Starting phenix.real_space_refine on Wed Aug 5 08:41:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v31_64746/08_2026/9v31_64746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v31_64746/08_2026/9v31_64746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v31_64746/08_2026/9v31_64746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v31_64746/08_2026/9v31_64746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v31_64746/08_2026/9v31_64746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v31_64746/08_2026/9v31_64746.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5627 2.51 5 N 1461 2.21 5 O 1691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8839 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1192 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain breaks: 3 Chain: "H" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1553 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 191} Chain breaks: 2 Chain: "L" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1680 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "C" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1553 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 191} Chain breaks: 2 Chain: "D" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1680 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "B" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1181 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain breaks: 3 Time building chain proxies: 2.01, per 1000 atoms: 0.23 Number of scatterers: 8839 At special positions: 0 Unit cell: (96.05, 220.15, 66.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1691 8.00 N 1461 7.00 C 5627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 63 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 94 " distance=2.04 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 63 " 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 557.6 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 21.0% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 3 through 27 removed outlier: 3.564A pdb=" N GLN A 7 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 4.506A pdb=" N ALA A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 145 removed outlier: 3.897A pdb=" N PHE A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.948A pdb=" N PHE A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'L' and resid 127 through 132 removed outlier: 3.762A pdb=" N LYS L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 194 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.582A pdb=" N ASN C 103 " --> pdb=" O TYR C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.989A pdb=" N LYS D 132 " --> pdb=" O ASP D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 195 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.625A pdb=" N THR B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 4.261A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 79 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 145 removed outlier: 3.743A pdb=" N PHE B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 194 removed outlier: 3.991A pdb=" N PHE B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 47 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.351A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.351A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N CYS H 96 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP H 108 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ARG H 98 " --> pdb=" O ASP H 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP H 106 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA H 104 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 125 through 127 removed outlier: 3.714A pdb=" N SER H 125 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS H 148 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU H 146 " --> pdb=" O PHE H 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 156 through 159 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.783A pdb=" N PHE L 77 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP L 76 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.865A pdb=" N LEU L 11 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA L 90 " --> pdb=" O VAL L 110 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE L 54 " --> pdb=" O TRP L 41 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 120 through 124 removed outlier: 6.206A pdb=" N TYR L 179 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 150 through 156 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.630A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.874A pdb=" N SER C 125 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 146 " --> pdb=" O PHE C 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.603A pdb=" N PHE D 77 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP D 76 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 73 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.869A pdb=" N LEU D 11 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 13 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA D 90 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.418A pdb=" N TYR D 179 " --> pdb=" O ASN D 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 160 through 161 removed outlier: 4.705A pdb=" N TRP D 154 " --> pdb=" O GLN D 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AC3, first strand: chain 'B' and resid 43 through 46 395 hydrogen bonds defined for protein. 