Starting phenix.real_space_refine on Fri Mar 14 05:46:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bsw_30169/03_2025/7bsw_30169_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bsw_30169/03_2025/7bsw_30169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bsw_30169/03_2025/7bsw_30169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bsw_30169/03_2025/7bsw_30169.map" model { file = "/net/cci-nas-00/data/ceres_data/7bsw_30169/03_2025/7bsw_30169_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bsw_30169/03_2025/7bsw_30169_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 1 5.49 5 S 45 5.16 5 C 6078 2.51 5 N 1504 2.21 5 O 1696 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9329 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6596 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 792} Chain breaks: 3 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ALF': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.24, per 1000 atoms: 0.56 Number of scatterers: 9329 At special positions: 0 Unit cell: (97.2, 105.3, 141.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 45 16.00 P 1 15.00 Al 1 13.00 F 4 9.00 O 1696 8.00 N 1504 7.00 C 6078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 9314 O5 NAG C 404 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9314 O5 NAG C 404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG C 402 " - " MAN C 403 " BETA1-4 " NAG C 401 " - " NAG C 402 " NAG-ASN " NAG C 401 " - " ASN C 180 " " NAG C 404 " - " ASN C 294 " " NAG C 405 " - " ASN C 107 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.0 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 11 sheets defined 44.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 removed outlier: 4.197A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.915A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 93 through 119 removed outlier: 3.686A pdb=" N ILE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 286 through 314 removed outlier: 3.752A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.503A pdb=" N LYS A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.772A 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 360 through 371 removed outlier: 4.097A pdb=" N MET A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.763A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 679 through 688 removed outlier: 4.005A pdb=" N SER A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 Processing helix chain 'A' and resid 754 through 762 removed outlier: 3.821A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 782 Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.657A pdb=" N LYS A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 853 through 862 removed outlier: 4.583A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 886 removed outlier: 4.246A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 892 through 894 No H-bonds generated for 'chain 'A' and resid 892 through 894' Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 918 through 926 Processing helix chain 'A' and resid 931 through 936 Processing helix chain 'A' and resid 938 through 945 removed outlier: 3.600A pdb=" N TYR A 942 " --> pdb=" O PRO A 939 " (cutoff:3.500A) removed outlier: 3.812A 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 976 removed outlier: 3.715A pdb=" N ALA A 964 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 992 through 1015 removed outlier: 3.762A pdb=" N GLY A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.717A pdb=" N HIS A1023 " --> pdb=" O THR A1019 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A1024 " --> pdb=" O TRP A1020 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1062 removed outlier: 3.676A pdb=" N GLN A1059 " --> pdb=" O PHE A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1077 removed outlier: 3.648A pdb=" N LEU A1068 " --> pdb=" O VAL A1064 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A1075 " --> pdb=" O ILE A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 52 through 71 removed outlier: 4.060A pdb=" N GLY C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.596A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.547A pdb=" N SER C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.681A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 removed outlier: 3.618A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 4.123A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 258 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 163 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.515A pdb=" N LEU A 245 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.814A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 