Starting phenix.real_space_refine on Sat Aug 23 00:07:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ote_17176/08_2025/8ote_17176.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ote_17176/08_2025/8ote_17176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ote_17176/08_2025/8ote_17176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ote_17176/08_2025/8ote_17176.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ote_17176/08_2025/8ote_17176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ote_17176/08_2025/8ote_17176.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 56 5.16 5 C 5544 2.51 5 N 1384 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8680 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "D" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "E" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "F" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "G" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "H" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 2.23, per 1000 atoms: 0.26 Number of scatterers: 8680 At special positions: 0 Unit cell: (191.992, 144.2, 36.256, 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 56 16.00 O 1696 8.00 N 1384 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 253 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 253 " distance=2.04 Simple disulfide: pdb=" SG CYS F 214 " - pdb=" SG CYS F 253 " distance=2.04 Simple disulfide: pdb=" SG CYS G 214 " - pdb=" SG CYS G 253 " distance=2.04 Simple disulfide: pdb=" SG CYS H 214 " - pdb=" SG CYS H 253 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 461.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 23 sheets defined 0.0% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 121 through 126 removed outlier: 6.905A pdb=" N ASP A 122 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A 121 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N LYS C 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 123 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE C 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR A 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE C 121 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N LYS G 124 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 123 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE G 126 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR C 125 " --> pdb=" O ILE G 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 129 through 130 removed outlier: 6.680A pdb=" N LYS A 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS C 129 " --> pdb=" O SER G 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.797A pdb=" N ILE E 146 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A 147 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN E 148 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N LEU A 144 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR C 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N ILE A 146 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N LEU C 144 " --> pdb=" O ASN G 145 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR G 147 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N ILE C 146 " --> pdb=" O THR G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 155 through 157 removed outlier: 6.668A pdb=" N ASN A 156 " --> pdb=" O TYR E 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 163 through 165 removed outlier: 6.409A pdb=" N GLU A 163 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 168 through 175 removed outlier: 6.894A pdb=" N VAL A 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N SER C 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE A 171 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR C 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 173 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 169 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N SER G 172 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE C 171 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR G 174 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS C 173 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 180 through 181 removed outlier: 6.644A pdb=" N ARG A 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG C 180 " --> pdb=" O LEU G 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.876A pdb=" N ILE A 184 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE E 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE A 186 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 201 through 206 removed outlier: 6.795A pdb=" N THR A 201 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ALA E 204 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 203 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLU E 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 205 " --> pdb=" O GLU E 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 224 through 230 removed outlier: 6.165A pdb=" N VAL A 225 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N MET E 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N MET A 227 " --> pdb=" O MET E 228 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL E 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLN A 229 