1086 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: 1.23 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2767 1.34 - 1.46: 2261 1.46 - 1.58: 3907 1.58 - 1.71: 1 1.71 - 1.83: 92 Bond restraints: 9028 Sorted by residual: bond pdb=" CB PRO C 154 " pdb=" CG PRO C 154 " ideal model delta sigma weight residual 1.506 1.593 -0.087 3.90e-02 6.57e+02 4.99e+00 bond pdb=" CA ASP D 66 " pdb=" C ASP D 66 " ideal model delta sigma weight residual 1.522 1.551 -0.029 1.72e-02 3.38e+03 2.83e+00 bond pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.20e+00 bond pdb=" CB MET H 81 " pdb=" CG MET H 81 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.91e-01 bond pdb=" CG PRO C 154 " pdb=" CD PRO C 154 " ideal model delta sigma weight residual 1.512 1.535 -0.023 2.70e-02 1.37e+03 7.34e-01 ... (remaining 9023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 12175 2.98 - 5.96: 76 5.96 - 8.94: 3 8.94 - 11.93: 0 11.93 - 14.91: 2 Bond angle restraints: 12256 Sorted by residual: angle pdb=" N ALA C 92 " pdb=" CA ALA C 92 " pdb=" C ALA C 92 " ideal model delta sigma weight residual 108.74 115.53 -6.79 1.38e+00 5.25e-01 2.42e+01 angle pdb=" C THR C 91 " pdb=" N ALA C 92 " pdb=" CA ALA C 92 " ideal model delta sigma weight residual 122.11 116.43 5.68 1.59e+00 3.96e-01 1.28e+01 angle pdb=" CA PRO C 154 " pdb=" N PRO C 154 " pdb=" CD PRO C 154 " ideal model delta sigma weight residual 111.50 106.53 4.97 1.40e+00 5.10e-01 1.26e+01 angle pdb=" C ASN H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta sigma weight residual 122.94 117.91 5.03 1.50e+00 4.44e-01 1.13e+01 angle pdb=" N VAL B 3 " pdb=" CA VAL B 3 " pdb=" C VAL B 3 " ideal model delta sigma weight residual 113.20 110.05 3.15 9.60e-01 1.09e+00 1.08e+01 ... (remaining 12251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4912 17.69 - 35.38: 348 35.38 - 53.08: 63 53.08 - 70.77: 8 70.77 - 88.46: 6 Dihedral angle restraints: 5337 sinusoidal: 2006 harmonic: 3331 Sorted by residual: dihedral pdb=" CB CYS L 140 " pdb=" SG CYS L 140 " pdb=" SG CYS L 200 " pdb=" CB CYS L 200 " ideal model delta sinusoidal sigma weight residual -86.00 -121.13 35.13 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA MET A 191 " pdb=" C MET A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP C 90 " pdb=" C ASP C 90 " pdb=" N THR C 91 " pdb=" CA THR C 91 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 857 0.031 - 0.062: 366 0.062 - 0.093: 123 0.093 - 0.124: 45 0.124 - 0.155: 12 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA ILE H 72 " pdb=" N ILE H 72 " pdb=" C ILE H 72 " pdb=" CB ILE H 72 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE H 200 " pdb=" N ILE H 200 " pdb=" C ILE H 200 " pdb=" CB ILE H 200 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE C 200 " pdb=" N ILE C 200 " pdb=" C ILE C 200 " pdb=" CB ILE C 200 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1400 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " 0.019 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP H 36 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 36 " -0.014 2.00e-02 2.50e+03 1.42e-02 5.01e+00 pdb=" CG TRP C 36 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 36 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 36 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 36 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 36 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 36 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 151 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO H 152 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 152 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 152 " 0.029 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 884 2.75 - 3.29: 8668 3.29 - 3.82: 13753 3.82 - 4.36: 14939 4.36 - 4.90: 26549 Nonbonded interactions: 64793 Sorted by model distance: nonbonded pdb=" NH1 ARG L 67 " pdb=" OE1 GLN L 85 " model vdw 2.211 3.120 nonbonded pdb=" OG SER H 17 " pdb=" O LEU H 83 " model vdw 2.215 3.040 nonbonded pdb=" NE2 GLN C 176 " pdb=" OG SER C 178 " model vdw 2.223 3.120 nonbonded pdb=" OG SER H 125 " pdb=" O LYS H 148 " model vdw 2.226 3.040 nonbonded pdb=" NZ LYS L 24 " pdb=" OD1 ASP L 76 " model vdw 2.232 3.120 ... (remaining 64788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 66 or resid 73 through 194)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'L' } 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 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 : 0.003 0.087 9038 Z= 0.132 Angle : 0.647 14.908 12276 Z= 0.343 Chirality : 0.041 0.155 1403 Planarity : 0.004 0.056 1536 Dihedral : 12.526 88.461 3181 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 0.95 (0.26), residues: 1133 helix: 2.84 (0.36), residues: 223 sheet: 1.18 (0.26), residues: 419 loop : -0.97 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.025 0.001 TYR H 54 PHE 0.023 0.001 PHE H 151 TRP 0.063 0.002 TRP H 36 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9028) covalent geometry : angle 0.64515 / 0.34 (12256) SS BOND : bond 0.00639 / 0.31 ( 10) SS BOND : angle 1.30480 / 0.85 ( 20) hydrogen bonds : bond 0.10011 / 6.73 ( 391) hydrogen bonds : angle 4.91235 / 3.46 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.6911 (mpp) cc_final: 0.6420 (mpp) REVERT: A 28 ASP cc_start: 0.7333 (m-30) cc_final: 0.7001 (m-30) REVERT: A 29 GLN cc_start: 0.8377 (mp10) cc_final: 0.7893 (mp10) REVERT: A 75 MET cc_start: 0.7551 (mmp) cc_final: 0.7225 (mmt) REVERT: A 84 ILE cc_start: 0.8267 (mm) cc_final: 0.7935 (mm) REVERT: A 145 THR cc_start: 0.8974 (m) cc_final: 0.8724 (m) REVERT: A 192 MET cc_start: 0.5743 (mmt) cc_final: 0.5497 (mmt) REVERT: H 6 GLN cc_start: 0.6646 (pt0) cc_final: 0.6387 (pt0) REVERT: H 99 MET cc_start: 0.7047 (ptp) cc_final: 0.6544 (ptp) REVERT: H 103 ASN cc_start: 0.8499 (t0) cc_final: 0.7847 (t0) REVERT: H 112 THR cc_start: 0.7282 (m) cc_final: 0.6615 (m) REVERT: L 51 LYS cc_start: 0.8183 (pttp) cc_final: 0.7815 (pttp) REVERT: L 53 LEU cc_start: 0.8459 (mm) cc_final: 0.8217 (mm) REVERT: L 67 ARG cc_start: 0.6641 (ttp-170) cc_final: 0.5737 (ttp-170) REVERT: L 130 GLN cc_start: 0.8115 (tt0) cc_final: 0.7560 (pt0) REVERT: C 74 LYS cc_start: 0.8610 (mppt) cc_final: 0.8306 (mppt) REVERT: C 103 ASN cc_start: 0.8316 (t0) cc_final: 0.7509 (t0) REVERT: C 108 TRP cc_start: 0.7639 (m100) cc_final: 0.6804 (m100) REVERT: C 110 GLN cc_start: 0.7791 (pm20) cc_final: 0.7425 (pm20) REVERT: C 112 THR cc_start: 0.7260 (m) cc_final: 0.6579 (m) REVERT: D 151 LYS cc_start: 0.8179 (tttt) cc_final: 0.7798 (tttt) REVERT: D 180 SER cc_start: 0.7498 (t) cc_final: 0.7295 (t) REVERT: B 64 ARG cc_start: 0.6909 (tmt170) cc_final: 0.6671 (tmt170) REVERT: B 191 MET cc_start: 0.8014 (ttp) cc_final: 0.7284 (ttp) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.0670 time to fit residues: 28.3341 Evaluate side-chains 281 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN H 110 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS D 6 GLN D 166 GLN B 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135440 restraints weight = 15852.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139872 restraints weight = 9815.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142978 restraints weight = 6622.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145004 restraints weight = 4757.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146556 restraints weight = 3648.178| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9038 Z= 0.166 Angle : 0.626 17.627 12276 Z= 0.320 Chirality : 0.042 0.166 1403 Planarity : 0.004 0.060 1536 Dihedral : 4.536 20.313 1235 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 0.96 (0.26), residues: 1133 helix: 2.85 (0.36), residues: 226 sheet: 1.15 (0.26), residues: 403 loop : -0.89 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 67 TYR 0.024 0.002 TYR D 55 PHE 0.027 0.002 PHE B 125 TRP 0.037 0.002 TRP H 36 HIS 0.008 0.002 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 9028) covalent geometry : angle 0.62383 / 0.32 (12256) SS BOND : bond 0.00750 / 0.35 ( 10) SS BOND : angle 1.50729 / 1.07 ( 20) hydrogen bonds : bond 0.04590 / 3.20 ( 391) hydrogen bonds : angle 4.69347 / 3.32 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8105 (tt) cc_final: 0.7887 (tt) REVERT: A 27 MET cc_start: 0.6775 (mpp) cc_final: 0.6480 (mpp) REVERT: A 29 GLN cc_start: 0.8351 (mp10) cc_final: 0.7909 (mp10) REVERT: A 75 MET cc_start: 0.7083 (mmp) cc_final: 0.6822 (mmp) REVERT: A 84 ILE cc_start: 0.8300 (mm) cc_final: 0.7865 (mm) REVERT: H 34 MET cc_start: 0.7619 (mmt) cc_final: 0.7354 (mmt) REVERT: H 60 TYR cc_start: 0.7121 (m-80) cc_final: 0.6463 (m-80) REVERT: H 98 ARG cc_start: 0.6945 (ptm-80) cc_final: 0.6705 (ptm-80) REVERT: H 99 MET cc_start: 0.7205 (ptp) cc_final: 0.6539 (ptp) REVERT: H 103 ASN cc_start: 0.8468 (t0) cc_final: 0.7911 (t0) REVERT: H 112 THR cc_start: 0.7364 (m) cc_final: 0.6752 (m) REVERT: L 27 GLN cc_start: 0.6962 (tm-30) cc_final: 0.6044 (tm-30) REVERT: L 29 LEU cc_start: 0.8020 (mt) cc_final: 0.7716 (mt) REVERT: L 67 ARG cc_start: 0.6821 (ttp-170) cc_final: 0.6282 (ttp-170) REVERT: C 39 GLN cc_start: 0.7792 (tp40) cc_final: 0.7423 (tp40) REVERT: C 74 LYS cc_start: 0.8579 (mppt) cc_final: 0.8350 (mppt) REVERT: C 90 ASP cc_start: 0.7065 (p0) cc_final: 0.6851 (p0) REVERT: C 103 ASN cc_start: 0.8081 (t0) cc_final: 0.7385 (t0) REVERT: C 110 GLN cc_start: 0.7847 (pm20) cc_final: 0.7424 (pm20) REVERT: C 112 THR cc_start: 0.7491 (m) cc_final: 0.6820 (m) REVERT: D 85 GLN cc_start: 0.7872 (pm20) cc_final: 0.7616 (pm20) REVERT: D 108 THR cc_start: 0.7515 (m) cc_final: 0.7290 (m) REVERT: D 109 LYS cc_start: 0.8080 (ptpp) cc_final: 0.7665 (ptpp) REVERT: D 151 LYS cc_start: 0.8091 (tttt) cc_final: 0.7753 (tttt) REVERT: B 22 ILE cc_start: 0.7712 (tt) cc_final: 0.7497 (tt) REVERT: B 27 MET cc_start: 0.6045 (tpp) cc_final: 0.5816 (tpp) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.0719 time to fit residues: 30.1707 Evaluate side-chains 277 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN H 160 ASN L 6 GLN C 39 GLN C 202 ASN D 6 GLN B 146 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.165534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133873 restraints weight = 16446.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138426 restraints weight = 10041.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141607 restraints weight = 6751.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143655 restraints weight = 4888.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145514 restraints weight = 3789.404| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9038 Z= 0.125 Angle : 0.593 16.318 12276 Z= 0.297 Chirality : 0.041 0.175 1403 Planarity : 0.004 0.055 1536 Dihedral : 4.366 21.597 1235 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 1.00 (0.26), residues: 1133 helix: 2.79 (0.36), residues: 226 sheet: 1.11 (0.26), residues: 411 loop : -0.77 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 67 TYR 0.024 0.001 TYR D 55 PHE 0.031 0.002 PHE B 139 TRP 0.023 0.002 TRP H 36 HIS 0.003 0.001 HIS L 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9028) covalent geometry : angle 0.59095 / 0.30 (12256) SS BOND : bond 0.00659 / 0.31 ( 10) SS BOND : angle 1.31556 / 0.87 ( 20) hydrogen bonds : bond 0.04049 / 2.82 ( 391) hydrogen bonds : angle 4.44709 / 3.15 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8418 (mp10) cc_final: 