250 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.855A pdb=" N GLY A 223 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.987A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N CYS A 788 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 751 " --> pdb=" O CYS A 788 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 748 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 812 through 815 removed outlier: 5.650A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.517A pdb=" N ARG C 309 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.588A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 188 " --> pdb=" O ARG C 290 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 936 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: 2.55 Time building geometry restraints manager: 2.89 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: 1518 1.32 - 1.45: 2643 1.45 - 1.57: 5325 1.57 - 1.69: 2 1.69 - 1.81: 71 Bond restraints: 9559 Sorted by residual: bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.800 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.797 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N THR C 100 " pdb=" CA THR C 100 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.13e+01 ... (remaining 9554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.11: 12955 14.11 - 28.22: 4 28.22 - 42.32: 0 42.32 - 56.43: 0 56.43 - 70.54: 2 Bond angle restraints: 12961 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.22 -70.54 3.00e+00 1.11e-01 5.53e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.69 -70.06 3.00e+00 1.11e-01 5.45e+02 angle pdb=" N LYS A1088 " pdb=" CA LYS A1088 " pdb=" C LYS A1088 " ideal model delta sigma weight residual 112.93 103.39 9.54 1.12e+00 7.97e-01 7.26e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.20 20.01 3.00e+00 1.11e-01 4.45e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.68 19.91 3.00e+00 1.11e-01 4.41e+01 ... (remaining 12956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 5428 26.09 - 52.18: 245 52.18 - 78.27: 23 78.27 - 104.35: 17 104.35 - 130.44: 13 Dihedral angle restraints: 5726 sinusoidal: 2383 harmonic: 3343 Sorted by residual: dihedral pdb=" C3 PEE A1102 " pdb=" C1 PEE A1102 " pdb=" C2 PEE A1102 " pdb=" O3P PEE A1102 " ideal model delta sinusoidal sigma weight residual 62.73 -67.71 130.44 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" O2 PEE A1102 " pdb=" C1 PEE A1102 " pdb=" C2 PEE A1102 " pdb=" O3P PEE A1102 " ideal model delta sinusoidal sigma weight residual 300.04 170.89 129.15 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" N PEE A1102 " pdb=" C4 PEE A1102 " pdb=" C5 PEE A1102 " pdb=" O4P PEE A1102 " ideal model delta sinusoidal sigma weight residual -56.97 -178.16 121.19 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 5723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.091: 1462 1.091 - 2.182: 0 2.182 - 3.272: 1 3.272 - 4.363: 0 4.363 - 5.454: 2 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" O4 NAG C 401 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 3.05 -5.45 2.00e-02 2.50e+03 7.44e+04 chirality pdb=" C1 MAN C 403 " pdb=" O4 NAG C 402 " pdb=" C2 MAN C 403 " pdb=" O5 MAN C 403 " both_signs ideal model delta sigma weight residual False 2.40 -2.42 4.82 2.00e-02 2.50e+03 5.81e+04 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.17 -2.23 2.00e-01 2.50e+01 1.25e+02 ... (remaining 1462 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 294 " 0.271 2.00e-02 2.50e+03 4.91e-01 3.01e+03 pdb=" CG ASN C 294 " -0.164 2.00e-02 2.50e+03 pdb=" OD1 ASN C 294 " 0.086 2.00e-02 2.50e+03 pdb=" ND2 ASN C 294 " -0.831 2.00e-02 2.50e+03 pdb=" C1 NAG C 404 " 0.639 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.275 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" C7 NAG C 402 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.377 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.130 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" C7 NAG C 401 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.104 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 56 2.36 - 2.99: 5632 2.99 - 3.63: 12950 3.63 - 4.26: 20676 4.26 - 4.90: 34904 Nonbonded interactions: 74218 Sorted by model distance: nonbonded pdb=" CD2 TYR A 876 " pdb=" CD1 ILE A 920 " model vdw 1.719 3.760 nonbonded pdb=" OE2 GLU A 181 " pdb=" OD2 ASP A 676 " model vdw 1.869 3.040 nonbonded pdb=" CG ASN C 294 " pdb=" O5 NAG C 404 " model vdw 1.919 2.616 nonbonded pdb=" OH TYR A 876 " pdb=" O VAL A1007 " model vdw 1.932 3.040 nonbonded pdb=" OD1 ASN C 294 " pdb=" O5 NAG C 404 " model vdw 1.962 3.040 ... (remaining 74213 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.005 0.115 9559 Z= 0.314 Angle : 1.225 70.538 12961 Z= 0.602 Chirality : 0.206 5.454 1465 Planarity : 0.008 0.227 1611 Dihedral : 16.587 130.443 3561 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 37.