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 230 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 230 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 235 through 237 removed outlier: 6.439A pdb=" N THR A 235 " --> pdb=" O TYR E 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 246 through 247 removed outlier: 6.278A pdb=" N GLU A 246 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU C 246 " --> pdb=" O ARG G 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 121 through 126 removed outlier: 6.902A pdb=" N ASP B 122 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE B 121 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N LYS D 124 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 123 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE D 126 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR B 125 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE D 121 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N LYS H 124 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 123 " --> pdb=" O LYS H 124 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE H 126 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR D 125 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 129 through 130 removed outlier: 6.678A pdb=" N LYS B 129 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS D 129 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 147 through 148 removed outlier: 6.128A pdb=" N THR B 147 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR D 147 " --> pdb=" O ASN H 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 155 through 157 removed outlier: 6.663A pdb=" N ASN B 156 " --> pdb=" O TYR F 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 165 removed outlier: 6.418A pdb=" N GLU B 163 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 168 through 175 removed outlier: 6.931A pdb=" N VAL B 169 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER D 172 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 171 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR D 174 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS B 173 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL D 169 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 172 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE D 171 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR H 174 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS D 173 " --> pdb=" O THR H 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 180 through 181 removed outlier: 6.650A pdb=" N ARG B 180 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG D 180 " --> pdb=" O LEU H 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.903A pdb=" N ILE B 184 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE F 187 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE B 186 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 201 through 204 removed outlier: 6.792A pdb=" N THR B 201 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ALA F 204 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 203 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 224 through 230 removed outlier: 6.161A pdb=" N VAL B 225 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N MET F 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET B 227 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN B 229 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 230 " --> pdb=" O GLN D 229 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 230 " --> pdb=" O GLN H 229 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 247 removed outlier: 6.274A pdb=" N GLU B 246 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU D 246 " --> pdb=" O ARG H 247 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 294 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: 1.30 Time building geometry restraints manager: 0.92 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: 1852 1.34 - 1.46: 2574 1.46 - 1.58: 4302 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 8824 Sorted by residual: bond pdb=" CA SER A 130 " pdb=" CB SER A 130 " ideal model delta sigma weight residual 1.534 1.478 0.056 1.76e-02 3.23e+03 1.02e+01 bond pdb=" CA SER G 130 " pdb=" CB SER G 130 " ideal model delta sigma weight residual 1.534 1.478 0.056 1.76e-02 3.23e+03 1.01e+01 bond pdb=" CA SER E 130 " pdb=" CB SER E 130 " ideal model delta sigma weight residual 1.534 1.478 0.056 1.76e-02 3.23e+03 9.96e+00 bond pdb=" CA SER C 130 " pdb=" CB SER C 130 " ideal model delta sigma weight residual 1.534 1.478 0.055 1.76e-02 3.23e+03 9.89e+00 bond pdb=" CA SER H 130 " pdb=" CB SER H 130 " ideal model delta sigma weight residual 1.533 1.476 0.057 1.82e-02 3.02e+03 9.66e+00 ... (remaining 8819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8740 1.61 - 3.22: 2385 3.22 - 4.84: 686 4.84 - 6.45: 165 6.45 - 8.06: 16 Bond angle restraints: 11992 Sorted by residual: angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" C GLU C 246 " ideal model delta sigma weight residual 108.14 116.20 -8.06 1.52e+00 4.33e-01 2.81e+01 angle pdb=" N GLU G 246 " pdb=" CA GLU G 246 " pdb=" C GLU G 246 " ideal model delta sigma weight residual 108.14 116.19 -8.05 1.52e+00 4.33e-01 2.81e+01 angle pdb=" N GLU A 246 " pdb=" CA GLU A 246 " pdb=" C GLU A 246 " ideal model delta sigma weight residual 108.14 116.19 -8.05 1.52e+00 4.33e-01 2.80e+01 angle pdb=" N GLU E 246 " pdb=" CA GLU E 246 " pdb=" C GLU E 246 " ideal model delta sigma weight residual 108.14 116.18 -8.04 1.52e+00 4.33e-01 2.80e+01 angle pdb=" CA ASP F 252 " pdb=" CB ASP F 252 " pdb=" CG ASP F 252 " ideal model delta sigma weight residual 112.60 117.87 -5.27 1.00e+00 1.00e+00 2.78e+01 ... (remaining 11987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.48: 4285 14.48 - 28.95: 683 28.95 - 43.42: 196 43.42 - 57.90: 116 57.90 - 72.37: 40 Dihedral angle restraints: 5320 sinusoidal: 2072 harmonic: 3248 Sorted by residual: dihedral pdb=" CA ALA G 131 " pdb=" C ALA G 131 " pdb=" N TYR G 132 " pdb=" CA TYR G 132 " ideal model delta harmonic sigma weight residual 180.00 149.61 30.39 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA ALA H 131 " pdb=" C ALA H 131 " pdb=" N TYR H 132 " pdb=" CA TYR H 132 " ideal model delta harmonic sigma weight residual 180.00 149.65 30.35 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA ALA A 131 " pdb=" C ALA A 131 " pdb=" N TYR A 132 " pdb=" CA TYR A 132 " ideal model delta harmonic sigma weight residual 180.00 149.65 30.35 0 5.00e+00 4.00e-02 3.68e+01 ... (remaining 5317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 508 0.056 - 0.112: 557 0.112 - 0.169: 244 0.169 - 0.225: 96 0.225 - 0.281: 35 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA THR D 153 " pdb=" N THR D 153 " pdb=" C THR D 153 " pdb=" CB THR D 153 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA THR B 153 " pdb=" N THR B 153 " pdb=" C THR B 153 " pdb=" CB THR B 153 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA THR H 153 " pdb=" N THR H 153 " pdb=" C THR H 153 " pdb=" CB THR H 153 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1437 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 180 " 0.257 9.50e-02 1.11e+02 1.15e-01 9.10e+00 pdb=" NE ARG C 180 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 180 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG C 180 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 180 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 180 " -0.256 9.50e-02 1.11e+02 1.15e-01 9.07e+00 pdb=" NE ARG D 180 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG D 180 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG D 180 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 180 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 180 " 0.257 9.50e-02 1.11e+02 1.15e-01 9.06e+00 pdb=" NE ARG A 180 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 180 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 180 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 180 " 0.015 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2959 2.88 - 3.39: 8779 3.39 - 3.89: 14955 3.89 - 4.40: 16737 4.40 - 4.90: 32031 Nonbonded interactions: 75461 Sorted by model distance: nonbonded pdb=" O GLN A 138 " pdb=" OG1 THR A 141 " model vdw 2.378 3.040 nonbonded pdb=" O GLN C 138 " pdb=" OG1 THR C 141 " model vdw 2.378 3.040 nonbonded pdb=" O GLN E 138 " pdb=" OG1 THR E 141 " model vdw 2.378 3.040 nonbonded pdb=" O GLN G 138 " pdb=" OG1 THR G 141 " model vdw 2.378 3.040 nonbonded pdb=" O GLN H 138 " pdb=" OG1 THR H 141 " model vdw 2.378 3.040 ... (remaining 75456 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.930 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.009 0.059 8832 Z= 0.565 Angle : 1.703 8.060 12008 Z= 1.089 Chirality : 0.101 0.281 1440 Planarity : 0.013 0.116 1488 Dihedral : 18.705 72.373 3216 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 6.35 % Allowed : 10.32 % Favored : 83.33 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % 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 aren not related in a simple way. whole: -4.51 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.005 ARG D 180 TYR 0.046 0.008 TYR C 143 PHE 0.011 0.004 PHE C 237 HIS 0.008 0.005 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00875 ( 8824) covalent geometry : angle 1.70053 (11992) SS BOND : bond 0.00718 ( 8) SS BOND : angle 2.95656 ( 16) hydrogen bonds : bond 0.16460 ( 98) hydrogen bonds : angle 8.06494 ( 294) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 0.327 Fit side-chains REVERT: A 129 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8027 (ptmt) REVERT: A 157 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: A 193 LYS cc_start: 0.8767 (tttt) cc_final: 0.8556 (ttmt) REVERT: A 246 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8705 (pt0) REVERT: B 157 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.5884 (m-80) REVERT: B 193 LYS cc_start: 0.8772 (tttt) cc_final: 0.8571 (ttmt) REVERT: B 246 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8720 (pt0) REVERT: C 129 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8201 (ptmt) REVERT: C 157 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: C 246 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8625 (pt0) REVERT: D 129 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8206 (ptmt) REVERT: D 157 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.5480 (m-80) REVERT: D 246 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8672 (pt0) REVERT: E 129 