0.7987 (mp10) REVERT: A 75 MET cc_start: 0.7098 (mmp) cc_final: 0.6818 (mmp) REVERT: A 84 ILE cc_start: 0.8284 (mm) cc_final: 0.7938 (mm) REVERT: A 145 THR cc_start: 0.9037 (m) cc_final: 0.8823 (m) REVERT: H 6 GLN cc_start: 0.6793 (pt0) cc_final: 0.6468 (pt0) REVERT: H 35 ASN cc_start: 0.8198 (m-40) cc_final: 0.7945 (m-40) REVERT: H 55 TYR cc_start: 0.6773 (m-10) cc_final: 0.6552 (m-10) REVERT: H 60 TYR cc_start: 0.7076 (m-80) cc_final: 0.6364 (m-80) REVERT: H 98 ARG cc_start: 0.6906 (ptm-80) cc_final: 0.6692 (ptm-80) REVERT: H 99 MET cc_start: 0.7248 (ptp) cc_final: 0.6495 (ptp) REVERT: H 103 ASN cc_start: 0.8430 (t0) cc_final: 0.7855 (t0) REVERT: H 112 THR cc_start: 0.7403 (m) cc_final: 0.6753 (m) REVERT: H 184 SER cc_start: 0.7715 (t) cc_final: 0.7429 (t) REVERT: L 27 GLN cc_start: 0.6942 (tm-30) cc_final: 0.5982 (tm-30) REVERT: L 29 LEU cc_start: 0.8010 (mt) cc_final: 0.7713 (mt) REVERT: L 67 ARG cc_start: 0.6920 (ttp-170) cc_final: 0.6675 (ttp-170) REVERT: L 130 GLN cc_start: 0.8119 (tt0) cc_final: 0.7340 (pt0) REVERT: C 39 GLN cc_start: 0.7560 (tp-100) cc_final: 0.7031 (tp-100) REVERT: C 74 LYS cc_start: 0.8570 (mppt) cc_final: 0.8331 (mppt) REVERT: C 103 ASN cc_start: 0.8200 (t0) cc_final: 0.7573 (t0) REVERT: C 112 THR cc_start: 0.7499 (m) cc_final: 0.6828 (m) REVERT: C 169 HIS cc_start: 0.7195 (m90) cc_final: 0.6948 (m90) REVERT: D 24 LYS cc_start: 0.8277 (tptt) cc_final: 0.7846 (tptt) REVERT: D 85 GLN cc_start: 0.7881 (pm20) cc_final: 0.7628 (pm20) REVERT: D 108 THR cc_start: 0.7568 (m) cc_final: 0.7354 (m) REVERT: D 109 LYS cc_start: 0.8098 (ptpp) cc_final: 0.7731 (ptpp) REVERT: D 151 LYS cc_start: 0.8115 (tttt) cc_final: 0.7786 (tttt) REVERT: B 22 ILE cc_start: 0.7627 (tt) cc_final: 0.7426 (tt) REVERT: B 27 MET cc_start: 0.6156 (tpp) cc_final: 0.5880 (tpp) REVERT: B 89 LEU cc_start: 0.7616 (mt) cc_final: 0.7406 (mt) REVERT: B 191 MET cc_start: 0.7896 (ttp) cc_final: 0.7189 (ttp) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.0689 time to fit residues: 29.2276 Evaluate side-chains 284 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 85 optimal weight: 0.0020 chunk 1 optimal weight: 0.5980 overall best weight: 0.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN H 110 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN C 110 GLN D 6 GLN B 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.167285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135846 restraints weight = 16545.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.140463 restraints weight = 10066.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.143706 restraints weight = 6747.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.146077 restraints weight = 4851.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147753 restraints weight = 3682.342| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9038 Z= 0.102 Angle : 0.573 15.766 12276 Z= 0.283 Chirality : 0.040 0.167 1403 Planarity : 0.004 0.051 1536 Dihedral : 4.172 19.432 1235 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 1.01 (0.26), residues: 1133 helix: 2.73 (0.36), residues: 226 sheet: 1.14 (0.25), residues: 411 loop : -0.75 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.015 0.001 TYR D 55 PHE 0.029 0.001 PHE B 125 TRP 0.020 0.001 TRP H 36 HIS 0.008 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 9028) covalent geometry : angle 0.57090 / 0.28 (12256) SS BOND : bond 0.00540 / 0.26 ( 10) SS BOND : angle 1.27648 / 0.82 ( 20) hydrogen bonds : bond 0.03549 / 2.48 ( 391) hydrogen bonds : angle 4.20095 / 2.99 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7963 (tt) cc_final: 0.7758 (tt) REVERT: A 27 MET cc_start: 0.6769 (mpp) cc_final: 0.6558 (mpp) REVERT: A 29 GLN cc_start: 0.8397 (mp10) cc_final: 0.7897 (mp10) REVERT: A 84 ILE cc_start: 0.8229 (mm) cc_final: 0.7864 (mm) REVERT: A 145 THR cc_start: 0.9031 (m) cc_final: 0.8830 (m) REVERT: H 6 GLN cc_start: 0.6690 (pt0) cc_final: 0.6437 (pt0) REVERT: H 35 ASN cc_start: 0.8136 (m-40) cc_final: 0.7834 (m-40) REVERT: H 60 TYR cc_start: 0.7005 (m-80) cc_final: 0.6374 (m-80) REVERT: H 98 ARG cc_start: 0.6885 (ptm-80) cc_final: 0.6671 (ptm-80) REVERT: H 99 MET cc_start: 0.7221 (ptp) cc_final: 0.6411 (ptp) REVERT: H 103 ASN cc_start: 0.8358 (t0) cc_final: 0.7807 (t0) REVERT: H 112 THR cc_start: 0.7314 (m) cc_final: 0.6779 (m) REVERT: H 184 SER cc_start: 0.7667 (t) cc_final: 0.7396 (t) REVERT: L 27 GLN cc_start: 0.6756 (tm-30) cc_final: 0.5921 (tm-30) REVERT: L 29 LEU cc_start: 0.8050 (mt) cc_final: 0.7827 (mt) REVERT: L 130 GLN cc_start: 0.8034 (tt0) cc_final: 0.7320 (pt0) REVERT: C 74 LYS cc_start: 0.8533 (mppt) cc_final: 0.8283 (mppt) REVERT: C 103 ASN cc_start: 0.8172 (t0) cc_final: 0.7591 (t0) REVERT: C 112 THR cc_start: 0.7195 (m) cc_final: 0.6591 (m) REVERT: C 169 HIS cc_start: 0.7152 (m90) cc_final: 0.6913 (m-70) REVERT: D 24 LYS cc_start: 0.8314 (tptt) cc_final: 0.7728 (tptt) REVERT: D 27 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6317 (tm-30) REVERT: D 51 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7772 (ptpt) REVERT: D 85 GLN cc_start: 0.7919 (pm20) cc_final: 0.7624 (pm20) REVERT: D 109 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7721 (ptpp) REVERT: D 151 LYS cc_start: 0.8132 (tttt) cc_final: 0.7781 (tttt) REVERT: B 22 ILE cc_start: 0.7578 (tt) cc_final: 0.7362 (tt) REVERT: B 27 MET cc_start: 0.6063 (tpp) cc_final: 0.5816 (tpp) REVERT: B 89 LEU cc_start: 0.7622 (mt) cc_final: 0.7369 (mt) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.0726 time to fit residues: 30.4917 Evaluate side-chains 285 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 86 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN B 29 GLN B 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133864 restraints weight = 16634.