Starting phenix.real_space_refine on Fri Sep 11 18:51:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k7k_9937/09_2026/6k7k_9937.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7k_9937/09_2026/6k7k_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6k7k_9937/09_2026/6k7k_9937.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k7k_9937/09_2026/6k7k_9937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k7k_9937/09_2026/6k7k_9937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7k_9937/09_2026/6k7k_9937.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7k_9937/09_2026/6k7k_9937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7k_9937/09_2026/6k7k_9937.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 chiralities: 2 Time building chain proxies: 2.36, per 1000 atoms: 0.22 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: 0.82 Conformation dependent library (CDL) restraints added in 454.9 milliseconds 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: 0.34 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: 1.83 Time building geometry restraints manager: 1.11 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: 6024 25.03 - 50.07: 336 50.07 - 75.10: 25 75.10 - 100.14: 7 100.14 - 125.17: 2 Dihedral angle restraints: 6394 sinusoidal: 2574 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 6391 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: 1.240 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 15.047 125.173 3921 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 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: -3.51 (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 ARG 0.009 0.001 ARG A 608 TYR 0.030 0.003 TYR C 122 PHE 0.026 0.004 PHE C 61 TRP 0.019 0.003 TRP C 260 HIS 0.007 0.002 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.01130 / 0.47 (10833) covalent geometry : angle 1.45207 / 0.67 (14712) SS BOND : bond 0.00681 / 0.34 ( 3) SS BOND : angle 2.75132 / 1.25 ( 6) hydrogen bonds : bond 0.12813 / 7.66 ( 508) hydrogen bonds : angle 6.68824 / 4.86 ( 1461) link_ALPHA1-4 : bond 0.01132 / 0.60 ( 1) link_ALPHA1-4 : angle 4.82033 / 2.52 ( 3) link_BETA1-4 : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : angle 2.09819 / 1.11 ( 3) link_NAG-ASN : bond 0.00995 / 0.48 ( 3) link_NAG-ASN : angle 4.76432 / 2.22 ( 9) *********************** 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 : 0.436 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: 0.1212 time to fit residues: 27.4992 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 : 0.374 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.185959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.149377 restraints weight = 10894.132| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.29 r_work: 0.3162 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10841 Z= 0.157 Angle : 0.703 12.880 14733 Z= 0.352 Chirality : 0.048 0.529 1683 Planarity : 0.006 0.073 1832 Dihedral : 8.138 117.552 1441 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.39 % Allowed : 9.83 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.08 % 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 (0.21), residues: 1299 helix: -0.75 (0.20), residues: 576 sheet: -0.77 (0.36), residues: 168 loop : -2.13 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 67 TYR 0.016 0.002 TYR C 122 PHE 0.020 0.002 PHE A 968 TRP 0.018 0.002 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10833) covalent geometry : angle 0.69513 / 0.35 (14712) SS BOND : bond 0.00554 / 0.28 ( 3) SS BOND : angle 1.26216 / 0.60 ( 6) hydrogen bonds : bond 0.05155 / 3.33 ( 508) hydrogen bonds : angle 5.42130 / 3.88 ( 1461) link_ALPHA1-4 : bond 0.01286 / 0.68 ( 1) link_ALPHA1-4 : angle 2.63344 / 1.37 ( 3) link_BETA1-4 : bond 0.00141 / 0.07 ( 1) link_BETA1-4 : angle 1.40693 / 0.76 ( 3) link_NAG-ASN : bond 0.00793 / 0.40 ( 3) link_NAG-ASN : angle 3.87039 / 1.80 ( 9) *********************** 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 157 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7621 (mmp-170) cc_final: 0.6835 (ttp-110) REVERT: A 139 ARG cc_start: 0.6328 (ttp-110) cc_final: 0.5747 (ttp80) REVERT: A 275 LYS cc_start: 0.6897 (mptt) cc_final: 0.6657 (mttt) REVERT: A 383 GLU cc_start: 0.6476 (mm-30) cc_final: 0.6259 (mm-30) REVERT: A 420 GLN cc_start: 0.7471 (pt0) cc_final: 0.7060 (mm-40) REVERT: A 525 ARG cc_start: 0.7610 (ttt-90) cc_final: 0.7247 (ttp80) REVERT: A 675 GLU cc_start: 0.6770 (pm20) cc_final: 0.5962 (mm-30) REVERT: A 754 LYS cc_start: 0.6494 (mttp) cc_final: 0.4762 (ttpt) REVERT: A 775 LYS cc_start: 0.8295 (tttt) cc_final: 0.8082 (tttp) REVERT: C 200 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8108 (ttpp) REVERT: C 291 TYR cc_start: 0.9074 (m-80) cc_final: 0.8520 (m-80) outliers start: 16 outliers final: 10 residues processed: 150 average time/residue: 0.1135 time to fit residues: 23.4079 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 : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 290 ARG 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 54 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 117 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 193 ASN A 331 ASN A 352 ASN A 353 ASN C 283 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.184743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.145757 restraints weight = 10955.252| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.31 r_work: 0.3126 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10841 Z= 0.176 Angle : 0.686 9.873 14733 Z= 0.342 Chirality : 0.048 0.497 1683 Planarity : 0.005 0.071 1832 Dihedral : 7.843 124.678 1438 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.26 % Allowed : 11.14 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.38 (0.22), residues: 1299 helix: -0.15 (0.21), residues: 589 sheet: -0.34 (0.36), residues: 179 loop : -1.95 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 67 TYR 0.019 0.002 TYR C 122 PHE 0.021 0.002 PHE A 968 TRP 0.015 0.002 TRP A 927 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (10833) covalent geometry : angle 0.67732 / 0.34 (14712) SS BOND : bond 0.00408 / 0.21 ( 3) SS BOND : angle 1.18154 / 0.56 ( 6) hydrogen bonds : bond 0.05056 / 3.26 ( 508) hydrogen bonds : angle 5.16367 / 3.68 ( 1461) link_ALPHA1-4 : bond 0.00932 / 0.49 ( 1) link_ALPHA1-4 : angle 2.74004 / 1.42 ( 3) link_BETA1-4 : bond 0.00138 / 0.07 ( 1) link_BETA1-4 : angle 1.51185 / 0.83 ( 3) link_NAG-ASN : bond 0.00867 / 0.43 ( 3) link_NAG-ASN : angle 3.98655 / 1.83 ( 9) *********************** 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 163 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6544 (p) REVERT: A 74 ARG cc_start: 0.7576 (mmp-170) cc_final: 0.6864 (ttp-170) REVERT: A 275 LYS cc_start: 0.6945 (mptt) cc_final: 0.6734 (mttt) REVERT: A 383 GLU cc_start: 0.6558 (mm-30) cc_final: 0.6343 (mm-30) REVERT: A 420 GLN cc_start: 0.7427 (pt0) cc_final: 0.7098 (mm-40) REVERT: A 583 GLN cc_start: 0.6549 (tt0) cc_final: 0.6163 (tp-100) REVERT: A 754 LYS cc_start: 0.6480 (mttp) cc_final: 0.4783 (ttpt) REVERT: A 775 LYS cc_start: 0.8265 (tttt) cc_final: 0.8042 (tttp) REVERT: C 200 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8288 (tttm) REVERT: C 263 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8844 (m) REVERT: C 291 TYR cc_start: 0.9080 (m-80) cc_final: 0.8509 (m-80) outliers start: 26 outliers final: 13 residues processed: 153 average time/residue: 0.0985 time to fit residues: 21.7198 Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 542 SER 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 341 VAL Chi-restraints excluded: chain C residue 342 VAL 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 78 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3989 