Starting phenix.real_space_refine on Tue Jul 29 04:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7k_9937/07_2025/6k7k_9937.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7k_9937/07_2025/6k7k_9937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7k_9937/07_2025/6k7k_9937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7k_9937/07_2025/6k7k_9937.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7k_9937/07_2025/6k7k_9937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7k_9937/07_2025/6k7k_9937.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 6851 2.51 5 N 1755 2.21 5 O 1915 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10586 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7835 Classifications: {'peptide': 984} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 953} Chain breaks: 3 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.37, per 1000 atoms: 0.60 Number of scatterers: 10586 At special positions: 0 Unit cell: (69.72, 109.56, 167.66, 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 56 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 1915 8.00 N 1755 7.00 C 6851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.04 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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 ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 48.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 131 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.695A pdb=" N ASP A 273 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 324 Processing helix chain 'A' and resid 341 through 352 removed outlier: 4.008A pdb=" N PHE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.956A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.288A pdb=" N ILE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.959A pdb=" N ASP A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 4.019A pdb=" N LYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 617 Processing helix chain 'A' and resid 621 through 632 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 742 through 752 Processing helix chain 'A' and resid 762 through 778 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.442A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 866 removed outlier: 4.294A pdb=" N ILE A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 880 Processing helix chain 'A' and resid 888 through 896 removed outlier: 4.579A pdb=" N GLY A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 896 " --> pdb=" O THR A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.534A pdb=" N THR A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.295A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 removed outlier: 3.656A pdb=" N HIS A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 3.971A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1061 removed outlier: 5.121A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.755A pdb=" N LEU C 95 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 146 through 151 removed outlier: 4.357A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.525A pdb=" N ARG C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.705A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 4.021A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.085A pdb=" N GLU A 144 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.856A pdb=" N TRP A 262 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 174 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.617A pdb=" N TYR A 182 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.564A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.985A pdb=" N VAL A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 542 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 530 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 546 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU A 528 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 7.357A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.103A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 163 508 hydrogen bonds defined for protein. 