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138568 restraints weight = 10091.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141870 restraints weight = 6794.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144239 restraints weight = 4933.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145768 restraints weight = 3786.564| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9038 Z= 0.128 Angle : 0.600 16.331 12276 Z= 0.299 Chirality : 0.041 0.172 1403 Planarity : 0.004 0.054 1536 Dihedral : 4.248 21.088 1235 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 0.92 (0.26), residues: 1133 helix: 2.58 (0.36), residues: 226 sheet: 1.12 (0.26), residues: 407 loop : -0.79 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.019 0.001 TYR H 54 PHE 0.032 0.002 PHE B 125 TRP 0.043 0.002 TRP H 36 HIS 0.003 0.001 HIS L 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9028) covalent geometry : angle 0.59732 / 0.30 (12256) SS BOND : bond 0.00675 / 0.32 ( 10) SS BOND : angle 1.58281 / 1.11 ( 20) hydrogen bonds : bond 0.04024 / 2.82 ( 391) hydrogen bonds : angle 4.35894 / 3.11 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.302 Fit side-chains REVERT: A 22 ILE cc_start: 0.8045 (tt) cc_final: 0.7823 (tt) REVERT: A 29 GLN cc_start: 0.8298 (mp10) cc_final: 0.7867 (mp10) REVERT: H 35 ASN cc_start: 0.7954 (m-40) cc_final: 0.7588 (m-40) REVERT: H 60 TYR cc_start: 0.7119 (m-80) cc_final: 0.6374 (m-80) REVERT: H 99 MET cc_start: 0.7206 (ptp) cc_final: 0.6468 (ptp) REVERT: H 103 ASN cc_start: 0.8322 (t0) cc_final: 0.7806 (t0) REVERT: L 27 GLN cc_start: 0.6896 (tm-30) cc_final: 0.5938 (tm-30) REVERT: L 29 LEU cc_start: 0.7974 (mt) cc_final: 0.7715 (mt) REVERT: L 67 ARG cc_start: 0.6808 (ttp-170) cc_final: 0.6258 (ttp-170) REVERT: L 108 THR cc_start: 0.7956 (m) cc_final: 0.7734 (m) REVERT: C 39 GLN cc_start: 0.7670 (tp-100) cc_final: 0.7332 (tp-100) REVERT: C 103 ASN cc_start: 0.8098 (t0) cc_final: 0.7553 (t0) REVERT: C 112 THR cc_start: 0.7367 (m) cc_final: 0.6725 (m) REVERT: C 169 HIS cc_start: 0.7223 (m90) cc_final: 0.6985 (m90) REVERT: D 24 LYS cc_start: 0.8300 (tptt) cc_final: 0.7769 (tptt) REVERT: D 27 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6424 (tm-30) REVERT: D 85 GLN cc_start: 0.7934 (pm20) cc_final: 0.7671 (pm20) REVERT: D 108 THR cc_start: 0.7551 (m) cc_final: 0.7311 (m) REVERT: D 109 LYS cc_start: 0.8069 (ptpp) cc_final: 0.7680 (ptpp) REVERT: D 151 LYS cc_start: 0.8101 (tttt) cc_final: 0.7759 (tttt) REVERT: D 173 ASP cc_start: 0.8734 (t70) cc_final: 0.8526 (t70) REVERT: B 22 ILE cc_start: 0.7641 (tt) cc_final: 0.7419 (tt) REVERT: B 27 MET cc_start: 0.6057 (tpp) cc_final: 0.5780 (tpp) REVERT: B 29 GLN cc_start: 0.8138 (mp10) cc_final: 0.7619 (mp10) REVERT: B 55 ARG cc_start: 0.7702 (ptt90) cc_final: 0.7499 (ptt-90) REVERT: B 89 LEU cc_start: 0.7665 (mt) cc_final: 0.7418 (mt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.0679 time to fit residues: 29.0339 Evaluate side-chains 288 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 94 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN L 22 ASN L 44 GLN C 110 GLN D 22 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.169360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138035 restraints weight = 16734.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142405 restraints weight = 10434.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145508 restraints weight = 7139.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147568 restraints weight = 5242.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149307 restraints weight = 4113.228| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9038 Z= 0.100 Angle : 0.581 15.866 12276 Z= 0.287 Chirality : 0.041 0.148 1403 Planarity : 0.004 0.051 1536 Dihedral : 4.101 19.460 1235 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 0.97 (0.26), residues: 1133 helix: 2.62 (0.36), residues: 226 sheet: 1.15 (0.26), residues: 411 loop : -0.76 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.014 0.001 TYR L 55 PHE 0.034 0.002 PHE A 139 TRP 0.034 0.002 TRP H 36 HIS 0.009 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 9028) covalent geometry : angle 0.57932 / 0.29 (12256) SS BOND : bond 0.00532 / 0.26 ( 10) SS BOND : angle 1.23855 / 0.85 ( 20) hydrogen bonds : bond 0.03461 / 2.46 ( 391) hydrogen bonds : angle 4.15186 / 2.96 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.325 Fit side-chains REVERT: A 22 ILE cc_start: 0.7976 (tt) cc_final: 0.7769 (tt) REVERT: A 27 MET cc_start: 0.6434 (mmt) cc_final: 0.6162 (mmt) REVERT: A 29 GLN cc_start: 0.8400 (mp10) cc_final: 0.7770 (mp10) REVERT: A 75 MET cc_start: 0.6952 (mmp) cc_final: 0.6539 (mmp) REVERT: A 84 ILE cc_start: 0.8156 (mm) cc_final: 0.7796 (mm) REVERT: A 191 MET cc_start: 0.7774 (ttt) cc_final: 0.7418 (ttt) REVERT: H 35 ASN cc_start: 0.7928 (m-40) cc_final: 0.7497 (m-40) REVERT: H 99 MET cc_start: 0.7216 (ptp) cc_final: 0.6629 (ptp) REVERT: H 103 ASN cc_start: 0.8306 (t0) cc_final: 0.7884 (t0) REVERT: H 184 SER cc_start: 0.7762 (t) cc_final: 0.7550 (t) REVERT: H 205 HIS cc_start: 0.7303 (t-170) cc_final: 0.7024 (t-170) REVERT: L 27 GLN cc_start: 0.6789 (tm-30) cc_final: 0.5958 (tm-30) REVERT: L 109 LYS cc_start: 0.8293 (ttpp) cc_final: 0.7949 (ttpp) REVERT: L 130 GLN cc_start: 0.8047 (tt0) cc_final: 0.7337 (pt0) REVERT: C 39 GLN cc_start: 0.7530 (tp-100) cc_final: 0.6947 (tp-100) REVERT: C 74 LYS cc_start: 0.8501 (mppt) cc_final: 0.8267 (mppt) REVERT: C 103 ASN cc_start: 0.8110 (t0) cc_final: 