Starting phenix.real_space_refine on Wed Feb 4 08:33:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsl_65302/02_2026/9vsl_65302_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsl_65302/02_2026/9vsl_65302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vsl_65302/02_2026/9vsl_65302_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsl_65302/02_2026/9vsl_65302_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vsl_65302/02_2026/9vsl_65302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsl_65302/02_2026/9vsl_65302.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 45 5.16 5 Be 1 3.05 5 C 6072 2.51 5 N 1502 2.21 5 O 1689 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9314 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6591 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 791} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {' MG': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.39, per 1000 atoms: 0.26 Number of scatterers: 9314 At special positions: 0 Unit cell: (92.496, 78.96, 159.424, 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 45 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 1689 8.00 N 1502 7.00 C 6072 6.00 Be 1 4.00 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=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 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 NAG-ASN " NAG C 403 " - " ASN C 294 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 560.7 milliseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 47.7% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.559A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.510A pdb=" N VAL A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.546A pdb=" N THR A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 122 removed outlier: 3.718A pdb=" N LYS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 190 through 194 removed outlier: 4.031A pdb=" N ILE A 194 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.570A pdb=" N ASN A 273 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 282 through 314 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.503A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.924A pdb=" N VAL A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.772A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.610A pdb=" N GLY A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 677 through 688 Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'A' and resid 716 through 721 removed outlier: 3.552A pdb=" N GLU A 721 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 770 through 780 Processing helix chain 'A' and resid 793 through 805 removed outlier: 3.531A pdb=" N GLN A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 805 " --> pdb=" O MET A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 853 through 861 removed outlier: 4.401A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 891 removed outlier: 3.659A pdb=" N LEU A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Proline residue: A 887 - end of helix Processing helix chain 'A' and resid 904 through 914 removed outlier: 3.595A pdb=" N THR A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET A 910 " --> pdb=" O ALA A 906 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 927 removed outlier: 3.521A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 945 removed outlier: 4.001A pdb=" N LEU A 941 " --> pdb=" O ASP A 938 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET A 943 " --> pdb=" O ARG A 940 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 945 " --> pdb=" O TYR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 978 removed outlier: 3.792A pdb=" N PHE A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1014 removed outlier: 3.536A pdb=" N VAL A 999 " --> pdb=" O PHE A 995 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.656A pdb=" N TRP A1027 " --> pdb=" O HIS A1023 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 3.756A pdb=" N TRP A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1089 removed outlier: 3.505A pdb=" N ASN A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 49 Processing helix chain 'C' and resid 50 through 75 removed outlier: 3.671A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix removed outlier: 3.522A pdb=" N ILE C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.739A pdb=" N CYS C 94 " --> pdb=" O CYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.604A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.940A 