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.69 % Allowed : 3.74 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.19), residues: 1129 helix: -2.91 (0.19), residues: 474 sheet: -3.89 (0.33), residues: 151 loop : -3.83 (0.22), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS C 348 PHE 0.012 0.001 PHE A 884 TYR 0.015 0.001 TYR C 350 ARG 0.005 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 226 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.7848 (t0) cc_final: 0.7585 (t0) REVERT: A 381 TYR cc_start: 0.7636 (t80) cc_final: 0.7287 (t80) REVERT: A 399 GLU cc_start: 0.8819 (tt0) cc_final: 0.8579 (mt-10) REVERT: A 826 GLU cc_start: 0.8349 (tp30) cc_final: 0.7988 (tp30) REVERT: A 914 CYS cc_start: 0.8052 (m) cc_final: 0.7751 (m) REVERT: A 1050 GLN cc_start: 0.8516 (pp30) cc_final: 0.8128 (pp30) REVERT: C 106 ILE cc_start: 0.8564 (mm) cc_final: 0.8300 (mm) REVERT: C 122 TYR cc_start: 0.8611 (p90) cc_final: 0.8410 (p90) REVERT: C 310 MET cc_start: 0.8525 (ttp) cc_final: 0.7885 (tmm) outliers start: 7 outliers final: 2 residues processed: 231 average time/residue: 0.2455 time to fit residues: 76.0280 Evaluate side-chains 145 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 275 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.3980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 243 ASN A 314 GLN A 352 ASN A 392 ASN A 402 GLN A 653 GLN A 716 HIS A 744 HIS A 828 HIS A 862 HIS A 864 HIS C 36 GLN C 129 GLN C 347 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.163809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.153428 restraints weight = 10720.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138699 restraints weight = 18216.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.137133 restraints weight = 17002.098| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9559 Z= 0.342 Angle : 0.731 7.922 12961 Z= 0.367 Chirality : 0.049 0.194 1465 Planarity : 0.004 0.031 1611 Dihedral : 12.706 103.672 1381 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.56 % Allowed : 12.78 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.22), residues: 1129 helix: -1.90 (0.21), residues: 477 sheet: -3.78 (0.31), residues: 158 loop : -2.76 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.009 0.002 HIS C 302 PHE 0.021 0.002 PHE A1075 TYR 0.016 0.002 TYR A 879 ARG 0.004 0.001 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7326 (mmmt) REVERT: A 747 TYR cc_start: 0.6989 (m-80) cc_final: 0.6743 (m-80) REVERT: A 826 GLU cc_start: 0.8611 (tp30) cc_final: 0.8197 (tp30) REVERT: A 877 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8032 (t80) REVERT: A 914 CYS cc_start: 0.8503 (m) cc_final: 0.8203 (m) REVERT: A 975 TYR cc_start: 0.9183 (t80) cc_final: 0.8841 (t80) REVERT: A 1014 ASP cc_start: 0.8625 (m-30) cc_final: 0.8419 (t0) REVERT: A 1050 GLN cc_start: 0.8917 (pp30) cc_final: 0.8260 (pp30) REVERT: C 310 MET cc_start: 0.8637 (ttp) cc_final: 0.8248 (tmm) outliers start: 26 outliers final: 18 residues processed: 191 average time/residue: 0.2280 time to fit residues: 62.6703 Evaluate side-chains 181 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 336 SER 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 56 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 6 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 397 ASN A 828 HIS C 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.165216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149738 restraints weight = 10721.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142935 restraints weight = 12700.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141432 restraints weight = 15915.940| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9559 Z= 0.212 Angle : 0.624 7.814 12961 Z= 0.313 Chirality : 0.045 0.209 1465 Planarity : 0.004 0.034 1611 Dihedral : 9.707 85.538 1376 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.05 % Allowed : 16.42 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.23), residues: 1129 helix: -1.16 (0.23), residues: 478 sheet: -3.23 (0.33), residues: 158 loop : -2.40 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.007 0.001 HIS C 302 PHE 0.015 0.001 PHE A1039 TYR 0.013 0.001 TYR C 350 ARG 0.004 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7413 (mmmt) REVERT: A 183 ASN cc_start: 0.8898 (p0) cc_final: 0.8686 (p0) REVERT: A 366 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 678 MET cc_start: 0.7985 (tpp) cc_final: 0.7355 (tpt) REVERT: A 698 LEU cc_start: 0.8498 (mt) cc_final: 0.8239 (tp) REVERT: A 747 TYR cc_start: 0.6850 (m-80) cc_final: 0.6439 (m-80) REVERT: A 826 GLU cc_start: 0.8514 (tp30) cc_final: 0.8170 (tp30) REVERT: A 877 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8148 (t80) REVERT: A 1050 GLN cc_start: 0.8981 (pp30) cc_final: 0.8498 (pp30) REVERT: C 310 MET cc_start: 0.8577 (ttp) cc_final: 0.8235 (tmm) outliers start: 31 outliers final: 17 residues processed: 180 average time/residue: 0.1896 time to fit residues: 49.7215 Evaluate side-chains 164 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.160260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149780 restraints weight = 10840.