0.7567 (t0) REVERT: C 112 THR cc_start: 0.7225 (m) cc_final: 0.6593 (m) REVERT: C 169 HIS cc_start: 0.7244 (m90) cc_final: 0.7002 (m90) REVERT: D 24 LYS cc_start: 0.8324 (tptt) cc_final: 0.8078 (tptt) REVERT: D 27 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6374 (tm-30) REVERT: D 51 LYS cc_start: 0.8010 (ptpt) cc_final: 0.7514 (ptpt) REVERT: D 85 GLN cc_start: 0.7899 (pm20) cc_final: 0.7596 (pm20) REVERT: D 108 THR cc_start: 0.7475 (m) cc_final: 0.7258 (m) REVERT: D 109 LYS cc_start: 0.8084 (ptpp) cc_final: 0.7684 (ptpp) REVERT: D 151 LYS cc_start: 0.8105 (tttt) cc_final: 0.7754 (tttt) REVERT: D 173 ASP cc_start: 0.8760 (t70) cc_final: 0.8434 (t70) REVERT: B 22 ILE cc_start: 0.7599 (tt) cc_final: 0.7387 (tt) REVERT: B 27 MET cc_start: 0.5997 (tpp) cc_final: 0.5656 (tpp) REVERT: B 84 ILE cc_start: 0.8143 (mm) cc_final: 0.7834 (mm) REVERT: B 89 LEU cc_start: 0.7618 (mt) cc_final: 0.7358 (mt) REVERT: B 191 MET cc_start: 0.7806 (ttp) cc_final: 0.7153 (ttp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.0750 time to fit residues: 31.1990 Evaluate side-chains 280 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 94 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 0.0670 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN C 110 GLN D 22 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.169874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138704 restraints weight = 16968.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143111 restraints weight = 10508.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146279 restraints weight = 7143.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.148451 restraints weight = 5199.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.150110 restraints weight = 4016.687| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9038 Z= 0.099 Angle : 0.580 15.790 12276 Z= 0.285 Chirality : 0.040 0.151 1403 Planarity : 0.004 0.048 1536 Dihedral : 4.039 19.832 1235 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 0.98 (0.26), residues: 1133 helix: 2.50 (0.36), residues: 226 sheet: 1.30 (0.26), residues: 393 loop : -0.75 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 67 TYR 0.013 0.001 TYR D 98 PHE 0.032 0.001 PHE B 125 TRP 0.027 0.001 TRP H 36 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 9028) covalent geometry : angle 0.57843 / 0.28 (12256) SS BOND : bond 0.00481 / 0.24 ( 10) SS BOND : angle 1.10350 / 0.75 ( 20) hydrogen bonds : bond 0.03402 / 2.41 ( 391) hydrogen bonds : angle 4.09063 / 2.92 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.6449 (mmt) cc_final: 0.6160 (mmt) REVERT: A 29 GLN cc_start: 0.8383 (mp10) cc_final: 0.7601 (mp10) REVERT: A 84 ILE cc_start: 0.8145 (mm) cc_final: 0.7800 (mm) REVERT: A 191 MET cc_start: 0.7769 (ttt) cc_final: 0.7468 (ttt) REVERT: H 35 ASN cc_start: 0.7875 (m-40) cc_final: 0.7490 (m-40) REVERT: H 99 MET cc_start: 0.7173 (ptp) cc_final: 0.6591 (ptp) REVERT: H 103 ASN cc_start: 0.8289 (t0) cc_final: 0.7910 (t0) REVERT: H 184 SER cc_start: 0.7733 (t) cc_final: 0.7522 (t) REVERT: L 18 ARG cc_start: 0.7754 (tmm-80) cc_final: 0.7548 (ttt-90) REVERT: L 27 GLN cc_start: 0.6890 (tm-30) cc_final: 0.5878 (tm-30) REVERT: L 29 LEU cc_start: 0.7827 (mt) cc_final: 0.7575 (mt) REVERT: L 109 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7937 (ttpp) REVERT: L 130 GLN cc_start: 0.8036 (tt0) cc_final: 0.7377 (pt0) REVERT: L 173 ASP cc_start: 0.8164 (t70) cc_final: 0.7762 (t0) REVERT: C 39 GLN cc_start: 0.7611 (tp-100) cc_final: 0.7081 (tp-100) REVERT: C 74 LYS cc_start: 0.8487 (mppt) cc_final: 0.8251 (mppt) REVERT: C 103 ASN cc_start: 0.8074 (t0) cc_final: 0.7588 (t0) REVERT: C 112 THR cc_start: 0.7167 (m) cc_final: 0.6529 (m) REVERT: C 169 HIS cc_start: 0.7266 (m90) cc_final: 0.7002 (m90) REVERT: D 24 LYS cc_start: 0.8331 (tptt) cc_final: 0.8124 (tptt) REVERT: D 51 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7504 (ptpt) REVERT: D 85 GLN cc_start: 0.7887 (pm20) cc_final: 0.7668 (pm20) REVERT: D 108 THR cc_start: 0.7478 (m) cc_final: 0.7229 (m) REVERT: D 109 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7678 (ptpp) REVERT: D 151 LYS cc_start: 0.8119 (tttt) cc_final: 0.7777 (tttt) REVERT: D 173 ASP cc_start: 0.8767 (t70) cc_final: 0.8370 (t70) REVERT: B 22 ILE cc_start: 0.7568 (tt) cc_final: 0.7340 (tt) REVERT: B 27 MET cc_start: 0.6007 (tpp) cc_final: 0.5674 (tpp) REVERT: B 47 GLN cc_start: 0.7680 (tt0) cc_final: 0.7254 (tt0) REVERT: B 89 LEU cc_start: 0.7641 (mt) cc_final: 0.7373 (mt) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.0831 time to fit residues: 34.8253 Evaluate side-chains 284 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 0.0040 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 110 optimal weight: 0.0770 chunk 87 optimal weight: 0.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN C 110 GLN D 22 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.170065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138620 restraints weight = 16711.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143027 restraints weight = 10321.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146160 restraints weight = 7026.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148398 restraints weight = 5152.