 0.8465 (m-30) cc_final: 0.8186 (m-30) REVERT: A 821 ASP cc_start: 0.9224 (t0) cc_final: 0.8980 (t0) REVERT: A 833 MET cc_start: 0.9321 (ppp) cc_final: 0.8996 (tmm) REVERT: B 559 MET cc_start: 0.9332 (mpp) cc_final: 0.9001 (mmp) REVERT: B 617 MET cc_start: 0.9533 (mmm) cc_final: 0.9222 (mmm) REVERT: B 626 ASP cc_start: 0.8470 (m-30) cc_final: 0.8191 (m-30) REVERT: B 696 MET cc_start: 0.9080 (mmm) cc_final: 0.8780 (mmm) REVERT: B 821 ASP cc_start: 0.9258 (t0) cc_final: 0.9014 (t0) REVERT: B 833 MET cc_start: 0.9321 (ppp) cc_final: 0.8995 (tmm) outliers start: 31 outliers final: 14 residues processed: 83 average time/residue: 0.0568 time to fit residues: 7.6558 Evaluate side-chains 75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 0.1980 chunk 101 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.044590 restraints weight = 37236.676| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.81 r_work: 0.2633 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8745 Z= 0.110 Angle : 0.567 9.442 11912 Z= 0.263 Chirality : 0.039 0.226 1428 Planarity : 0.005 0.044 1402 Dihedral : 7.726 59.972 1243 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.45 % Allowed : 12.92 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.27), residues: 1024 helix: 2.01 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.84 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.015 0.001 TYR A 824 PHE 0.014 0.001 PHE B 411 TRP 0.013 0.001 TRP A 848 HIS 0.002 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8741) covalent geometry : angle 0.56637 / 0.26 (11900) hydrogen bonds : bond 0.03544 / 2.43 ( 508) hydrogen bonds : angle 3.90648 / 2.78 ( 1488) link_BETA1-4 : bond 0.00818 / 0.43 ( 2) link_BETA1-4 : angle 1.00879 / 0.65 ( 6) link_NAG-ASN : bond 0.00112 / 0.06 ( 2) link_NAG-ASN : angle 0.86180 / 0.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.328 Fit side-chains REVERT: A 559 MET cc_start: 0.9355 (mpp) cc_final: 0.9031 (mmp) REVERT: A 617 MET cc_start: 0.9531 (mmm) cc_final: 0.9266 (mmm) REVERT: A 626 ASP cc_start: 0.8413 (m-30) cc_final: 0.8121 (m-30) REVERT: A 821 ASP cc_start: 0.9148 (t0) cc_final: 0.8908 (t0) REVERT: A 833 MET cc_start: 0.9367 (ppp) cc_final: 0.9123 (ppp) REVERT: A 880 ASN cc_start: 0.9439 (p0) cc_final: 0.9046 (t0) REVERT: B 559 MET cc_start: 0.9310 (mpp) cc_final: 0.9017 (mmp) REVERT: B 626 ASP cc_start: 0.8376 (m-30) cc_final: 0.8080 (m-30) REVERT: B 696 MET cc_start: 0.9000 (mmm) cc_final: 0.8707 (mmm) REVERT: B 821 ASP cc_start: 0.9176 (t0) cc_final: 0.8927 (t0) REVERT: B 833 MET cc_start: 0.9357 (ppp) cc_final: 0.9001 (tmm) REVERT: B 880 ASN cc_start: 0.9379 (p0) cc_final: 0.8937 (t0) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 0.0596 time to fit residues: 7.6057 Evaluate side-chains 70 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 48 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.043482 restraints weight = 37609.292| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.67 r_work: 0.2607 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8745 Z= 0.164 Angle : 0.605 9.320 11912 Z= 0.277 Chirality : 0.040 0.222 1428 Planarity : 0.004 0.042 1402 Dihedral : 7.692 59.772 1243 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.34 % Allowed : 14.70 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.27), residues: 1024 helix: 2.08 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.71 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 760 TYR 0.013 0.001 TYR B 824 PHE 0.015 0.001 PHE A 471 TRP 0.010 0.001 TRP A 492 HIS 0.002 0.001 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 8741) covalent geometry : angle 0.60405 / 0.28 (11900) hydrogen bonds : bond 0.03679 / 2.51 ( 508) hydrogen bonds : angle 3.95252 / 2.82 ( 1488) link_BETA1-4 : bond 0.00498 / 0.26 ( 2) link_BETA1-4 : angle 0.87411 / 0.53 ( 6) link_NAG-ASN : bond 0.00081 / 0.04 ( 2) link_NAG-ASN : angle 1.33783 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.307 Fit side-chains REVERT: A 559 MET cc_start: 0.9323 (mpp) cc_final: 0.9024 (mmp) REVERT: A 626 ASP cc_start: 0.8395 (m-30) cc_final: 0.8105 (m-30) REVERT: A 696 MET cc_start: 0.9130 (mmm) cc_final: 0.8925 (mmm) REVERT: A 821 ASP cc_start: 0.9065 (t0) cc_final: 0.8816 (t0) REVERT: A 833 MET cc_start: 0.9432 (ppp) cc_final: 0.9093 (tmm) REVERT: A 880 ASN cc_start: 0.9468 (p0) cc_final: 0.8997 (t0) REVERT: B 559 MET cc_start: 0.9306 (mpp) cc_final: 0.9044 (mmp) REVERT: B 617 MET cc_start: 0.9553 (mmm) cc_final: 0.9294 (mmm) REVERT: B 626 ASP cc_start: 0.8368 (m-30) cc_final: 0.8087 (m-30) REVERT: B 821 ASP cc_start: 0.9107 (t0) cc_final: 0.8852 (t0) REVERT: B 833 MET cc_start: 0.9418 (ppp) cc_final: 0.9044 (tmm) REVERT: B 880 ASN cc_start: 0.9400 (p0) cc_final: 0.8926 (t0) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.0571 time to fit residues: 6.4191 Evaluate side-chains 70 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.043835 restraints weight = 38717.436| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.85 r_work: 0.2609 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8745 Z= 0.150 Angle : 0.584 9.329 11912 Z= 0.268 Chirality : 0.039 0.225 1428 Planarity : 0.004 0.042 1402 Dihedral : 7.580 59.672 1243 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.90 % Allowed : 13.25 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.94 (0.27), residues: 1024 helix: 2.15 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.64 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 389 TYR 0.013 0.001 TYR A 824 PHE 0.014 0.001 PHE A 471 TRP 0.010 0.001 TRP B 492 HIS 0.001 0.000 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 8741) covalent geometry : angle 0.58313 / 0.27 (11900) hydrogen bonds : bond 0.03540 / 2.42 ( 508) hydrogen bonds : angle 3.87317 / 2.75 ( 1488) link_BETA1-4 : bond 0.00774 / 0.41 ( 2) link_BETA1-4 : angle 0.98316 / 0.67 ( 6) link_NAG-ASN : bond 0.00057 / 0.03 ( 2) link_NAG-ASN : angle 1.20146 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.320 Fit side-chains REVERT: A 557 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8693 (m) REVERT: A 559 MET cc_start: 0.9361 (mpp) cc_final: 0.9069 (mpp) REVERT: A 587 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8578 (mmm) REVERT: A 626 ASP cc_start: 0.8414 (m-30) cc_final: 0.8107 (m-30) REVERT: A 821 ASP cc_start: 0.9131 (t0) cc_final: 0.8878 (t0) REVERT: A 833 MET cc_start: 0.9417 (ppp) cc_final: 0.9049 (tmm) REVERT: A 880 ASN cc_start: 0.9468 (p0) cc_final: 0.9039 (t0) REVERT: B 557 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8618 (m) REVERT: B 559 MET cc_start: 0.9339 (mpp) cc_final: 0.9049 (mpp) REVERT: B 626 ASP cc_start: 0.8410 (m-30) cc_final: 0.8116 (m-30) REVERT: B 696 MET cc_start: 0.9174 (mmm) cc_final: 0.8851 (mmm) REVERT: B 821 ASP cc_start: 0.9120 (t0) cc_final: 0.8874 (t0) REVERT: B 833 MET cc_start: 0.9428 (ppp) cc_final: 0.9065 (tmm) REVERT: B 880 ASN cc_start: 0.9419 (p0) cc_final: 0.8943 (t0) outliers start: 26 outliers final: 15 residues processed: 78 average time/residue: 0.0619 time to fit residues: 7.8740 Evaluate side-chains 79 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 HIS ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.044573 restraints weight = 37508.840| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.72 r_work: 0.2635 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8745 Z= 0.124 Angle : 0.596 9.419 11912 Z= 0.269 Chirality : 0.039 0.229 1428 Planarity : 0.004 0.042 1402 Dihedral : 7.500 59.261 1243 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.23 % Allowed : 13.92 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.00 (0.27), residues: 1024 helix: 2.19 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.57 