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: 3.581A pdb=" N ARG C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.700A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.944A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 322 through 347 removed outlier: 4.614A pdb=" N GLY C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 removed outlier: 4.548A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR A 258 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP A 158 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.766A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.593A pdb=" N TYR A 847 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 670 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N CYS A 787 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 672 " --> pdb=" O CYS A 787 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 784 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP A 752 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.088A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 104 through 110 removed outlier: 5.033A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 162 through 163 391 hydrogen bonds defined for protein. 1101 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: 1.70 Time building geometry restraints manager: 1.03 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: 1537 1.32 - 1.45: 2626 1.45 - 1.57: 5311 1.57 - 1.70: 3 1.70 - 1.82: 67 Bond restraints: 9544 Sorted by residual: bond pdb=" OD1 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.737 1.595 0.142 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C BFD A 409 " pdb=" N LYS A 410 " ideal model delta sigma weight residual 1.329 1.267 0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CA THR A 408 " pdb=" C THR A 408 " ideal model delta sigma weight residual 1.525 1.472 0.053 2.10e-02 2.27e+03 6.42e+00 bond pdb=" N SER A 91 " pdb=" CA SER A 91 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.14e-02 7.69e+03 6.36e+00 bond pdb=" N PRO A 85 " pdb=" CD PRO A 85 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.81e+00 ... (remaining 9539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 12898 4.32 - 8.65: 42 8.65 - 12.97: 1 12.97 - 17.30: 0 17.30 - 21.62: 2 Bond angle restraints: 12943 Sorted by residual: angle pdb=" F2 BFD A 409 " pdb="BE BFD A 409 " pdb=" F3 BFD A 409 " ideal model delta sigma weight residual 112.60 90.98 21.62 3.00e+00 1.11e-01 5.20e+01 angle pdb=" CG BFD A 409 " pdb=" OD1 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 124.84 104.01 20.83 3.00e+00 1.11e-01 4.82e+01 angle pdb=" N VAL C 50 " pdb=" CA VAL C 50 " pdb=" C VAL C 50 " ideal model delta sigma weight residual 113.53 107.89 5.64 9.80e-01 1.04e+00 3.32e+01 angle pdb=" N PRO A 85 " pdb=" CA PRO A 85 " pdb=" C PRO A 85 " ideal model delta sigma weight residual 114.68 108.88 5.80 1.04e+00 9.25e-01 3.11e+01 angle pdb=" F1 BFD A 409 " pdb="BE BFD A 409 " pdb=" F3 BFD A 409 " ideal model delta sigma weight residual 111.29 123.78 -12.49 3.00e+00 1.11e-01 1.73e+01 ... (remaining 12938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 5004 21.52 - 43.04: 567 43.04 - 64.57: 101 64.57 - 86.09: 20 86.09 - 107.61: 10 Dihedral angle restraints: 5702 sinusoidal: 2362 harmonic: 3340 Sorted by residual: dihedral pdb=" CA THR C 263 " pdb=" C THR C 263 " pdb=" N ALA C 264 " pdb=" CA ALA C 264 " ideal model delta harmonic sigma weight residual 180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" C1 NAG C 403 " pdb=" C2 NAG C 403 " pdb=" C3 NAG C 403 " pdb=" O3 NAG C 403 " ideal model delta sinusoidal sigma weight residual -175.09 -67.48 -107.61 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C1 NAG C 403 " pdb=" C2 NAG C 403 " pdb=" C3 NAG C 403 " pdb=" C4 NAG C 403 " ideal model delta sinusoidal sigma weight residual -52.39 54.55 -106.94 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1210 0.057 - 0.113: 230 0.113 - 0.170: 13 0.170 - 0.226: 2 0.226 - 0.283: 1 Chirality restraints: 1456 Sorted by residual: chirality pdb=" C1 NAG C 403 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 403 " pdb=" O5 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA BFD A 409 " pdb=" N BFD A 409 " pdb=" C BFD A 409 " pdb=" CB BFD A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE A 705 " pdb=" CA ILE A 705 " pdb=" CG1 ILE A 705 " pdb=" CG2 ILE A 705 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 1453 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 PCW