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149806 restraints weight = 3979.789| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9038 Z= 0.104 Angle : 0.580 15.908 12276 Z= 0.288 Chirality : 0.041 0.155 1403 Planarity : 0.004 0.049 1536 Dihedral : 4.036 23.511 1235 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 1.08 (0.26), residues: 1133 helix: 2.64 (0.36), residues: 226 sheet: 1.34 (0.27), residues: 397 loop : -0.72 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 87 TYR 0.013 0.001 TYR D 55 PHE 0.031 0.001 PHE A 139 TRP 0.044 0.002 TRP H 36 HIS 0.002 0.001 HIS L 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 9028) covalent geometry : angle 0.57925 / 0.29 (12256) SS BOND : bond 0.00511 / 0.26 ( 10) SS BOND : angle 1.07800 / 0.69 ( 20) hydrogen bonds : bond 0.03496 / 2.46 ( 391) hydrogen bonds : angle 4.11571 / 2.95 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 CYS cc_start: 0.6792 (m) cc_final: 0.6557 (m) REVERT: A 27 MET cc_start: 0.6481 (mmt) cc_final: 0.6276 (mmt) REVERT: A 29 GLN cc_start: 0.8394 (mp10) cc_final: 0.7527 (mp10) REVERT: A 55 ARG cc_start: 0.7868 (ptt90) cc_final: 0.7620 (ppt170) REVERT: A 84 ILE cc_start: 0.8143 (mm) cc_final: 0.7786 (mm) REVERT: A 191 MET cc_start: 0.7803 (ttt) cc_final: 0.7402 (ttt) REVERT: H 35 ASN cc_start: 0.7855 (m-40) cc_final: 0.7522 (m-40) REVERT: H 60 TYR cc_start: 0.6580 (m-10) cc_final: 0.6081 (m-80) REVERT: H 99 MET cc_start: 0.7162 (ptp) cc_final: 0.6547 (ptp) REVERT: H 103 ASN cc_start: 0.8297 (t0) cc_final: 0.7941 (t0) REVERT: H 184 SER cc_start: 0.7676 (t) cc_final: 0.7446 (t) REVERT: L 18 ARG cc_start: 0.7787 (tmm-80) cc_final: 0.7566 (ttt-90) REVERT: L 27 GLN cc_start: 0.6753 (tm-30) cc_final: 0.5867 (tm-30) REVERT: L 108 THR cc_start: 0.7871 (m) cc_final: 0.7656 (m) REVERT: L 109 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7950 (ttpp) REVERT: L 130 GLN cc_start: 0.8016 (tt0) cc_final: 0.7353 (pt0) REVERT: L 173 ASP cc_start: 0.8070 (t70) cc_final: 0.7660 (t0) REVERT: C 39 GLN cc_start: 0.7667 (tp-100) cc_final: 0.7344 (tp-100) REVERT: C 74 LYS cc_start: 0.8501 (mppt) cc_final: 0.8250 (mppt) REVERT: C 103 ASN cc_start: 0.8081 (t0) cc_final: 0.7611 (t0) REVERT: C 112 THR cc_start: 0.7191 (m) cc_final: 0.6551 (m) REVERT: C 169 HIS cc_start: 0.7300 (m90) cc_final: 0.7009 (m90) REVERT: D 24 LYS cc_start: 0.8360 (tptt) cc_final: 0.8136 (tptt) REVERT: D 51 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7494 (ptpt) REVERT: D 85 GLN cc_start: 0.7944 (pm20) cc_final: 0.7726 (pm20) REVERT: D 151 LYS cc_start: 0.8125 (tttt) cc_final: 0.7752 (tttt) REVERT: D 173 ASP cc_start: 0.8775 (t70) cc_final: 0.8444 (t70) REVERT: B 22 ILE cc_start: 0.7618 (tt) cc_final: 0.7396 (tt) REVERT: B 27 MET cc_start: 0.6039 (tpp) cc_final: 0.5703 (tpp) REVERT: B 47 GLN cc_start: 0.7656 (tt0) cc_final: 0.7207 (tt0) REVERT: B 75 MET cc_start: 0.7591 (mmp) cc_final: 0.7310 (mmp) REVERT: B 89 LEU cc_start: 0.7676 (mt) cc_final: 0.7372 (mt) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.0819 time to fit residues: 34.8766 Evaluate side-chains 284 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 0.0030 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 90 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN C 110 GLN D 6 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.164672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132559 restraints weight = 16481.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137135 restraints weight = 10081.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140350 restraints weight = 6811.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142645 restraints weight = 4960.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.144281 restraints weight = 3820.410| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9038 Z= 0.187 Angle : 0.668 16.944 12276 Z= 0.342 Chirality : 0.043 0.164 1403 Planarity : 0.005 0.054 1536 Dihedral : 4.509 27.616 1235 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 0.95 (0.26), residues: 1133 helix: 2.59 (0.36), residues: 227 sheet: 1.25 (0.27), residues: 389 loop : -0.79 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 67 TYR 0.025 0.002 TYR L 55 PHE 0.034 0.002 PHE A 139 TRP 0.083 0.003 TRP H 36 HIS 0.004 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 ( 9028) covalent geometry : angle 0.66536 / 0.34 (12256) SS BOND : bond 0.00877 / 0.41 ( 10) SS BOND : angle 1.58063 / 0.99 ( 20) hydrogen bonds : bond 0.04721 / 3.33 ( 391) hydrogen bonds : angle 4.64895 / 3.33 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.6606 (mmt) cc_final: 0.6305 (mmt) REVERT: A 29 GLN cc_start: 0.8415 (mp10) cc_final: 0.7502 (mp10) REVERT: A 84 ILE cc_start: 0.8211 (mm) cc_final: 0.7853 (mm) REVERT: A 145 THR cc_start: 0.9099 (m) cc_final: 0.8895 (m) REVERT: A 191 MET cc_start: 0.7878 (ttt) cc_final: 0.7513 (ttt) REVERT: H 30 THR cc_start: 0.8393 (m) cc_final: 0.8044 (t) REVERT: H 35 ASN cc_start: 0.7706 (m-40) cc_final: 0.7499 (m-40) REVERT: H 98 ARG cc_start: 0.6866 (ptm-80) cc_final: 0.6662 (ptm-80) REVERT: H 99 MET cc_start: 0.7187 (ptp) cc_final: 0.6339 (ptp) REVERT: H 103 ASN cc_start: 0.8318 (t0) cc_final: 0.7795 (t0) REVERT: L 27 GLN cc_start: 0.6959 (tm-30) cc_final: 0.6171 (tm-30) REVERT: L 108 THR cc_start: 0.7930 (m) cc_final: 0.7708 (m) REVERT: L 130 GLN cc_start: 0.8003 (tt0) cc_final: 0.7337 (pt0) REVERT: L 173 ASP cc_start: 0.8132 (t70) cc_final: 0.7734 (t0) REVERT: C 39 GLN cc_start: 0.7760 (tp-100) cc_final: 0.7368 (tp-100) REVERT: C 103 ASN cc_start: 0.8119 (t0) cc_final: 0.7559 (t0) REVERT: C 112 THR cc_start: 0.7511 (m) cc_final: 0.6885 (m) REVERT: C 127 PHE cc_start: 0.7495 (m-10) cc_final: 0.7283 (m-10) REVERT: C 169 HIS cc_start: 0.7105 (m90) cc_final: 0.6872 (m90) REVERT: D 24 LYS cc_start: 0.8312 (tptt) cc_final: 0.7734 (tptt) REVERT: D 27 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6384 (tm-30) REVERT: D 51 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7582 (ptpt) REVERT: D 85 GLN cc_start: 0.8002 (pm20) cc_final: 0.7751 (pm20) REVERT: D 151 LYS cc_start: 0.8099 (tttt) cc_final: 0.7782 (tttt) REVERT: D 173 ASP cc_start: 0.8809 (t70) cc_final: 0.8463 (t70) REVERT: B 22 ILE cc_start: 0.7724 (tt) cc_final: 0.7488 (tt) REVERT: B 27 MET cc_start: 0.6143 (tpp) cc_final: 0.5817 (tpp) REVERT: B 75 MET cc_start: 0.7737 (mmp) cc_final: 0.7494 (mmp) REVERT: B 89 LEU cc_start: 0.7699 (mt) cc_final: 0.7426 (mt) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.0790 time to fit residues: 34.4914 Evaluate side-chains 289 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 17 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN C 110 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.167210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135449 restraints weight = 16618.