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.014 0.001 TYR B 824 PHE 0.014 0.001 PHE A 471 TRP 0.009 0.001 TRP A 492 HIS 0.002 0.000 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 8741) covalent geometry : angle 0.59528 / 0.27 (11900) hydrogen bonds : bond 0.03445 / 2.36 ( 508) hydrogen bonds : angle 3.82818 / 2.72 ( 1488) link_BETA1-4 : bond 0.00728 / 0.38 ( 2) link_BETA1-4 : angle 0.97827 / 0.68 ( 6) link_NAG-ASN : bond 0.00051 / 0.03 ( 2) link_NAG-ASN : angle 1.07427 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.335 Fit side-chains REVERT: A 435 MET cc_start: 0.8967 (mmm) cc_final: 0.8631 (tpt) REVERT: A 557 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8675 (m) REVERT: A 559 MET cc_start: 0.9360 (mpp) cc_final: 0.9051 (mpp) REVERT: A 587 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8606 (mmm) REVERT: A 626 ASP cc_start: 0.8356 (m-30) cc_final: 0.8063 (m-30) REVERT: A 821 ASP cc_start: 0.9112 (t0) cc_final: 0.8854 (t0) REVERT: A 833 MET cc_start: 0.9420 (ppp) cc_final: 0.9045 (tmm) REVERT: A 880 ASN cc_start: 0.9468 (p0) cc_final: 0.9031 (t0) REVERT: B 557 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8615 (m) REVERT: B 559 MET cc_start: 0.9331 (mpp) cc_final: 0.9035 (mpp) REVERT: B 587 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8633 (mmm) REVERT: B 626 ASP cc_start: 0.8355 (m-30) cc_final: 0.8058 (m-30) REVERT: B 696 MET cc_start: 0.9094 (mmm) cc_final: 0.8717 (mmm) REVERT: B 821 ASP cc_start: 0.9078 (t0) cc_final: 0.8831 (t0) REVERT: B 833 MET cc_start: 0.9427 (ppp) cc_final: 0.9058 (tmm) REVERT: B 880 ASN cc_start: 0.9411 (p0) cc_final: 0.8934 (t0) outliers start: 20 outliers final: 13 residues processed: 78 average time/residue: 0.0594 time to fit residues: 7.6264 Evaluate side-chains 80 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 0.0570 chunk 98 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.044381 restraints weight = 38591.624| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.83 r_work: 0.2639 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8745 Z= 0.114 Angle : 0.608 9.579 11912 Z= 0.271 Chirality : 0.039 0.230 1428 Planarity : 0.004 0.040 1402 Dihedral : 7.392 59.455 1243 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.34 % Allowed : 14.70 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.01 (0.27), residues: 1024 helix: 2.19 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 490 TYR 0.014 0.001 TYR A 824 PHE 0.013 0.001 PHE A 471 TRP 0.009 0.001 TRP A 496 HIS 0.002 0.000 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 8741) covalent geometry : angle 0.60743 / 0.27 (11900) hydrogen bonds : bond 0.03355 / 2.30 ( 508) hydrogen bonds : angle 3.79863 / 2.70 ( 1488) link_BETA1-4 : bond 0.00710 / 0.37 ( 2) link_BETA1-4 : angle 0.96801 / 0.68 ( 6) link_NAG-ASN : bond 0.00072 / 0.04 ( 2) link_NAG-ASN : angle 0.96705 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.343 Fit side-chains REVERT: A 435 MET cc_start: 0.8934 (mmm) cc_final: 0.8636 (tpt) REVERT: A 557 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8663 (m) REVERT: A 559 MET cc_start: 0.9330 (mpp) cc_final: 0.8997 (mpp) REVERT: A 587 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8595 (mmm) REVERT: A 672 LEU cc_start: 0.9492 (tp) cc_final: 0.9273 (pp) REVERT: A 821 ASP cc_start: 0.9066 (t0) cc_final: 0.8806 (t0) REVERT: A 833 MET cc_start: 0.9448 (ppp) cc_final: 0.9074 (tmm) REVERT: A 880 ASN cc_start: 0.9477 (p0) cc_final: 0.9055 (t0) REVERT: B 557 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8688 (m) REVERT: B 559 MET cc_start: 0.9288 (mpp) cc_final: 0.8981 (mpp) REVERT: B 587 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8604 (mmm) REVERT: B 696 MET cc_start: 0.9150 (mmm) cc_final: 0.8755 (mmm) REVERT: B 776 MET cc_start: 0.9625 (ptp) cc_final: 0.9411 (ptp) REVERT: B 821 ASP cc_start: 0.9031 (t0) cc_final: 0.8782 (t0) REVERT: B 833 MET cc_start: 0.9446 (ppp) cc_final: 0.9079 (tmm) REVERT: B 880 ASN cc_start: 0.9430 (p0) cc_final: 0.8977 (t0) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 0.0573 time to fit residues: 7.9318 Evaluate side-chains 81 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.044848 restraints weight = 38188.888| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.87 r_work: 0.2653 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8745 Z= 0.112 Angle : 0.629 9.463 11912 Z= 0.277 Chirality : 0.039 0.231 1428 Planarity : 0.004 0.039 1402 Dihedral : 7.267 59.759 1243 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.23 % Allowed : 14.81 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.27), residues: 1024 helix: 2.19 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.013 0.001 TYR B 824 PHE 0.013 0.001 PHE A 471 TRP 0.009 0.001 TRP A 496 HIS 0.002 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 8741) covalent geometry : angle 0.62823 / 0.28 (11900) hydrogen bonds : bond 0.03349 / 2.30 ( 508) hydrogen bonds : angle 3.81852 / 2.73 ( 1488) link_BETA1-4 : bond 0.00753 / 0.39 ( 2) link_BETA1-4 : angle 1.00040 / 0.72 ( 6) link_NAG-ASN : bond 0.00085 / 0.04 ( 2) link_NAG-ASN : angle 0.93593 / 0.77 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.321 Fit side-chains REVERT: A 435 MET cc_start: 0.8932 (mmm) cc_final: 0.8659 (tpt) REVERT: A 557 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8679 (m) REVERT: A 559 MET cc_start: 0.9324 (mpp) cc_final: 0.9006 (mpp) REVERT: A 587 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8641 (mmm) REVERT: A 617 MET cc_start: 0.9332 (mmm) cc_final: 0.9128 (mmt) REVERT: A 672 LEU cc_start: 0.9489 (tp) cc_final: 0.9277 (pp) REVERT: A 821 ASP cc_start: 0.9044 (t0) cc_final: 0.8790 (t0) REVERT: A 880 ASN cc_start: 0.9460 (p0) cc_final: 0.9046 (t0) REVERT: B 557 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 559 MET cc_start: 0.9285 (mpp) cc_final: 0.9000 (mpp) REVERT: B 587 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8608 (mmm) REVERT: B 617 MET cc_start: 0.9340 (mmm) cc_final: 0.9115 (mmt) REVERT: B 696 MET cc_start: 0.9156 (mmm) cc_final: 0.8756 (mmm) REVERT: B 776 MET cc_start: 0.9597 (ptp) cc_final: 0.9396 (ptp) REVERT: B 821 ASP cc_start: 0.9031 (t0) cc_final: 0.8774 (t0) REVERT: B 833 MET cc_start: 0.9463 (ppp) cc_final: 0.9097 (tmm) REVERT: B 880 ASN cc_start: 0.9424 (p0) cc_final: 0.8985 (t0) outliers start: 20 outliers final: 11 residues processed: 81 average time/residue: 0.0539 time to fit residues: 7.1293 Evaluate side-chains 79 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.050326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.044063 restraints weight = 38263.894| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.82 r_work: 0.2633 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8745 Z= 0.144 Angle : 0.648 9.484 11912 Z= 0.288 Chirality : 0.040 0.228 1428 Planarity : 0.004 0.037 1402 Dihedral : 7.257 59.696 1243 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.12 % Allowed : 15.70 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.11 (0.27), residues: 1024 helix: 2.25 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 490 TYR 0.013 0.001 TYR A 824 PHE 0.013 0.001 PHE A 471 TRP 0.010 0.001 TRP B 492 HIS 0.002 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 8741) covalent geometry : angle 0.64800 / 0.29 (11900) hydrogen bonds : bond 0.03452 / 2.36 ( 508) hydrogen bonds : angle 3.81370 / 2.72 ( 1488) link_BETA1-4 : bond 0.00685 / 0.36 ( 2) link_BETA1-4 : angle 0.97920 / 0.71 ( 6) link_NAG-ASN : bond 0.00060 / 0.03 ( 2) link_NAG-ASN : angle 1.06263 / 0.89 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.50 seconds wall clock time: 27 minutes 23.33 seconds (1643.33 seconds total)