A1101 " -0.073 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C39 PCW A1101 " 0.190 2.00e-02 2.50e+03 pdb=" C40 PCW A1101 " -0.190 2.00e-02 2.50e+03 pdb=" C41 PCW A1101 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A1101 " 0.090 2.00e-02 2.50e+03 8.95e-02 8.01e+01 pdb=" C19 PCW A1101 " -0.091 2.00e-02 2.50e+03 pdb=" C20 PCW A1101 " -0.087 2.00e-02 2.50e+03 pdb=" C21 PCW A1101 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 89 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C VAL A 89 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 89 " -0.018 2.00e-02 2.50e+03 pdb=" N THR A 90 " -0.016 2.00e-02 2.50e+03 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 21 2.34 - 2.98: 4563 2.98 - 3.62: 13365 3.62 - 4.26: 22054 4.26 - 4.90: 37872 Nonbonded interactions: 77875 Sorted by model distance: nonbonded pdb=" OD2 BFD A 409 " pdb=" F1 BFD A 409 " model vdw 1.698 2.990 nonbonded pdb=" F1 BFD A 409 " pdb="MG MG A1100 " model vdw 2.115 2.120 nonbonded pdb=" OE2 GLU A 109 " pdb=" OG SER A 394 " model vdw 2.219 3.040 nonbonded pdb=" OG SER A 282 " pdb=" OE2 GLU A 398 " model vdw 2.220 3.040 nonbonded pdb=" O GLY A 370 " pdb=" OH TYR A 866 " model vdw 2.223 3.040 ... (remaining 77870 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: 9.450 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.004 0.142 9548 Z= 0.229 Angle : 0.809 21.625 12952 Z= 0.467 Chirality : 0.044 0.283 1456 Planarity : 0.006 0.144 1610 Dihedral : 18.388 107.608 3539 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.27 % Allowed : 29.26 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.24), residues: 1125 helix: -0.53 (0.24), residues: 481 sheet: -0.51 (0.43), residues: 156 loop : -1.54 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 714 TYR 0.012 0.001 TYR A1054 PHE 0.015 0.001 PHE A 72 TRP 0.016 0.001 TRP A1040 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9544) covalent geometry : angle 0.80719 (12943) SS BOND : bond 0.00521 ( 3) SS BOND : angle 1.12534 ( 6) hydrogen bonds : bond 0.23482 ( 391) hydrogen bonds : angle 7.97217 ( 1101) link_NAG-ASN : bond 0.01029 ( 1) link_NAG-ASN : angle 3.92484 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: C 215 ARG cc_start: 0.7513 (mmp-170) cc_final: 0.7303 (mtm110) outliers start: 23 outliers final: 19 residues processed: 109 average time/residue: 0.3985 time to fit residues: 47.6051 Evaluate side-chains 102 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 329 GLN A 761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102408 restraints weight = 13581.938| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.13 r_work: 0.3141 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9548 Z= 0.154 Angle : 0.604 7.859 12952 Z= 0.311 Chirality : 0.044 0.222 1456 Planarity : 0.004 0.041 1610 Dihedral : 10.525 92.021 1387 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.93 % Allowed : 24.33 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.86 (0.25), residues: 1125 helix: 0.12 (0.23), residues: 494 sheet: -0.37 (0.42), residues: 163 loop : -1.32 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 714 TYR 0.010 0.001 TYR A 324 PHE 0.013 0.001 PHE A 971 TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9544) covalent geometry : angle 0.60106 (12943) SS BOND : bond 0.00635 ( 3) SS BOND : angle 1.16341 ( 6) hydrogen bonds : bond 0.04700 ( 391) hydrogen bonds : angle 4.93560 ( 1101) link_NAG-ASN : bond 0.01296 ( 1) link_NAG-ASN : angle 3.69258 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 339 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6912 (mmtt) REVERT: C 53 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7142 (mm) REVERT: C 146 ASP cc_start: 0.7977 (t0) cc_final: 0.7748 (t70) REVERT: C 154 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8449 (p) REVERT: C 215 ARG cc_start: 0.7898 (mmp-170) cc_final: 0.7317 (mtm110) outliers start: 50 outliers final: 24 residues processed: 136 average time/residue: 0.4151 time to fit residues: 61.5309 Evaluate side-chains 117 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 100 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 329 GLN A 761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104538 restraints weight = 13328.574| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.14 r_work: 0.3192 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9548 Z= 0.120 Angle : 0.557 7.764 12952 Z= 0.284 Chirality : 0.043 0.307 1456 Planarity : 0.004 0.037 1610 Dihedral : 9.210 89.975 1367 