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.146486 restraints weight = 17495.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144603 restraints weight = 20946.341| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9559 Z= 0.326 Angle : 0.682 10.413 12961 Z= 0.339 Chirality : 0.047 0.190 1465 Planarity : 0.004 0.032 1611 Dihedral : 8.868 83.189 1376 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.52 % Allowed : 16.81 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.23), residues: 1129 helix: -1.03 (0.23), residues: 477 sheet: -2.94 (0.34), residues: 158 loop : -2.29 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.006 0.002 HIS C 302 PHE 0.028 0.002 PHE A1075 TYR 0.019 0.002 TYR A 722 ARG 0.002 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 142 LYS cc_start: 0.7883 (mtpp) cc_final: 0.7452 (mmmt) REVERT: A 366 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8229 (tm-30) REVERT: A 678 MET cc_start: 0.7992 (tpp) cc_final: 0.7474 (tpt) REVERT: A 877 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8199 (t80) REVERT: A 910 MET cc_start: 0.8768 (mmm) cc_final: 0.8535 (mmm) REVERT: A 1014 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.7626 (t0) REVERT: A 1050 GLN cc_start: 0.9013 (pp30) cc_final: 0.8570 (pp30) REVERT: C 310 MET cc_start: 0.8819 (ttp) cc_final: 0.8390 (tmm) outliers start: 46 outliers final: 31 residues processed: 179 average time/residue: 0.2256 time to fit residues: 57.9069 Evaluate side-chains 168 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.165283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154163 restraints weight = 10714.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150428 restraints weight = 18995.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149169 restraints weight = 21313.269| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9559 Z= 0.182 Angle : 0.597 9.540 12961 Z= 0.294 Chirality : 0.043 0.191 1465 Planarity : 0.003 0.033 1611 Dihedral : 7.987 82.769 1376 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.95 % Allowed : 19.57 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.24), residues: 1129 helix: -0.53 (0.24), residues: 470 sheet: -2.47 (0.37), residues: 158 loop : -2.04 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 260 HIS 0.005 0.001 HIS C 302 PHE 0.013 0.001 PHE A1039 TYR 0.015 0.001 TYR A 722 ARG 0.003 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.940 Fit side-chains REVERT: A 145 ASP cc_start: 0.8040 (p0) cc_final: 0.7744 (p0) REVERT: A 399 GLU cc_start: 0.8736 (tt0) cc_final: 0.8178 (mt-10) REVERT: A 402 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8460 (mm-40) REVERT: A 678 MET cc_start: 0.7833 (tpp) cc_final: 0.7488 (tpt) REVERT: A 747 TYR cc_start: 0.7099 (m-80) cc_final: 0.6853 (m-80) REVERT: A 844 ASN cc_start: 0.8384 (m-40) cc_final: 0.8137 (m-40) REVERT: A 877 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8181 (t80) REVERT: A 1014 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7585 (t0) REVERT: A 1050 GLN cc_start: 0.8994 (pp30) cc_final: 0.8674 (pp30) REVERT: C 310 MET cc_start: 0.8741 (ttp) cc_final: 0.8378 (tmm) REVERT: C 343 LEU cc_start: 0.7779 (mp) cc_final: 0.7355 (mp) outliers start: 30 outliers final: 22 residues processed: 179 average time/residue: 0.2230 time to fit residues: 57.1423 Evaluate side-chains 161 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.164213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153059 restraints weight = 10673.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139726 restraints weight = 17487.