r_free = 0.3989 target = 0.186593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148576 restraints weight = 10926.287| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.34 r_work: 0.3151 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10841 Z= 0.133 Angle : 0.633 9.589 14733 Z= 0.315 Chirality : 0.046 0.495 1683 Planarity : 0.005 0.069 1832 Dihedral : 7.555 122.113 1438 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.26 % Allowed : 12.01 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.96 (0.23), residues: 1299 helix: 0.29 (0.22), residues: 587 sheet: -0.15 (0.37), residues: 179 loop : -1.86 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.016 0.001 TYR A1054 PHE 0.018 0.001 PHE A 935 TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10833) covalent geometry : angle 0.62457 / 0.31 (14712) SS BOND : bond 0.00428 / 0.22 ( 3) SS BOND : angle 1.08100 / 0.51 ( 6) hydrogen bonds : bond 0.04500 / 2.93 ( 508) hydrogen bonds : angle 4.94323 / 3.52 ( 1461) link_ALPHA1-4 : bond 0.00807 / 0.42 ( 1) link_ALPHA1-4 : angle 2.28184 / 1.18 ( 3) link_BETA1-4 : bond 0.00271 / 0.14 ( 1) link_BETA1-4 : angle 1.24289 / 0.68 ( 3) link_NAG-ASN : bond 0.00810 / 0.41 ( 3) link_NAG-ASN : angle 3.87451 / 1.77 ( 9) *********************** 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 163 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6738 (OUTLIER) cc_final: 0.6432 (p) REVERT: A 74 ARG cc_start: 0.7528 (mmp-170) cc_final: 0.6808 (ttp-170) REVERT: A 258 ARG cc_start: 0.8264 (mmm-85) cc_final: 0.7974 (mmm-85) REVERT: A 383 GLU cc_start: 0.6463 (mm-30) cc_final: 0.6241 (mm-30) REVERT: A 420 GLN cc_start: 0.7255 (pt0) cc_final: 0.7036 (mm-40) REVERT: A 583 GLN cc_start: 0.6531 (tt0) cc_final: 0.6143 (tp-100) REVERT: A 754 LYS cc_start: 0.6389 (mttp) cc_final: 0.4776 (ttpt) REVERT: C 200 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8281 (tttm) REVERT: C 263 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8822 (m) REVERT: C 291 TYR cc_start: 0.9049 (m-80) cc_final: 0.8531 (m-80) outliers start: 26 outliers final: 17 residues processed: 151 average time/residue: 0.1013 time to fit residues: 22.0358 Evaluate side-chains 149 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 263 THR 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 100 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.0060 chunk 59 optimal weight: 4.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4006 r_free = 0.4006 target = 0.187945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.151215 restraints weight = 10896.856| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.27 r_work: 0.3178 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10841 Z= 0.139 Angle : 0.629 9.754 14733 Z= 0.312 Chirality : 0.046 0.491 1683 Planarity : 0.004 0.069 1832 Dihedral : 7.474 122.484 1438 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.35 % Allowed : 12.88 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.75 (0.23), residues: 1299 helix: 0.45 (0.22), residues: 590 sheet: 0.05 (0.37), residues: 176 loop : -1.76 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 67 TYR 0.016 0.001 TYR C 122 PHE 0.017 0.001 PHE A 968 TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10833) covalent geometry : angle 0.62076 / 0.31 (14712) SS BOND : bond 0.00432 / 0.22 ( 3) SS BOND : angle 1.12482 / 0.53 ( 6) hydrogen bonds : bond 0.04503 / 2.94 ( 508) hydrogen bonds : angle 4.88953 / 3.49 ( 1461) link_ALPHA1-4 : bond 0.00658 / 0.35 ( 1) link_ALPHA1-4 : angle 2.34439 / 1.22 ( 3) link_BETA1-4 : bond 0.00081 / 0.04 ( 1) link_BETA1-4 : angle 1.28308 / 0.70 ( 3) link_NAG-ASN : bond 0.00828 / 0.41 ( 3) link_NAG-ASN : angle 3.90618 / 1.79 ( 9) *********************** 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 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6868 (OUTLIER) cc_final: 0.6539 (p) REVERT: A 74 ARG cc_start: 0.7563 (mmp-170) cc_final: 0.6897 (ttp-170) REVERT: A 139 ARG cc_start: 0.6080 (ttp-110) cc_final: 0.5709 (ttp80) REVERT: A 258 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.8103 (mmm-85) REVERT: A 468 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7482 (ttp) REVERT: A 583 GLN cc_start: 0.6600 (tt0) cc_final: 0.6231 (tp-100) REVERT: A 754 LYS cc_start: 0.6368 (mttp) cc_final: 0.4772 (ttpt) REVERT: C 200 LYS cc_start: 0.8518 (ttpt) cc_final: 0.8312 (tttm) REVERT: C 263 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8814 (m) REVERT: C 291 TYR cc_start: 0.9034 (m-80) cc_final: 0.8552 (m-80) outliers start: 27 outliers final: 18 residues processed: 147 average time/residue: 0.1076 time to fit residues: 22.2685 Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.188680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.150687 restraints weight = 10910.025| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.24 r_work: 0.3186 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2161 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= 0.121 Angle : 0.615 9.629 14733 Z= 0.304 Chirality : 0.045 0.488 1683 Planarity : 0.004 0.070 1832 Dihedral : 7.374 122.918 1438 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.44 % Allowed : 13.93 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.56 (0.23), residues: 1299 helix: 0.63 (0.22), residues: 589 sheet: 0.17 (0.37), residues: 176 loop : -1.70 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 525 TYR 0.014 0.001 TYR A1054 PHE 0.017 0.001 PHE A 935 TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10833) covalent geometry : angle 0.60693 / 0.30 (14712) SS BOND : bond 0.00395 / 0.20 ( 3) SS BOND : angle 1.01623 / 0.48 ( 6) hydrogen bonds : bond 0.04296 / 2.81 ( 508) hydrogen bonds : angle 4.79300 / 3.41 ( 1461) link_ALPHA1-4 : bond 0.00738 / 0.39 ( 1) link_ALPHA1-4 : angle 2.16671 / 1.12 ( 3) link_BETA1-4 : bond 0.00208 / 0.11 ( 1) link_BETA1-4 : angle 1.15587 / 0.63 ( 3) link_NAG-ASN : bond 0.00821 / 0.41 ( 3) link_NAG-ASN : angle 3.84529 / 1.76 ( 9) *********************** 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 158 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6457 (p) REVERT: A 74 ARG cc_start: 0.7606 (mmp-170) cc_final: 0.6923 (ttp-170) REVERT: A 139 ARG cc_start: 0.6071 (ttp-110) cc_final: 0.5605 (ttp80) REVERT: A 258 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.7948 (mmm-85) REVERT: A 468 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7468 (ttp) REVERT: A 583 GLN cc_start: 0.6544 (tt0) cc_final: 0.6165 (tp-100) REVERT: A 754 LYS cc_start: 0.6201 (mttp) cc_final: 0.4691 (ttpt) REVERT: A 758 CYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7075 (m) REVERT: C 263 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8809 (m) REVERT: C 291 TYR cc_start: 0.9021 (m-80) cc_final: 0.8534 (m-80) outliers start: 28 outliers final: 19 residues processed: 144 average time/residue: 0.1076 time to fit residues: 21.6813 Evaluate side-chains 153 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU 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 660 MET Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 758 CYS 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 5 optimal weight: 0.0870 chunk 123 optimal weight: 0.0570 chunk 49 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 331 ASN A 917 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.191793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.155936 restraints weight = 10767.221| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.24 r_work: 0.3228 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2365 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= 0.109 Angle : 0.593 9.446 14733 Z= 0.292 Chirality : 0.045 0.486 1683 Planarity : 0.004 0.071 1832 Dihedral : 7.254 123.253 1438 