1461 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: 4.28 Time building geometry restraints manager: 3.12 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: 1833 1.32 - 1.45: 2848 1.45 - 1.57: 6060 1.57 - 1.70: 3 1.70 - 1.82: 89 Bond restraints: 10833 Sorted by residual: bond pdb=" C4 ADP A1201 " pdb=" C5 ADP A1201 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.796 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.794 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.793 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.790 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 10828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.03: 14705 14.03 - 28.07: 5 28.07 - 42.10: 0 42.10 - 56.13: 0 56.13 - 70.17: 2 Bond angle restraints: 14712 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.85 -70.17 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 178.35 -68.72 3.00e+00 1.11e-01 5.25e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 87.20 23.01 3.00e+00 1.11e-01 5.88e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.69 87.79 21.90 3.00e+00 1.11e-01 5.33e+01 angle pdb=" C ASN C 163 " pdb=" N GLU C 164 " pdb=" CA GLU C 164 " ideal model delta sigma weight residual 121.54 133.48 -11.94 1.91e+00 2.74e-01 3.91e+01 ... (remaining 14707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 6162 25.03 - 50.07: 347 50.07 - 75.10: 35 75.10 - 100.14: 9 100.14 - 125.17: 2 Dihedral angle restraints: 6555 sinusoidal: 2735 harmonic: 3820 Sorted by residual: dihedral pdb=" CA GLU C 164 " pdb=" C GLU C 164 " pdb=" N ASP C 165 " pdb=" CA ASP C 165 " ideal model delta harmonic sigma weight residual 180.00 131.13 48.87 0 5.00e+00 4.00e-02 9.55e+01 dihedral pdb=" CA THR C 100 " pdb=" C THR C 100 " pdb=" N PRO C 101 " pdb=" CA PRO C 101 " ideal model delta harmonic sigma weight residual 0.00 34.24 -34.24 0 5.00e+00 4.00e-02 4.69e+01 dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 174.82 125.17 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 6552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1340 0.079 - 0.158: 297 0.158 - 0.237: 40 0.237 - 0.317: 5 0.317 - 0.396: 1 Chirality restraints: 1683 Sorted by residual: chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB ILE A 41 " pdb=" CA ILE A 41 " pdb=" CG1 ILE A 41 " pdb=" CG2 ILE A 41 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB THR C 263 " pdb=" CA THR C 263 " pdb=" OG1 THR C 263 " pdb=" CG2 THR C 263 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1680 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.295 2.00e-02 2.50e+03 2.51e-01 7.90e+02 pdb=" C7 NAG C 402 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.438 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.186 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" C7 NAG C 401 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.135 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.253 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.088 2.00e-02 2.50e+03 7.52e-02 7.07e+01 pdb=" C7 NAG B 2 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.121 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.072 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 97 2.58 - 3.16: 8078 3.16 - 3.74: 16667 3.74 - 4.32: 23714 4.32 - 4.90: 39925 Nonbonded interactions: 88481 Sorted by model distance: nonbonded pdb=" F3 ALF A1202 " pdb="MG MG A1204 " model vdw 2.000 2.120 nonbonded pdb=" O THR A 411 " pdb="MG MG A1204 " model vdw 2.082 2.170 nonbonded pdb=" OD1 ASP A 786 " pdb="MG MG A1204 " model vdw 2.156 2.170 nonbonded pdb=" O THR A 411 " pdb=" F3 ALF A1202 " model vdw 2.248 2.990 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.255 3.040 ... (remaining 88476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.011 0.132 10841 Z= 0.467 Angle : 1.459 70.169 