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139998 restraints weight = 10229.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.143130 restraints weight = 6926.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145453 restraints weight = 5042.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147145 restraints weight = 3881.305| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9038 Z= 0.120 Angle : 0.623 16.494 12276 Z= 0.310 Chirality : 0.042 0.166 1403 Planarity : 0.004 0.055 1536 Dihedral : 4.311 24.261 1235 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 1.02 (0.26), residues: 1133 helix: 2.68 (0.36), residues: 227 sheet: 1.17 (0.26), residues: 407 loop : -0.73 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 55 TYR 0.016 0.001 TYR L 55 PHE 0.032 0.001 PHE A 139 TRP 0.073 0.002 TRP H 36 HIS 0.007 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9028) covalent geometry : angle 0.62131 / 0.31 (12256) SS BOND : bond 0.00692 / 0.33 ( 10) SS BOND : angle 1.39413 / 0.91 ( 20) hydrogen bonds : bond 0.04024 / 2.84 ( 391) hydrogen bonds : angle 4.43566 / 3.18 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.320 Fit side-chains REVERT: A 27 MET cc_start: 0.6543 (mmt) cc_final: 0.6292 (mmt) REVERT: A 29 GLN cc_start: 0.8415 (mp10) cc_final: 0.7500 (mp10) REVERT: A 145 THR cc_start: 0.9109 (m) cc_final: 0.8903 (m) REVERT: A 191 MET cc_start: 0.7847 (ttt) cc_final: 0.7446 (ttt) REVERT: H 35 ASN cc_start: 0.7828 (m-40) cc_final: 0.7486 (m-40) REVERT: H 99 MET cc_start: 0.7183 (ptp) cc_final: 0.6440 (ptp) REVERT: H 103 ASN cc_start: 0.8279 (t0) cc_final: 0.7736 (t0) REVERT: L 27 GLN cc_start: 0.6772 (tm-30) cc_final: 0.6117 (tm-30) REVERT: L 67 ARG cc_start: 0.6405 (ttp-170) cc_final: 0.6188 (ttp-170) REVERT: L 108 THR cc_start: 0.7954 (m) cc_final: 0.7669 (m) REVERT: L 130 GLN cc_start: 0.7974 (tt0) cc_final: 0.7278 (pt0) REVERT: L 173 ASP cc_start: 0.8168 (t70) cc_final: 0.7777 (t0) REVERT: C 39 GLN cc_start: 0.7575 (tp-100) cc_final: 0.6996 (tp-100) REVERT: C 103 ASN cc_start: 0.8012 (t0) cc_final: 0.7475 (t0) REVERT: C 112 THR cc_start: 0.7412 (m) cc_final: 0.6796 (m) REVERT: C 169 HIS cc_start: 0.7174 (m90) cc_final: 0.6889 (m90) REVERT: D 24 LYS cc_start: 0.8371 (tptt) cc_final: 0.8045 (tptt) REVERT: D 27 GLN cc_start: 0.7294 (tm-30) cc_final: 0.6416 (tm-30) REVERT: D 51 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7552 (ptpt) REVERT: D 85 GLN cc_start: 0.7912 (pm20) cc_final: 0.7599 (pm20) REVERT: D 108 THR cc_start: 0.7500 (m) cc_final: 0.7276 (m) REVERT: D 151 LYS cc_start: 0.8077 (tttt) cc_final: 0.7738 (tttt) REVERT: D 170 THR cc_start: 0.8109 (t) cc_final: 0.7644 (p) REVERT: D 173 ASP cc_start: 0.8803 (t70) cc_final: 0.8462 (t70) REVERT: B 22 ILE cc_start: 0.7634 (tt) cc_final: 0.7408 (tt) REVERT: B 27 MET cc_start: 0.6120 (tpp) cc_final: 0.5785 (tpp) REVERT: B 47 GLN cc_start: 0.7458 (tt0) cc_final: 0.7119 (tt0) REVERT: B 75 MET cc_start: 0.7718 (mmp) cc_final: 0.7420 (mmp) REVERT: B 89 LEU cc_start: 0.7642 (mt) cc_final: 0.7343 (mt) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.0757 time to fit residues: 32.6463 Evaluate side-chains 289 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 0.0770 chunk 52 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.0470 chunk 101 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.1636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN C 110 GLN D 22 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.170087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138678 restraints weight = 16649.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143097 restraints weight = 10327.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146280 restraints weight = 7060.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148603 restraints weight = 5164.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150038 restraints weight = 3979.531| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9038 Z= 0.104 Angle : 0.607 16.058 12276 Z= 0.300 Chirality : 0.041 0.161 1403 Planarity : 0.004 0.048 1536 Dihedral : 4.133 24.258 1235 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.83 % 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: 1.02 (0.26), residues: 1133 helix: 2.62 (0.36), residues: 227 sheet: 1.27 (0.26), residues: 395 loop : -0.74 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 55 TYR 0.012 0.001 TYR C 95 PHE 0.036 0.002 PHE B 125 TRP 0.098 0.002 TRP H 36 HIS 0.011 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 9028) covalent geometry : angle 0.60552 / 0.30 (12256) SS BOND : bond 0.00581 / 0.29 ( 10) SS BOND : angle 1.14482 / 0.69 ( 20) hydrogen bonds : bond 0.03475 / 2.45 ( 391) hydrogen bonds : angle 4.23480 / 3.06 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1607.05 seconds wall clock time: 28 minutes 27.55 seconds (1707.55 seconds total)