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.52 % Allowed : 13.32 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 1299 helix: 0.86 (0.22), residues: 592 sheet: 0.41 (0.37), residues: 174 loop : -1.66 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.014 0.001 TYR A1054 PHE 0.016 0.001 PHE A 935 TRP 0.012 0.001 TRP A 927 HIS 0.003 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (10833) covalent geometry : angle 0.58542 / 0.29 (14712) SS BOND : bond 0.00364 / 0.19 ( 3) SS BOND : angle 0.91266 / 0.43 ( 6) hydrogen bonds : bond 0.04056 / 2.66 ( 508) hydrogen bonds : angle 4.69592 / 3.34 ( 1461) link_ALPHA1-4 : bond 0.00791 / 0.42 ( 1) link_ALPHA1-4 : angle 1.98575 / 1.03 ( 3) link_BETA1-4 : bond 0.00318 / 0.17 ( 1) link_BETA1-4 : angle 1.07321 / 0.58 ( 3) link_NAG-ASN : bond 0.00817 / 0.41 ( 3) link_NAG-ASN : angle 3.75917 / 1.71 ( 9) *********************** 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 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6823 (OUTLIER) cc_final: 0.6492 (p) REVERT: A 74 ARG cc_start: 0.7625 (mmp-170) cc_final: 0.6944 (ttp-170) REVERT: A 136 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7723 (mp10) REVERT: A 258 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.8049 (mmm-85) REVERT: A 468 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7428 (ttp) REVERT: A 502 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7811 (tt0) REVERT: A 527 GLU cc_start: 0.6942 (tp30) cc_final: 0.6705 (tp30) REVERT: A 583 GLN cc_start: 0.6549 (tt0) cc_final: 0.6182 (tp40) REVERT: C 78 ILE cc_start: 0.9169 (tp) cc_final: 0.8938 (tp) REVERT: C 183 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8805 (mt) REVERT: C 263 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8817 (m) REVERT: C 291 TYR cc_start: 0.9005 (m-80) cc_final: 0.8576 (m-80) outliers start: 29 outliers final: 17 residues processed: 147 average time/residue: 0.0977 time to fit residues: 20.8745 Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3996 r_free = 0.3996 target = 0.186802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.145859 restraints weight = 10880.472| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.34 r_work: 0.3129 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10841 Z= 0.185 Angle : 0.656 10.328 14733 Z= 0.324 Chirality : 0.048 0.495 1683 Planarity : 0.005 0.072 1832 Dihedral : 7.426 121.340 1438 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.18 % Allowed : 14.27 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.48 (0.23), residues: 1299 helix: 0.69 (0.22), residues: 592 sheet: 0.21 (0.38), residues: 173 loop : -1.65 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 525 TYR 0.022 0.002 TYR C 122 PHE 0.020 0.002 PHE A 968 TRP 0.012 0.002 TRP C 260 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10833) covalent geometry : angle 0.64674 / 0.32 (14712) SS BOND : bond 0.00455 / 0.23 ( 3) SS BOND : angle 1.39577 / 0.65 ( 6) hydrogen bonds : bond 0.04853 / 3.12 ( 508) hydrogen bonds : angle 4.86268 / 3.48 ( 1461) link_ALPHA1-4 : bond 0.00837 / 0.44 ( 1) link_ALPHA1-4 : angle 2.79485 / 1.45 ( 3) link_BETA1-4 : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : angle 1.44241 / 0.79 ( 3) link_NAG-ASN : bond 0.00888 / 0.44 ( 3) link_NAG-ASN : angle 4.10066 / 1.88 ( 9) *********************** 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 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6498 (p) REVERT: A 74 ARG cc_start: 0.7661 (mmp-170) cc_final: 0.6956 (ttp-170) REVERT: A 258 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.7915 (mmm-85) REVERT: A 468 MET cc_start: 0.7736 (ttp) cc_final: 0.7407 (ttp) REVERT: A 502 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7739 (tt0) REVERT: A 525 ARG cc_start: 0.7442 (ttp80) cc_final: 0.6954 (tmm160) REVERT: A 583 GLN cc_start: 0.6555 (tt0) cc_final: 0.6168 (tp40) REVERT: C 183 