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.63 % Allowed : 24.63 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1125 helix: 0.57 (0.24), residues: 494 sheet: -0.23 (0.42), residues: 162 loop : -1.23 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 714 TYR 0.011 0.001 TYR A 324 PHE 0.012 0.001 PHE A 72 TRP 0.017 0.001 TRP A 323 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9544) covalent geometry : angle 0.55454 (12943) SS BOND : bond 0.00523 ( 3) SS BOND : angle 0.95119 ( 6) hydrogen bonds : bond 0.04080 ( 391) hydrogen bonds : angle 4.61140 ( 1101) link_NAG-ASN : bond 0.01428 ( 1) link_NAG-ASN : angle 3.38130 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.8273 (tp) cc_final: 0.8073 (mp) REVERT: A 399 GLU cc_start: 0.7703 (pt0) cc_final: 0.7405 (tt0) REVERT: A 709 GLU cc_start: 0.5698 (pm20) cc_final: 0.4790 (mp0) REVERT: A 1067 TRP cc_start: 0.6570 (m-10) cc_final: 0.5325 (m100) REVERT: A 1085 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7986 (mp) REVERT: C 154 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8366 (p) outliers start: 47 outliers final: 27 residues processed: 128 average time/residue: 0.3607 time to fit residues: 50.8454 Evaluate side-chains 119 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 130 ASN A 329 GLN A 761 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104150 restraints weight = 13507.178| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.16 r_work: 0.3166 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9548 Z= 0.117 Angle : 0.544 6.807 12952 Z= 0.276 Chirality : 0.043 0.362 1456 Planarity : 0.004 0.038 1610 Dihedral : 8.511 88.147 1366 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.42 % Allowed : 23.74 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.26), residues: 1125 helix: 0.80 (0.24), residues: 494 sheet: -0.16 (0.42), residues: 162 loop : -1.14 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 224 TYR 0.011 0.001 TYR A 324 PHE 0.012 0.001 PHE A 72 TRP 0.016 0.001 TRP A 323 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9544) covalent geometry : angle 0.54018 (12943) SS BOND : bond 0.00649 ( 3) SS BOND : angle 1.31577 ( 6) hydrogen bonds : bond 0.03858 ( 391) hydrogen bonds : angle 4.37915 ( 1101) link_NAG-ASN : bond 0.01284 ( 1) link_NAG-ASN : angle 3.77956 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 98 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 225 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7685 (tp) REVERT: A 399 GLU cc_start: 0.7696 (pt0) cc_final: 0.7439 (tt0) REVERT: A 709 GLU cc_start: 0.5530 (pm20) cc_final: 0.4757 (mp0) REVERT: A 713 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7355 (t0) REVERT: A 714 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6636 (ptm-80) REVERT: A 717 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: A 836 LYS cc_start: 0.7794 (mttp) cc_final: 0.7411 (mmtt) REVERT: A 1067 TRP cc_start: 0.6547 (m-10) cc_final: 0.5251 (m100) REVERT: A 1085 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7925 (mp) REVERT: C 154 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8320 (p) REVERT: C 215 ARG cc_start: 0.7829 (mmp-170) cc_final: 0.7253 (mtm110) outliers start: 55 outliers final: 26 residues processed: 134 average time/residue: 0.3764 time to fit residues: 55.3838 Evaluate side-chains 119 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 130 ASN A 329 GLN A 761 ASN ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101552 restraints weight = 13457.159| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.16 r_work: 0.3127 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9548 Z= 0.154 Angle : 0.576 8.097 12952 Z= 0.294 Chirality : 0.044 0.343 1456 Planarity : 0.004 0.043 1610 Dihedral : 8.394 88.052 1366 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.02 % Allowed : 24.73 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.19 (0.26), residues: 1125 helix: 0.82 (0.24), residues: 495 sheet: -0.14 (0.41), residues: 162 loop : -1.10 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 224 TYR 0.011 0.001 TYR A 311 PHE 0.017 0.001 PHE A1055 TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9544) covalent geometry : angle 0.57229 (12943) SS BOND : bond 0.00851 ( 3) SS BOND : angle 1.34397 ( 6) hydrogen bonds : bond 0.04191 ( 391) hydrogen bonds : angle 4.42758 ( 1101) link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 4.19773 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 96 