14733 Z= 0.670 Chirality : 0.067 0.396 1683 Planarity : 0.011 0.251 1832 Dihedral : 15.373 125.173 4082 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.35 % Allowed : 6.01 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.19), residues: 1299 helix: -2.32 (0.16), residues: 575 sheet: -0.87 (0.36), residues: 174 loop : -2.73 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 260 HIS 0.007 0.002 HIS C 131 PHE 0.026 0.004 PHE C 61 TYR 0.030 0.003 TYR C 122 ARG 0.009 0.001 ARG A 608 Details of bonding type rmsd link_NAG-ASN : bond 0.00995 ( 3) link_NAG-ASN : angle 4.76432 ( 9) link_ALPHA1-4 : bond 0.01132 ( 1) link_ALPHA1-4 : angle 4.82033 ( 3) link_BETA1-4 : bond 0.00055 ( 1) link_BETA1-4 : angle 2.09819 ( 3) hydrogen bonds : bond 0.12813 ( 508) hydrogen bonds : angle 6.68824 ( 1461) SS BOND : bond 0.00681 ( 3) SS BOND : angle 2.75132 ( 6) covalent geometry : bond 0.01130 (10833) covalent geometry : angle 1.45207 (14712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7186 (mmp-170) cc_final: 0.6412 (ttp-110) REVERT: A 139 ARG cc_start: 0.6177 (ttp-110) cc_final: 0.5442 (ttp80) REVERT: A 275 LYS cc_start: 0.6335 (mptt) cc_final: 0.6097 (mttt) REVERT: A 278 GLN cc_start: 0.6169 (tt0) cc_final: 0.5905 (tt0) REVERT: A 420 GLN cc_start: 0.6832 (pt0) cc_final: 0.6412 (mt0) REVERT: A 525 ARG cc_start: 0.7167 (ttt-90) cc_final: 0.6940 (ttp80) REVERT: A 532 LEU cc_start: 0.6262 (mm) cc_final: 0.6025 (mm) REVERT: A 675 GLU cc_start: 0.6618 (pm20) cc_final: 0.5762 (mm-30) REVERT: A 754 LYS cc_start: 0.6286 (mttp) cc_final: 0.4620 (ttpt) REVERT: C 55 PHE cc_start: 0.8529 (m-80) cc_final: 0.8294 (m-80) REVERT: C 155 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7612 (mtmt) REVERT: C 200 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8283 (tttm) outliers start: 4 outliers final: 3 residues processed: 167 average time/residue: 0.3002 time to fit residues: 67.6670 Evaluate side-chains 134 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 136 GLN A 147 HIS A 227 HIS A 249 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 ASN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS A 765 GLN A 798 HIS A 917 ASN A 993 HIS C 216 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.186965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.150661 restraints weight = 10763.717| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.20 r_work: 0.3181 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10841 Z= 0.161 Angle : 0.699 12.574 14733 Z= 0.349 Chirality : 0.046 0.207 1683 Planarity : 0.006 0.072 1832 Dihedral : 9.946 118.159 1602 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.22 % Allowed : 10.27 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.21), residues: 1299 helix: -0.71 (0.20), residues: 578 sheet: -0.61 (0.37), residues: 161 loop : -2.12 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.020 0.002 PHE A 968 TYR 0.016 0.002 TYR C 122 ARG 0.004 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 3) link_NAG-ASN : angle 4.08599 ( 9) link_ALPHA1-4 : bond 0.01818 ( 1) link_ALPHA1-4 : angle 3.95690 ( 3) link_BETA1-4 : bond 0.00659 ( 1) link_BETA1-4 : angle 1.34667 ( 3) hydrogen bonds : bond 0.05015 ( 508) hydrogen bonds : angle 5.37613 ( 1461) SS BOND : bond 0.00524 ( 3) SS BOND : angle 1.26587 ( 6) covalent geometry : bond 0.00367 (10833) covalent geometry : angle 0.68862 (14712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7625 (mmp-170) cc_final: 0.6878 (ttp-110) REVERT: A 139 ARG cc_start: 0.6284 (ttp-110) cc_final: 0.5617 (ttp80) REVERT: A 275 LYS cc_start: 0.6925 (mptt) cc_final: 0.6694 (mttt) REVERT: A 383 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6173 (mm-30) REVERT: A 420 GLN cc_start: 0.7513 (pt0) cc_final: 0.7148 (mm-40) REVERT: A 675 GLU cc_start: 0.6816 (pm20) cc_final: 0.6063 (mm-30) REVERT: A 754 LYS cc_start: 0.6546 (mttp) cc_final: 0.4803 (ttpt) REVERT: A 775 LYS cc_start: 0.8270 (tttt) cc_final: 0.8058 (tttp) REVERT: C 200 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8076 (ttpp) REVERT: C 291 TYR cc_start: 0.9044 (m-80) cc_final: 0.8480 (m-80) outliers start: 14 outliers final: 10 residues processed: 149 average time/residue: 0.2599 time to fit residues: 53.5213 Evaluate side-chains 143 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 193 ASN A 331 ASN A 352 ASN A 353 ASN A 453 GLN C 283 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.186807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.150027 restraints weight = 11003.095| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.23 r_work: 0.3175 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10841 Z= 0.141 Angle : 0.649 9.363 14733 Z= 0.323 Chirality : 0.045 0.170 1683 Planarity : 0.005 0.071 1832 Dihedral : 9.438 124.511 1599 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.00 % Allowed : 11.75 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1299 helix: -0.05 (0.21), residues: 587 sheet: -0.30 (0.36), residues: 179 loop : -1.97 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS C 131 PHE 0.019 0.001 PHE A 968 TYR 0.016 0.001 TYR C 122 ARG 0.003 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 3) link_NAG-ASN : angle 3.08205 ( 9) link_ALPHA1-4 : bond 0.02017 ( 1) link_ALPHA1-4 : angle 4.12158 ( 3) link_BETA1-4 : bond 0.00093 ( 1) link_BETA1-4 : angle 1.39958 ( 3) hydrogen bonds : bond 0.04661 ( 508) hydrogen bonds : angle 5.10228 ( 1461) SS BOND : bond 0.00410 ( 3) SS BOND : angle 1.09433 ( 6) covalent geometry : bond 0.00319 (10833) covalent geometry : angle 0.64165 (14712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6549 (p) REVERT: A 74 ARG cc_start: 0.7501 (mmp-170) cc_final: 0.6810 (ttp-170) REVERT: A 139 ARG cc_start: 0.6135 (ttp-110) cc_final: 0.5502 (ttp80) REVERT: A 213 MET cc_start: 0.7532 (mmt) cc_final: 0.6887 (mmt) REVERT: A 383 GLU cc_start: 0.6405 (mm-30) cc_final: 0.6192 (mm-30) REVERT: A 420 GLN cc_start: 0.7405 (pt0) cc_final: 0.7057 (mm-40) REVERT: A 583 GLN cc_start: 0.6576 (tt0) cc_final: 0.6191 (tp-100) REVERT: A 754 LYS cc_start: 0.6481 (mttp) cc_final: 0.4795 (ttpt) REVERT: A 775 LYS cc_start: 0.8228 (tttt) cc_final: 0.8001 (tttp) REVERT: C 200 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8099 (ttpp) REVERT: C 263 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8824 (m) REVERT: C 291 TYR cc_start: 0.9030 (m-80) cc_final: 0.8532 (m-80) outliers start: 23 outliers final: 10 residues processed: 151 average time/residue: 0.2342 time to fit residues: 50.2950 Evaluate side-chains 146 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.0970 chunk 55 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 272 HIS A 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.181599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.142055 restraints weight = 10934.910| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.19 r_work: 0.3078 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 10841 Z= 0.306 Angle : 0.773 9.416 14733 Z= 0.383 Chirality : 0.051 0.181 1683 Planarity : 0.006 0.069 1832 Dihedral : 9.570 118.190 1599 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.79 % Allowed : 12.53 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.22), residues: 1299 helix: -0.14 (0.21), residues: 581 sheet: -0.30 (0.36), residues: 180 loop : -1.97 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 876 HIS 0.005 0.001 HIS A 323 PHE 0.026 0.002 PHE A 968 TYR 0.025 0.002 TYR C 122 ARG 0.006 0.001 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 3) link_NAG-ASN : angle 3.41960 ( 9) link_ALPHA1-4 : bond 0.01526 ( 1) link_ALPHA1-4 : angle 4.67549 ( 3) link_BETA1-4 : bond 0.00182 ( 1) link_BETA1-4 : angle 1.96270 ( 3) hydrogen bonds : bond 0.05858 ( 508) hydrogen bonds : angle 5.25126 ( 1461) SS BOND : bond 0.00529 ( 3) SS BOND : angle 1.76316 ( 6) covalent geometry : bond 0.00745 (10833) covalent geometry : angle 0.76464 (14712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6998 (OUTLIER) cc_final: 0.6643 (p) REVERT: A 74 ARG cc_start: 0.7667 (mmp-170) cc_final: 0.6953 (ttp-170) REVERT: A 275 LYS cc_start: 0.7265 (mttt) cc_final: 0.6988 (mttt) REVERT: A 383 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6343 (mm-30) REVERT: A 420 GLN cc_start: 0.7484 (pt0) cc_final: 0.7269 (mm-40) REVERT: A 583 GLN cc_start: 0.6672 (tt0) cc_final: 0.6305 (tp-100) REVERT: A 754 LYS cc_start: 0.6508 (mttp) cc_final: 0.4790 (ttpt) REVERT: A 775 LYS cc_start: 0.8253 (tttt) cc_final: 0.7949 (tttp) REVERT: C 200 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8445 (tttm) REVERT: C 263 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8853 (m) REVERT: C 291 TYR cc_start: 0.9079 (m-80) cc_final: 0.8551 (m-80) outliers start: 32 outliers final: 21 residues processed: 153 average time/residue: 0.2541 time to fit residues: 55.0969 Evaluate side-chains 159 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 49 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 0.0040 chunk 117 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 331 ASN C 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.190946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.150999 restraints weight = 10689.881| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.30 r_work: 0.3151 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10841 Z= 0.120 Angle : 0.634 9.079 14733 Z= 0.314 Chirality : 0.044 0.163 1683 Planarity : 0.005 0.070 1832 Dihedral : 9.157 123.049 1599 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.44 % Allowed : 13.58 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1299 helix: 0.39 (0.22), residues: 582 sheet: -0.05 (0.37), residues: 179 loop : -1.83 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS C 131 PHE 0.018 0.001 PHE A 935 TYR 0.014 0.001 TYR A1054 ARG 0.003 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 3) link_NAG-ASN : angle 2.73217 ( 9) link_ALPHA1-4 : bond 0.01779 ( 1) link_ALPHA1-4 : angle 3.99402 ( 3) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 1.22069 ( 3) hydrogen bonds : bond 0.04462 ( 508) hydrogen bonds : angle 4.92862 ( 1461) SS BOND : bond 0.00429 ( 3) SS BOND : angle 1.02071 ( 6) covalent geometry : bond 0.00261 (10833) covalent geometry : angle 0.62805 (14712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7613 (mmp-170) cc_final: 0.6831 (ttp-170) REVERT: A 258 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.8028 (mmm-85) REVERT: A 275 LYS cc_start: 0.7215 (mttt) cc_final: 0.6887 (mttt) REVERT: A 383 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6346 (mm-30) REVERT: A 420 GLN cc_start: 0.7331 (pt0) cc_final: 0.7130 (mm-40) REVERT: A 583 GLN cc_start: 0.6594 (tt0) cc_final: 0.6220 (tp-100) REVERT: A 754 LYS cc_start: 0.6210 (mttp) cc_final: 0.4606 (ttpt) REVERT: C 200 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8330 (tttm) REVERT: C 263 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8825 (m) REVERT: C 291 TYR cc_start: 0.9048 (m-80) cc_final: 0.8552 (m-80) outliers start: 28 outliers final: 18 residues processed: 150 average time/residue: 0.2766 time to fit residues: 59.6940 Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.190281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151175 restraints weight = 10752.591| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.29 r_work: 0.3138 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10841 Z= 0.147 Angle : 0.634 9.129 14733 Z= 0.314 Chirality : 0.045 0.154 1683 Planarity : 0.005 0.070 1832 Dihedral : 8.967 122.132 1599 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.70 % Allowed : 14.36 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1299 helix: 0.52 (0.22), residues: 582 sheet: 0.05 (0.37), residues: 179 loop : -1.80 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 798 PHE 0.017 0.001 PHE A 968 TYR 0.017 0.001 TYR C 122 ARG 0.003 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 