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8822 (mt) REVERT: C 263 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8841 (m) REVERT: C 291 TYR cc_start: 0.9030 (m-80) cc_final: 0.8568 (m-80) outliers start: 25 outliers final: 19 residues processed: 145 average time/residue: 0.0971 time to fit residues: 20.1869 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 : 0.251 ------------------------------------------------------------------------------- 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 219 ILE 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 A residue 913 LYS 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 341 VAL 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 123 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.189038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147979 restraints weight = 10760.575| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.29 r_work: 0.3162 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2338 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= 0.127 Angle : 0.605 9.786 14733 Z= 0.299 Chirality : 0.046 0.485 1683 Planarity : 0.004 0.072 1832 Dihedral : 7.345 123.197 1438 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.35 % Allowed : 14.01 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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 (0.24), residues: 1299 helix: 0.85 (0.22), residues: 592 sheet: 0.27 (0.38), residues: 173 loop : -1.59 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 525 TYR 0.015 0.001 TYR A1054 PHE 0.016 0.001 PHE A 968 TRP 0.013 0.001 TRP A 927 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10833) covalent geometry : angle 0.59630 / 0.30 (14712) SS BOND : bond 0.00403 / 0.21 ( 3) SS BOND : angle 1.06785 / 0.50 ( 6) hydrogen bonds : bond 0.04332 / 2.83 ( 508) hydrogen bonds : angle 4.75858 / 3.40 ( 1461) link_ALPHA1-4 : bond 0.00815 / 0.43 ( 1) link_ALPHA1-4 : angle 2.24023 / 1.16 ( 3) link_BETA1-4 : bond 0.00252 / 0.13 ( 1) link_BETA1-4 : angle 1.15053 / 0.63 ( 3) link_NAG-ASN : bond 0.00852 / 0.43 ( 3) link_NAG-ASN : angle 3.89572 / 1.79 ( 9) *********************** 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 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6793 (OUTLIER) cc_final: 0.6456 (p) REVERT: A 74 ARG cc_start: 0.7623 (mmp-170) cc_final: 0.6924 (ttp-170) REVERT: A 258 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: A 468 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7412 (ttp) REVERT: A 502 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7727 (tt0) REVERT: A 525 ARG cc_start: 0.7392 (ttp80) cc_final: 0.6962 (tmm160) REVERT: A 583 GLN cc_start: 0.6513 (tt0) cc_final: 0.6138 (tp40) REVERT: A 587 GLU cc_start: 0.7584 (tt0) cc_final: 0.7246 (tp30) REVERT: A 743 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.5798 (ttt180) REVERT: C 80 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8753 (mp) REVERT: C 183 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8813 (mt) REVERT: C 263 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8823 (m) REVERT: C 291 TYR cc_start: 0.9021 (m-80) cc_final: 0.8532 (m-80) outliers start: 27 outliers final: 17 residues processed: 144 average time/residue: 0.0963 time to fit residues: 19.9760 Evaluate side-chains 150 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 660 MET Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 80 ILE 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 81 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.188157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146515 restraints weight = 10746.005| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.31 r_work: 0.3152 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2434 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= 0.126 Angle : 0.603 9.808 14733 Z= 0.296 Chirality : 0.046 0.487 1683 