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7938 (pttp) REVERT: E 246 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: F 129 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7913 (pttp) REVERT: F 246 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8442 (pt0) REVERT: G 129 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8054 (ptmt) REVERT: G 157 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: G 210 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7749 (ttm) REVERT: H 129 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7981 (ptmt) REVERT: H 157 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6441 (m-80) outliers start: 64 outliers final: 34 residues processed: 211 average time/residue: 0.1076 time to fit residues: 30.3150 Evaluate side-chains 195 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 157 TYR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 253 CYS Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 157 TYR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 170 GLN A 194 GLN A 242 GLN A 245 GLN B 154 ASN B 170 GLN B 194 GLN B 242 GLN B 245 GLN C 154 ASN C 170 GLN C 242 GLN D 154 ASN D 170 GLN D 242 GLN E 154 ASN E 170 GLN E 242 GLN E 245 GLN F 154 ASN F 170 GLN F 242 GLN F 245 GLN G 154 ASN G 170 GLN G 242 GLN H 154 ASN H 170 GLN H 242 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.136396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.121102 restraints weight = 13477.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.123986 restraints weight = 5933.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.125946 restraints weight = 3335.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.127241 restraints weight = 2214.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.128103 restraints weight = 1650.325| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8832 Z= 0.113 Angle : 0.597 3.673 12008 Z= 0.341 Chirality : 0.053 0.133 1440 Planarity : 0.003 0.033 1488 Dihedral : 11.099 59.075 1317 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.56 % Allowed : 11.61 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.20 (0.19), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.14), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 247 TYR 0.023 0.002 TYR D 236 PHE 0.015 0.002 PHE D 237 HIS 0.002 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8824) covalent geometry : angle 0.59713 (11992) SS BOND : bond 0.00220 ( 8) SS BOND : angle 0.35503 ( 16) hydrogen bonds : bond 0.02365 ( 98) hydrogen bonds : angle 5.08466 ( 294) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6608 (pttp) REVERT: A 193 LYS cc_start: 0.8389 (tttt) cc_final: 0.7969 (ttmt) REVERT: A 206 GLU cc_start: 0.5565 (pt0) cc_final: 0.5207 (tm-30) REVERT: A 224 ILE cc_start: 0.8409 (mt) cc_final: 0.8201 (mt) REVERT: B 193 LYS cc_start: 0.8413 (tttt) cc_final: 0.8000 (ttmt) REVERT: B 206 GLU cc_start: 0.5558 (pt0) cc_final: 0.5275 (tm-30) REVERT: B 224 ILE cc_start: 0.8408 (mt) cc_final: 0.8208 (mt) REVERT: C 129 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6393 (pttp) REVERT: D 129 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6401 (pttp) REVERT: D 206 GLU cc_start: 0.5772 (pt0) cc_final: 0.5338 (tm-30) REVERT: E 129 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6116 (pttp) REVERT: E 153 THR cc_start: 0.7047 (OUTLIER) cc_final: 0.6804 (p) REVERT: E 182 ASN cc_start: 0.8098 (t0) cc_final: 0.7760 (t0) REVERT: E 193 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8348 (mttt) REVERT: E 206 GLU cc_start: 0.6247 (pt0) cc_final: 0.5473 (tm-30) REVERT: E 244 SER cc_start: 0.9023 (t) cc_final: 0.8763 (t) REVERT: F 129 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6135 (pttp) REVERT: F 153 THR cc_start: 0.7053 (OUTLIER) cc_final: 0.6792 (p) REVERT: F 182 ASN cc_start: 0.8103 (t0) cc_final: 0.7766 (t0) REVERT: F 193 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8116 (mtpt) REVERT: F 244 SER cc_start: 0.9017 (t) cc_final: 0.8748 (t) REVERT: G 129 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7412 (ptmt) REVERT: G 193 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8317 (mttt) REVERT: G 234 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8210 (m) REVERT: H 129 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7236 (ptmt) REVERT: H 193 LYS cc_start: 0.8923 (mttt) cc_final: 0.8618 (mttt) outliers start: 46 outliers final: 27 residues processed: 195 average time/residue: 0.0929 time to fit residues: 25.1194 Evaluate side-chains 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 0.1980 chunk 18 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 GLN H 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.129938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.115460 restraints weight = 14115.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.118219 restraints weight = 6127.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.120011 restraints weight = 3434.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.121251 restraints weight = 2287.