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.137631 restraints weight = 17252.082| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9559 Z= 0.213 Angle : 0.597 8.610 12961 Z= 0.297 Chirality : 0.043 0.186 1465 Planarity : 0.003 0.030 1611 Dihedral : 7.549 84.137 1376 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.64 % Allowed : 20.65 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.24), residues: 1129 helix: -0.40 (0.24), residues: 467 sheet: -2.15 (0.39), residues: 158 loop : -1.89 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.017 0.001 PHE A1039 TYR 0.017 0.001 TYR A 722 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.960 Fit side-chains REVERT: A 145 ASP cc_start: 0.8279 (p0) cc_final: 0.7937 (p0) REVERT: A 678 MET cc_start: 0.7962 (tpp) cc_final: 0.7493 (tpt) REVERT: A 747 TYR cc_start: 0.6967 (m-80) cc_final: 0.6712 (m-80) REVERT: A 790 MET cc_start: 0.8951 (mmm) cc_final: 0.8068 (mmm) REVERT: A 844 ASN cc_start: 0.8475 (m-40) cc_final: 0.8185 (m-40) REVERT: A 877 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8005 (t80) REVERT: A 1014 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7637 (t0) REVERT: A 1050 GLN cc_start: 0.9064 (pp30) cc_final: 0.8764 (pp30) REVERT: C 343 LEU cc_start: 0.7822 (mp) cc_final: 0.7416 (mp) outliers start: 37 outliers final: 30 residues processed: 174 average time/residue: 0.1914 time to fit residues: 48.7267 Evaluate side-chains 177 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 54 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 chunk 110 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.161251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134801 restraints weight = 10890.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134257 restraints weight = 15678.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134428 restraints weight = 13427.166| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9559 Z= 0.232 Angle : 0.607 9.020 12961 Z= 0.299 Chirality : 0.043 0.181 1465 Planarity : 0.004 0.032 1611 Dihedral : 7.273 82.470 1376 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.93 % Allowed : 20.85 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.25), residues: 1129 helix: -0.27 (0.24), residues: 467 sheet: -2.06 (0.40), residues: 163 loop : -1.78 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.020 0.001 PHE A1039 TYR 0.017 0.001 TYR A 722 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.117 Fit side-chains REVERT: A 145 ASP cc_start: 0.8353 (p0) cc_final: 0.8007 (p0) REVERT: A 399 GLU cc_start: 0.8721 (tt0) cc_final: 0.8098 (mt-10) REVERT: A 678 MET cc_start: 0.7927 (tpp) cc_final: 0.7525 (tpt) REVERT: A 747 TYR cc_start: 0.6887 (m-80) cc_final: 0.6658 (m-80) REVERT: A 844 ASN cc_start: 0.8452 (m-40) cc_final: 0.8144 (m-40) REVERT: A 877 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 1014 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7700 (t0) REVERT: A 1050 GLN cc_start: 0.9099 (pp30) cc_final: 0.8764 (pp30) REVERT: C 310 MET cc_start: 0.8895 (tmm) cc_final: 0.8442 (tmm) REVERT: C 343 LEU cc_start: 0.7675 (mp) cc_final: 0.7194 (mp) outliers start: 40 outliers final: 35 residues processed: 169 average time/residue: 0.1953 time to fit residues: 47.7168 Evaluate side-chains 179 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127950 restraints weight = 11725.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125931 restraints weight = 22689.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125168 restraints weight = 23556.668| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9559 Z= 0.196 Angle : 0.575 9.145 12961 Z= 0.286 Chirality : 0.042 0.182 1465 Planarity : 0.003 0.032 1611 Dihedral : 6.869 81.584 1376 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.83 % Allowed : 21.04 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.25), residues: 1129 helix: -0.10 (0.24), residues: 473 sheet: -1.82 (0.41), residues: 163 loop : -1.70 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 323 HIS 0.004 0.001 HIS C 302 PHE 0.021 0.001 PHE A 775 TYR 0.020 0.001 TYR A 722 ARG 0.003 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.000 Fit side-chains REVERT: A 145 ASP cc_start: 0.8142 (p0) cc_final: 0.7771 (p0) REVERT: A 399 GLU cc_start: 0.8710 (tt0) cc_final: 0.8070 (mt-10) REVERT: A 698 LEU cc_start: 0.8396 (mm) cc_final: 0.8013 (tp) REVERT: A 747 TYR cc_start: 0.7048 (m-80) cc_final: 0.6746 (m-80) REVERT: A 844 ASN cc_start: 0.8437 (m-40) cc_final: 0.8172 (m-40) REVERT: A 877 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8081 (t80) REVERT: A 986 ASN cc_start: 0.8846 (p0) cc_final: 0.8628 (p0) REVERT: A 1014 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7475 (t0) REVERT: A 1050 GLN cc_start: 0.9059 (pp30) cc_final: 0.8756 (pp30) REVERT: C 310 MET cc_start: 0.8973 (tmm) cc_final: 0.8497 (tmm) REVERT: C 343 LEU cc_start: 0.7694 (mp) cc_final: 0.7242 (mp) outliers start: 39 outliers final: 31 residues processed: 170 average time/residue: 0.1942 time to fit residues: 47.6643 Evaluate side-chains 170 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.157428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141155 restraints weight = 10866.