3) link_NAG-ASN : angle 2.66902 ( 9) link_ALPHA1-4 : bond 0.01652 ( 1) link_ALPHA1-4 : angle 4.11451 ( 3) link_BETA1-4 : bond 0.00169 ( 1) link_BETA1-4 : angle 1.35305 ( 3) hydrogen bonds : bond 0.04572 ( 508) hydrogen bonds : angle 4.87594 ( 1461) SS BOND : bond 0.00423 ( 3) SS BOND : angle 1.13290 ( 6) covalent geometry : bond 0.00339 (10833) covalent geometry : angle 0.62742 (14712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6441 (p) REVERT: A 74 ARG cc_start: 0.7552 (mmp-170) cc_final: 0.6807 (ttp-170) REVERT: A 258 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.8048 (mmm-85) REVERT: A 468 MET cc_start: 0.7726 (ttp) cc_final: 0.7432 (ttp) REVERT: A 525 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7415 (ttp80) REVERT: A 583 GLN cc_start: 0.6564 (tt0) cc_final: 0.6184 (tp-100) REVERT: A 754 LYS cc_start: 0.6220 (mttp) cc_final: 0.4630 (ttpt) REVERT: C 261 MET cc_start: 0.9143 (mmm) cc_final: 0.8928 (mmm) REVERT: C 263 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8826 (m) REVERT: C 291 TYR cc_start: 0.9026 (m-80) cc_final: 0.8556 (m-80) outliers start: 31 outliers final: 21 residues processed: 150 average time/residue: 0.2549 time to fit residues: 54.5153 Evaluate side-chains 155 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 114 optimal weight: 0.0170 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.191397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.151581 restraints weight = 10854.803| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.27 r_work: 0.3165 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10841 Z= 0.130 Angle : 0.620 9.337 14733 Z= 0.305 Chirality : 0.044 0.170 1683 Planarity : 0.004 0.070 1832 Dihedral : 8.774 122.722 1599 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.96 % Allowed : 14.10 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1299 helix: 0.63 (0.22), residues: 592 sheet: 0.23 (0.37), residues: 176 loop : -1.72 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.002 0.001 HIS A 798 PHE 0.017 0.001 PHE A 935 TYR 0.015 0.001 TYR A1054 ARG 0.003 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 3) link_NAG-ASN : angle 2.58159 ( 9) link_ALPHA1-4 : bond 0.01780 ( 1) link_ALPHA1-4 : angle 4.14414 ( 3) link_BETA1-4 : bond 0.00295 ( 1) link_BETA1-4 : angle 1.19412 ( 3) hydrogen bonds : bond 0.04394 ( 508) hydrogen bonds : angle 4.79773 ( 1461) SS BOND : bond 0.00396 ( 3) SS BOND : angle 1.05958 ( 6) covalent geometry : bond 0.00293 (10833) covalent geometry : angle 0.61374 (14712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6748 (OUTLIER) cc_final: 0.6404 (p) REVERT: A 74 ARG cc_start: 0.7625 (mmp-170) cc_final: 0.6920 (ttp-170) REVERT: A 258 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7972 (mmm-85) REVERT: A 468 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7517 (ttp) REVERT: A 525 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7429 (ttp80) REVERT: A 583 GLN cc_start: 0.6526 (tt0) cc_final: 0.6163 (tp40) REVERT: A 754 LYS cc_start: 0.6160 (mttp) cc_final: 0.4638 (ttpt) REVERT: C 261 MET cc_start: 0.9102 (mmm) cc_final: 0.8890 (mmm) REVERT: C 263 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8827 (m) REVERT: C 291 TYR cc_start: 0.9038 (m-80) cc_final: 0.8571 (m-80) outliers start: 34 outliers final: 21 residues processed: 148 average time/residue: 0.2478 time to fit residues: 52.4629 Evaluate side-chains 151 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 86 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.188513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.150089 restraints weight = 10748.357| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.24 r_work: 0.3187 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10841 Z= 0.122 Angle : 0.600 9.320 14733 Z= 0.295 Chirality : 0.043 0.162 1683 Planarity : 0.004 0.070 1832 Dihedral : 8.296 123.019 1599 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.52 % Allowed : 14.88 