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7080 (pt0) REVERT: A 225 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7759 (tp) REVERT: A 384 GLU cc_start: 0.8296 (pt0) cc_final: 0.7725 (tt0) REVERT: A 709 GLU cc_start: 0.5626 (pm20) cc_final: 0.4794 (mp0) REVERT: A 717 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8293 (pt0) REVERT: A 769 ASN cc_start: 0.7229 (m-40) cc_final: 0.6794 (t0) REVERT: A 836 LYS cc_start: 0.7856 (mttp) cc_final: 0.7476 (mmtt) REVERT: A 926 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8635 (pp) REVERT: A 1067 TRP cc_start: 0.6575 (m-10) cc_final: 0.5279 (m100) REVERT: A 1085 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7972 (mp) outliers start: 51 outliers final: 28 residues processed: 131 average time/residue: 0.3491 time to fit residues: 50.0980 Evaluate side-chains 124 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 314 GLN A 329 GLN A 761 ASN A 864 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100198 restraints weight = 13522.068| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.12 r_work: 0.3110 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9548 Z= 0.180 Angle : 0.610 10.064 12952 Z= 0.310 Chirality : 0.045 0.252 1456 Planarity : 0.004 0.038 1610 Dihedral : 8.252 88.886 1366 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.22 % Allowed : 24.14 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.26), residues: 1125 helix: 0.68 (0.24), residues: 505 sheet: 0.02 (0.43), residues: 155 loop : -1.10 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 224 TYR 0.014 0.002 TYR A 311 PHE 0.019 0.002 PHE A1055 TRP 0.016 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9544) covalent geometry : angle 0.60722 (12943) SS BOND : bond 0.00750 ( 3) SS BOND : angle 1.44332 ( 6) hydrogen bonds : bond 0.04391 ( 391) hydrogen bonds : angle 4.43847 ( 1101) link_NAG-ASN : bond 0.00393 ( 1) link_NAG-ASN : angle 3.30151 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 96 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7119 (pt0) REVERT: A 225 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 384 GLU cc_start: 0.8260 (pt0) cc_final: 0.7743 (tt0) REVERT: A 709 GLU cc_start: 0.5758 (pm20) cc_final: 0.4933 (mp0) REVERT: A 717 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: A 722 TYR cc_start: 0.7308 (t80) cc_final: 0.6676 (t80) REVERT: A 769 ASN cc_start: 0.7317 (m-40) cc_final: 0.6866 (t0) REVERT: A 926 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8668 (pp) REVERT: A 1067 TRP cc_start: 0.6590 (m-10) cc_final: 0.5317 (m100) REVERT: C 37 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8060 (mtm180) REVERT: C 215 ARG cc_start: 0.7896 (mmp-170) cc_final: 0.7282 (mtm110) outliers start: 53 outliers final: 29 residues processed: 136 average time/residue: 0.3553 time to fit residues: 53.1568 Evaluate side-chains 127 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 0.0970 chunk 63 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 213 GLN A 329 GLN A 761 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104033 restraints weight = 13465.856| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.18 r_work: 0.3166 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9548 Z= 0.106 Angle : 0.537 9.030 12952 Z= 0.271 Chirality : 0.042 0.232 1456 Planarity : 0.003 0.034 1610 Dihedral : 7.478 87.707 1365 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.24 % Allowed : 25.42 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.00 (0.26), residues: 1125 helix: 0.93 (0.24), residues: 500 sheet: -0.02 (0.42), residues: 161 loop : -0.96 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 723 TYR 0.013 0.001 TYR A 324 PHE 0.011 0.001 PHE A 72 TRP 0.019 0.001 TRP A 323 HIS 0.002 0.000 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9544) covalent geometry : angle 0.53564 (12943) SS BOND : bond 0.00494 ( 3) SS BOND : angle 0.84357 ( 6) hydrogen bonds : bond 0.03580 ( 391) hydrogen bonds : angle 4.20015 ( 1101) link_NAG-ASN : bond 0.00716 ( 1) link_NAG-ASN : angle 2.53227 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7157 (tt0) REVERT: A 218 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 225 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7692 (tp) REVERT: A 255 GLU cc_start: 0.8201 (tp30) cc_final: 0.7574 (tt0) REVERT: A 345 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8501 (mm) REVERT: A 384 GLU cc_start: 0.8269 (pt0) cc_final: 0.7811 (tt0) REVERT: A 399 GLU cc_start: 0.7612 (pt0) cc_final: 0.7301 (tt0) REVERT: A 709 GLU cc_start: 0.5659 (pm20) cc_final: 0.4952 (mp0) REVERT: A 769 ASN cc_start: 0.7283 (m-40) cc_final: 0.6885 (t0) REVERT: A 926 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8526 (pp) REVERT: A 1016 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8032 (mmt-90) REVERT: A 1067 TRP cc_start: 0.6563 (m-10) cc_final: 0.5304 (m100) REVERT: A 1081 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: A 1085 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7967 (mp) REVERT: C 215 ARG cc_start: 0.7976 (mmp-170) cc_final: 0.7371 (mtm110) outliers start: 43 outliers final: 24 residues processed: 129 average time/residue: 0.3689 time to fit residues: 52.2926 Evaluate side-chains 123 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1016 ARG Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098292 restraints weight = 13393.782| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.17 r_work: 0.3089 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9548 Z= 0.200 Angle : 0.624 9.423 12952 Z= 0.317 Chirality : 0.046 0.231 1456 Planarity : 0.004 0.043 1610 Dihedral : 7.763 89.520 1365 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.24 % Allowed : 25.62 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.18 (0.26), residues: 1125 helix: 0.68 (0.24), residues: 510 sheet: 0.08 (0.43), residues: 155 loop : -1.04 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 723 TYR 0.013 0.002 TYR C 297 PHE 0.017 0.002 PHE A1055 TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9544) covalent geometry : angle 0.62094 (12943) SS BOND : bond 0.00729 ( 3) SS BOND : angle 1.54067 ( 6) hydrogen bonds : bond 0.04534 ( 391) hydrogen bonds : angle 4.41443 ( 1101) link_NAG-ASN : bond 0.00592 ( 1) link_NAG-ASN : angle 3.28041 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7180 (pt0) REVERT: A 225 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7786 (tp) REVERT: A 345 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 384 GLU cc_start: 0.8273 (pt0) cc_final: 0.7811 (tt0) REVERT: A 709 GLU cc_start: 0.5754 (pm20) cc_final: 0.5023 (mp0) REVERT: A 722 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6693 (t80) REVERT: A 769 ASN cc_start: 0.7293 (m-40) cc_final: 0.6911 (t0) REVERT: A 926 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8678 (pp) REVERT: A 1016 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7978 (mmt-90) REVERT: A 1053 MET cc_start: 0.5657 (OUTLIER) cc_final: 0.5253 (mmm) REVERT: A 1067 TRP cc_start: 0.6673 (m-10) cc_final: 0.5375 (m100) REVERT: A 1081 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: A 1085 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8066 (mp) REVERT: C 60 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8602 (mt) REVERT: C 215 ARG cc_start: 0.7923 (mmp-170) cc_final: 0.7281 (mtm110) REVERT: C 318 MET cc_start: 0.8582 (ptt) cc_final: 0.8381 (ptt) outliers start: 43 outliers final: 24 residues processed: 124 average time/residue: 0.3796 time to fit residues: 51.2990 Evaluate side-chains 122 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1016 ARG Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 329 GLN A 761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101099 restraints weight = 13420.791| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.10 r_work: 0.3135 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9548 Z= 0.135 Angle : 0.573 9.749 12952 Z= 0.290 Chirality : 0.043 0.228 1456 Planarity : 0.004 0.035 1610 Dihedral : 7.387 89.902 1365 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.84 % Allowed : 26.11 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.06 (0.26), residues: 1125 helix: 0.80 (0.24), residues: 511 sheet: 0.10 (0.42), residues: 155 loop : -0.99 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 723 TYR 0.012 0.001 TYR A 324 PHE 0.013 0.001 PHE A 971 TRP 0.017 0.001 TRP A 323 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9544) covalent geometry : angle 0.57119 (12943) SS BOND : bond 0.00602 ( 3) SS BOND : angle 1.08907 ( 6) hydrogen bonds : bond 0.03961 ( 391) hydrogen bonds : angle 4.27176 ( 1101) link_NAG-ASN : bond 0.00718 ( 1) link_NAG-ASN : angle 2.99011 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7204 (tt0) REVERT: A 225 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7758 (tp) REVERT: A 345 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 384 GLU cc_start: 0.8196 (pt0) cc_final: 0.7795 (tt0) REVERT: A 709 GLU cc_start: 0.5765 (pm20) cc_final: 0.5129 (mp0) REVERT: A 722 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 769 ASN cc_start: 0.7306 (m-40) cc_final: 0.6929 (t0) REVERT: A 926 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8562 (pp) REVERT: A 1016 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8048 (mmt-90) REVERT: A 1053 MET cc_start: 0.5645 (OUTLIER) cc_final: 0.5271 (mmm) REVERT: A 1067 TRP cc_start: 0.6595 (m-10) cc_final: 0.5334 (m100) REVERT: A 1081 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: A 1085 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8051 (mp) REVERT: C 60 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8592 (mt) REVERT: C 215 ARG cc_start: 0.7977 (mmp-170) cc_final: 0.7381 (mtm110) outliers start: 39 outliers final: 25 residues processed: 122 average time/residue: 0.3759 time to fit residues: 50.3286 Evaluate side-chains 124 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1016 ARG Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 761 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101803 restraints weight = 13437.794| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.15 r_work: 0.3139 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9548 Z= 0.130 Angle : 0.571 8.646 12952 Z= 0.289 Chirality : 0.043 0.239 1456 Planarity : 0.004 0.039 1610 Dihedral : 7.123 89.738 1365 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.84 % Allowed : 26.11 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.10 (0.26), residues: 1125 helix: 0.99 (0.24), residues: 500 sheet: 0.13 (0.42), residues: 155 loop : -0.91 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 723 TYR 0.012 0.001 TYR A 324 PHE 0.013 0.001 PHE A 971 TRP 0.016 0.001 TRP A 323 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9544) covalent geometry : angle 0.56948 (12943) SS BOND : bond 0.00561 ( 3) SS BOND : angle 1.02726 ( 6) hydrogen bonds : bond 0.03856 ( 391) hydrogen bonds : angle 4.23510 ( 1101) link_NAG-ASN : bond 0.00734 ( 1) link_NAG-ASN : angle 2.95038 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7189 (tt0) REVERT: A 225 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7736 (tp) REVERT: A 345 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8516 (mm) REVERT: A 384 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: A 709 GLU cc_start: 0.5790 (pm20) cc_final: 0.5171 (mp0) REVERT: A 926 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8571 (pp) REVERT: A 1016 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8058 (mmt-90) REVERT: A 1053 MET cc_start: 0.5643 (OUTLIER) cc_final: 0.5256 (mmm) REVERT: A 1067 TRP cc_start: 0.6627 (m-10) cc_final: 0.5386 (m100) REVERT: A 1081 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: A 1085 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8065 (mp) REVERT: C 60 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 66 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8426 (mt) REVERT: C 215 ARG cc_start: 0.7997 (mmp-170) cc_final: 0.7379 (mtm110) outliers start: 39 outliers final: 25 residues processed: 118 average time/residue: 0.4273 time to fit residues: 55.1915 Evaluate side-chains 125 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 722 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1016 ARG Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.0060 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 101 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103276 restraints weight = 13272.494| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.09 r_work: 0.3165 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9548 Z= 0.116 Angle : 0.558 8.122 12952 Z= 0.282 Chirality : 0.042 0.234 1456 Planarity : 0.004 0.044 1610 Dihedral : 6.889 89.787 1365 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.55 % Allowed : 26.70 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.21 (0.26), residues: 1125 helix: 1.14 (0.24), residues: 493 sheet: 0.19 (0.42), residues: 155 loop : -0.90 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 714 TYR 0.013 0.001 TYR A 324 PHE 0.011 0.001 PHE A 72 TRP 0.017 0.001 TRP A 323 HIS 0.002 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9544) covalent geometry : angle 0.55577 (12943) SS BOND : bond 0.00532 ( 3) SS BOND : angle 0.90812 ( 6) hydrogen bonds : bond 0.03667 ( 391) hydrogen bonds : angle 4.16821 ( 1101) link_NAG-ASN : bond 0.00781 ( 1) link_NAG-ASN : angle 2.81987 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.94 seconds wall clock time: 48 minutes 42.94 seconds (2922.94 seconds total)