Planarity : 0.004 0.072 1832 Dihedral : 7.270 122.869 1438 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.26 % Allowed : 14.27 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.22 (0.24), residues: 1299 helix: 0.92 (0.22), residues: 592 sheet: 0.34 (0.38), residues: 173 loop : -1.55 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 525 TYR 0.015 0.001 TYR C 122 PHE 0.016 0.001 PHE A 968 TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10833) covalent geometry : angle 0.59456 / 0.29 (14712) SS BOND : bond 0.00377 / 0.19 ( 3) SS BOND : angle 1.07260 / 0.50 ( 6) hydrogen bonds : bond 0.04253 / 2.79 ( 508) hydrogen bonds : angle 4.69193 / 3.35 ( 1461) link_ALPHA1-4 : bond 0.00801 / 0.42 ( 1) link_ALPHA1-4 : angle 2.22971 / 1.16 ( 3) link_BETA1-4 : bond 0.00271 / 0.14 ( 1) link_BETA1-4 : angle 1.22224 / 0.67 ( 3) link_NAG-ASN : bond 0.00854 / 0.43 ( 3) link_NAG-ASN : angle 3.88225 / 1.78 ( 9) ********************** 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 157 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6485 (p) REVERT: A 74 ARG cc_start: 0.7596 (mmp-170) cc_final: 0.6915 (ttp-170) REVERT: A 258 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.8142 (mmm-85) REVERT: A 468 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7430 (ttp) REVERT: A 502 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7696 (tt0) REVERT: A 525 ARG cc_start: 0.7422 (ttp80) cc_final: 0.6970 (tmm160) REVERT: A 583 GLN cc_start: 0.6441 (tt0) cc_final: 0.6060 (tp40) REVERT: A 587 GLU cc_start: 0.7550 (tt0) cc_final: 0.7227 (tp30) REVERT: A 691 MET cc_start: 0.1387 (tpp) cc_final: -0.0030 (pmm) REVERT: A 743 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.5815 (ttt180) REVERT: A 1023 MET cc_start: 0.8691 (mmm) cc_final: 0.8428 (tpt) REVERT: C 80 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8741 (mp) REVERT: C 183 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8791 (mt) REVERT: C 263 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8827 (m) REVERT: C 291 TYR cc_start: 0.9015 (m-80) cc_final: 0.8544 (m-80) outliers start: 26 outliers final: 20 residues processed: 145 average time/residue: 0.0975 time to fit residues: 20.5031 Evaluate side-chains 154 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 136 GLN 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 660 MET Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 80 ILE 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 48 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.186239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.143977 restraints weight = 10803.679| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.30 r_work: 0.3121 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10841 Z= 0.166 Angle : 0.631 10.190 14733 Z= 0.311 Chirality : 0.047 0.489 1683 Planarity : 0.005 0.073 1832 Dihedral : 7.358 122.338 1438 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.44 % Allowed : 14.45 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.32 (0.23), residues: 1299 helix: 0.82 (0.22), residues: 593 sheet: 0.31 (0.38), residues: 173 loop : -1.59 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 525 TYR 0.019 0.001 TYR C 122 PHE 0.018 0.001 PHE A 968 TRP 0.011 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (10833) covalent geometry : angle 0.62185 / 0.31 (14712) SS BOND : bond 0.00434 / 0.22 ( 3) SS BOND : angle 1.27468 / 0.59 ( 6) hydrogen bonds : bond 0.04618 / 2.99 ( 508) hydrogen bonds : angle 4.77115 / 3.41 ( 1461) link_ALPHA1-4 : bond 0.00792 / 0.42 ( 1) link_ALPHA1-4 : angle 2.59478 / 1.34 ( 3) link_BETA1-4 : bond 0.00038 / 0.02 ( 1) link_BETA1-4 : angle 1.32920 / 0.73 ( 3) link_NAG-ASN : bond 0.00892 / 0.45 ( 3) link_NAG-ASN : angle 4.03488 / 1.86 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.78 seconds wall clock time: 52 minutes 5.17 seconds (3125.17 seconds total)