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1299 helix: 0.83 (0.22), residues: 591 sheet: 0.33 (0.38), residues: 172 loop : -1.65 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.002 0.001 HIS A 798 PHE 0.017 0.001 PHE A 935 TYR 0.014 0.001 TYR A1054 ARG 0.002 0.000 ARG A 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 3) link_NAG-ASN : angle 2.46131 ( 9) link_ALPHA1-4 : bond 0.02077 ( 1) link_ALPHA1-4 : angle 4.43164 ( 3) link_BETA1-4 : bond 0.00304 ( 1) link_BETA1-4 : angle 1.11521 ( 3) hydrogen bonds : bond 0.04193 ( 508) hydrogen bonds : angle 4.67222 ( 1461) SS BOND : bond 0.00362 ( 3) SS BOND : angle 0.99290 ( 6) covalent geometry : bond 0.00272 (10833) covalent geometry : angle 0.59356 (14712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6795 (OUTLIER) cc_final: 0.6451 (p) REVERT: A 74 ARG cc_start: 0.7610 (mmp-170) cc_final: 0.6912 (ttp-170) REVERT: A 139 ARG cc_start: 0.6068 (ttp-110) cc_final: 0.5645 (ttp80) REVERT: A 258 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.8005 (mmm-85) REVERT: A 275 LYS cc_start: 0.7440 (mttt) cc_final: 0.7129 (mttt) REVERT: A 468 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7483 (ttp) REVERT: A 502 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7784 (tt0) REVERT: A 525 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7428 (ttp80) REVERT: A 527 GLU cc_start: 0.6971 (tp30) cc_final: 0.6732 (tp30) REVERT: A 583 GLN cc_start: 0.6554 (tt0) cc_final: 0.6203 (tp40) REVERT: A 754 LYS cc_start: 0.6186 (mttp) cc_final: 0.4720 (ttpt) REVERT: C 261 MET cc_start: 0.9093 (mmm) cc_final: 0.8883 (mmm) REVERT: C 263 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8819 (m) REVERT: C 291 TYR cc_start: 0.9014 (m-80) cc_final: 0.8553 (m-80) outliers start: 29 outliers final: 19 residues processed: 145 average time/residue: 0.2350 time to fit residues: 48.3150 Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 93 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.189400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.150540 restraints weight = 10879.487| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.29 r_work: 0.3195 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10841 Z= 0.112 Angle : 0.591 9.579 14733 Z= 0.289 Chirality : 0.043 0.163 1683 Planarity : 0.004 0.071 1832 Dihedral : 7.842 123.165 1599 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.26 % Allowed : 15.40 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1299 helix: 0.96 (0.22), residues: 592 sheet: 0.43 (0.38), residues: 174 loop : -1.61 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 264 PHE 0.017 0.001 PHE A 935 TYR 0.014 0.001 TYR A1054 ARG 0.003 0.000 ARG A 590 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 3) link_NAG-ASN : angle 2.40860 ( 9) link_ALPHA1-4 : bond 0.02290 ( 1) link_ALPHA1-4 : angle 5.30871 ( 3) link_BETA1-4 : bond 0.00301 ( 1) link_BETA1-4 : angle 0.93901 ( 3) hydrogen bonds : bond 0.04053 ( 508) hydrogen bonds : angle 4.66923 ( 1461) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.94978 ( 6) covalent geometry : bond 0.00245 (10833) covalent geometry : angle 0.58256 (14712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6783 (OUTLIER) cc_final: 0.6448 (p) REVERT: A 74 ARG cc_start: 0.7624 (mmp-170) cc_final: 0.6933 (ttp-170) REVERT: A 258 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8083 (mmm-85) REVERT: A 275 LYS cc_start: 0.7420 (mttt) cc_final: 0.7107 (mttt) REVERT: A 468 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7470 (ttp) REVERT: A 502 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7755 (tt0) REVERT: A 525 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7391 (ttp80) REVERT: A 583 GLN cc_start: 0.6446 (tt0) cc_final: 0.6084 (tp40) REVERT: A 587 GLU cc_start: 0.7465 (tt0) cc_final: 0.7135 (tp30) REVERT: A 754 LYS cc_start: 0.6225 (mttp) cc_final: 0.4645 (ttpt) REVERT: A 1023 MET cc_start: 0.8650 (mmm) cc_final: 0.8249 (tpt) REVERT: C 261 MET cc_start: 0.9088 (mmm) cc_final: 