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128996 restraints weight = 15108.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127039 restraints weight = 14843.430| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9559 Z= 0.373 Angle : 0.690 9.325 12961 Z= 0.344 Chirality : 0.047 0.173 1465 Planarity : 0.004 0.033 1611 Dihedral : 7.130 81.414 1376 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.93 % Allowed : 21.63 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.25), residues: 1129 helix: -0.37 (0.23), residues: 473 sheet: -1.74 (0.41), residues: 163 loop : -1.82 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.006 0.001 HIS A 114 PHE 0.023 0.002 PHE A1039 TYR 0.013 0.002 TYR C 350 ARG 0.005 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.979 Fit side-chains REVERT: A 111 TRP cc_start: 0.8127 (t60) cc_final: 0.7778 (t-100) REVERT: A 145 ASP cc_start: 0.8379 (p0) cc_final: 0.8012 (p0) REVERT: A 399 GLU cc_start: 0.8746 (tt0) cc_final: 0.8140 (mt-10) REVERT: A 747 TYR cc_start: 0.6967 (m-80) cc_final: 0.6728 (m-80) REVERT: A 776 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8793 (mp) REVERT: A 877 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8063 (t80) REVERT: A 910 MET cc_start: 0.8762 (mmm) cc_final: 0.8372 (tpt) REVERT: A 1014 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.7702 (t0) REVERT: A 1050 GLN cc_start: 0.9126 (pp30) cc_final: 0.8699 (pp30) REVERT: C 310 MET cc_start: 0.8987 (tmm) cc_final: 0.8460 (tmm) REVERT: C 343 LEU cc_start: 0.7819 (mp) cc_final: 0.7334 (mp) outliers start: 40 outliers final: 34 residues processed: 163 average time/residue: 0.2221 time to fit residues: 52.9989 Evaluate side-chains 172 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.163575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.154226 restraints weight = 10946.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152014 restraints weight = 17134.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.150914 restraints weight = 20499.061| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9559 Z= 0.312 Angle : 0.658 9.095 12961 Z= 0.327 Chirality : 0.045 0.179 1465 Planarity : 0.004 0.033 1611 Dihedral : 7.014 79.714 1376 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.64 % Allowed : 22.22 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.25), residues: 1129 helix: -0.35 (0.23), residues: 479 sheet: -1.85 (0.40), residues: 168 loop : -1.80 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.006 0.001 HIS A 114 PHE 0.023 0.002 PHE A 775 TYR 0.017 0.002 TYR C 122 ARG 0.004 0.000 ARG A 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.068 Fit side-chains REVERT: A 111 TRP cc_start: 0.8268 (t60) cc_final: 0.7999 (t-100) REVERT: A 145 ASP cc_start: 0.7928 (p0) cc_final: 0.7518 (p0) REVERT: A 399 GLU cc_start: 0.8733 (tt0) cc_final: 0.8057 (mt-10) REVERT: A 679 GLU cc_start: 0.7984 (pp20) cc_final: 0.7107 (pp20) REVERT: A 790 MET cc_start: 0.8967 (mmm) cc_final: 0.8105 (mmm) REVERT: A 844 ASN cc_start: 0.8512 (m-40) cc_final: 0.8257 (m-40) REVERT: A 877 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8249 (t80) REVERT: A 910 MET cc_start: 0.8808 (mmm) cc_final: 0.8419 (tpt) REVERT: A 1014 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7624 (t0) REVERT: A 1050 GLN cc_start: 0.9108 (pp30) cc_final: 0.8764 (pp30) REVERT: C 310 MET cc_start: 0.8974 (tmm) cc_final: 0.8525 (tmm) REVERT: C 343 LEU cc_start: 0.7776 (mp) cc_final: 0.7261 (mp) outliers start: 37 outliers final: 34 residues processed: 164 average time/residue: 0.1876 time to fit residues: 44.9934 Evaluate side-chains 173 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.161394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.149996 restraints weight = 10814.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147026 restraints weight = 16873.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145913 restraints weight = 20931.806| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9559 Z= 0.293 Angle : 0.652 9.055 12961 Z= 0.325 Chirality : 0.045 0.179 1465 Planarity : 0.004 0.032 1611 Dihedral : 6.935 78.959 1376 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.54 % Allowed : 22.91 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.25), residues: 1129 helix: -0.36 (0.23), residues: 485 sheet: -1.81 (0.40), residues: 167 loop : -1.83 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 114 PHE 0.021 0.001 PHE A1039 TYR 0.016 0.001 TYR C 122 ARG 0.003 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.33 seconds wall clock time: 49 minutes 11.32 seconds (2951.32 seconds total)