0.8880 (mmm) REVERT: C 263 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8814 (m) REVERT: C 291 TYR cc_start: 0.9010 (m-80) cc_final: 0.8563 (m-80) outliers start: 26 outliers final: 19 residues processed: 147 average time/residue: 0.2662 time to fit residues: 55.8525 Evaluate side-chains 154 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 917 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.188042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.148419 restraints weight = 10824.316| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.25 r_work: 0.3134 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10841 Z= 0.209 Angle : 0.667 9.600 14733 Z= 0.328 Chirality : 0.047 0.162 1683 Planarity : 0.005 0.073 1832 Dihedral : 8.010 121.624 1599 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.35 % Allowed : 15.49 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1299 helix: 0.74 (0.22), residues: 589 sheet: 0.29 (0.38), residues: 173 loop : -1.64 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.021 0.002 PHE A 968 TYR 0.024 0.002 TYR C 122 ARG 0.004 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 3) link_NAG-ASN : angle 2.51180 ( 9) link_ALPHA1-4 : bond 0.01707 ( 1) link_ALPHA1-4 : angle 5.92028 ( 3) link_BETA1-4 : bond 0.00029 ( 1) link_BETA1-4 : angle 1.51594 ( 3) hydrogen bonds : bond 0.04944 ( 508) hydrogen bonds : angle 4.83247 ( 1461) SS BOND : bond 0.00490 ( 3) SS BOND : angle 1.45062 ( 6) covalent geometry : bond 0.00505 (10833) covalent geometry : angle 0.65827 (14712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6842 (OUTLIER) cc_final: 0.6498 (p) REVERT: A 74 ARG cc_start: 0.7726 (mmp-170) cc_final: 0.6998 (ttp-170) REVERT: A 258 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8098 (mmm-85) REVERT: A 275 LYS cc_start: 0.7446 (mttt) cc_final: 0.7112 (mttt) REVERT: A 468 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7516 (ttp) REVERT: A 502 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7765 (tt0) REVERT: A 583 GLN cc_start: 0.6589 (tt0) cc_final: 0.6213 (tp40) REVERT: A 587 GLU cc_start: 0.7660 (tt0) cc_final: 0.7341 (tp30) REVERT: A 754 LYS cc_start: 0.6184 (mttp) cc_final: 0.4662 (ttpt) REVERT: C 183 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8812 (mt) REVERT: C 263 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8830 (m) REVERT: C 291 TYR cc_start: 0.9050 (m-80) cc_final: 0.8574 (m-80) outliers start: 27 outliers final: 22 residues processed: 154 average time/residue: 0.2628 time to fit residues: 57.0392 Evaluate side-chains 158 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 108 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.188326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.148685 restraints weight = 10790.888| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.30 r_work: 0.3134 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 10841 Z= 0.204 Angle : 0.953 59.192 14733 Z= 0.535 Chirality : 0.046 0.223 1683 Planarity : 0.005 0.072 1832 Dihedral : 8.018 121.764 1599 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.26 % Allowed : 15.84 % Favored : 81.90 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1299 helix: 0.73 (0.22), residues: 589 sheet: 0.28 (0.38), residues: 173 loop : -1.65 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.020 0.002 PHE A 968 TYR 0.022 0.002 TYR C 122 ARG 0.005 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 3) link_NAG-ASN : angle 2.52425 ( 9) link_ALPHA1-4 : bond 0.01752 ( 1) link_ALPHA1-4 : angle 5.96387 ( 3) link_BETA1-4 : bond 0.00475 ( 1) link_BETA1-4 : angle 1.42820 ( 3) hydrogen bonds : bond 0.04850 ( 508) hydrogen bonds : angle 4.83166 ( 1461) SS BOND : bond 0.00464 ( 3) SS BOND : angle 1.39990 ( 6) covalent geometry : bond 0.00456 (10833) covalent geometry : angle 0.94716 (14712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6707.88 seconds wall clock time: 117 minutes 19.35 seconds (7039.35 seconds total)