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.122032 restraints weight = 1705.498| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8832 Z= 0.133 Angle : 0.587 4.377 12008 Z= 0.336 Chirality : 0.052 0.129 1440 Planarity : 0.003 0.033 1488 Dihedral : 9.178 59.587 1272 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.96 % Allowed : 11.81 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.05 (0.19), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.14), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 140 TYR 0.024 0.003 TYR D 236 PHE 0.011 0.002 PHE A 213 HIS 0.001 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8824) covalent geometry : angle 0.58684 (11992) SS BOND : bond 0.00230 ( 8) SS BOND : angle 0.26120 ( 16) hydrogen bonds : bond 0.02011 ( 98) hydrogen bonds : angle 4.66206 ( 294) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8411 (tttt) cc_final: 0.8006 (ttmt) REVERT: A 206 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5156 (tm-30) REVERT: B 193 LYS cc_start: 0.8449 (tttt) cc_final: 0.8037 (ttmt) REVERT: B 206 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5419 (tm-30) REVERT: C 206 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5318 (tm-30) REVERT: E 193 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8192 (mtpt) REVERT: F 192 MET cc_start: 0.7921 (mtt) cc_final: 0.7457 (mtt) REVERT: F 193 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8142 (mtpt) REVERT: F 244 SER cc_start: 0.9047 (t) cc_final: 0.8841 (t) REVERT: G 193 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8324 (mtmt) REVERT: G 234 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8320 (m) REVERT: G 236 TYR cc_start: 0.8561 (t80) cc_final: 0.8206 (t80) REVERT: H 193 LYS cc_start: 0.8916 (mttt) cc_final: 0.8620 (mttt) REVERT: H 236 TYR cc_start: 0.8629 (t80) cc_final: 0.8293 (t80) outliers start: 50 outliers final: 36 residues processed: 178 average time/residue: 0.0868 time to fit residues: 22.1630 Evaluate side-chains 174 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 194 GLN B 156 ASN C 156 ASN D 156 ASN E 156 ASN F 156 ASN G 156 ASN H 156 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.124942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.111097 restraints weight = 15148.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.113519 restraints weight = 6602.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.115199 restraints weight = 3809.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.116306 restraints weight = 2560.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.117037 restraints weight = 1943.847| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8832 Z= 0.182 Angle : 0.626 4.751 12008 Z= 0.357 Chirality : 0.053 0.136 1440 Planarity : 0.003 0.029 1488 Dihedral : 8.656 58.962 1244 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 6.55 % Allowed : 13.69 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.04 (0.19), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.024 0.003 TYR D 236 PHE 0.011 0.003 PHE C 237 HIS 0.002 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8824) covalent geometry : angle 0.62610 (11992) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.25217 ( 16) hydrogen bonds : bond 0.01960 ( 98) hydrogen bonds : angle 4.98533 ( 294) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6654 (pttp) REVERT: A 193 LYS cc_start: 0.8519 (tttt) cc_final: 0.8149 (ttmt) REVERT: A 206 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5344 (tm-30) REVERT: B 193 LYS cc_start: 0.8505 (tttt) cc_final: 0.8138 (ttmt) REVERT: C 124 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7334 (mttm) REVERT: D 124 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7328 (mttm) REVERT: E 129 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6906 (pttp) REVERT: E 193 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8172 (mtpt) REVERT: F 129 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6270 (pttp) REVERT: F 193 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8184 (mtpt) REVERT: G 129 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7161 (ptmt) REVERT: G 193 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8343 (mtmt) REVERT: G 228 MET cc_start: 0.7872 (ttt) cc_final: 0.7490 (ttt) REVERT: H 129 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7165 (ptmt) REVERT: H 193 LYS cc_start: 0.8966 (mttt) cc_final: 0.8590 (mttp) REVERT: H 228 MET cc_start: 0.7855 (ttt) cc_final: 0.7472 (ttt) REVERT: H 236 TYR cc_start: 0.8751 (t80) cc_final: 0.8437 (t80) outliers start: 66 outliers final: 49 residues processed: 200 average time/residue: 0.0884 time to fit residues: 24.8799 Evaluate side-chains 192 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 44 optimal weight: 20.0000 chunk 78 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN H 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.128190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.114037 restraints weight = 14847.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.116595 restraints weight = 6411.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.118356 restraints weight = 3655.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.119519 restraints weight = 2436.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.120271 restraints weight = 1845.895| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8832 Z= 0.137 Angle : 0.583 4.998 12008 Z= 0.330 Chirality : 0.052 0.134 1440 Planarity : 0.002 0.023 1488 Dihedral : 7.592 59.612 1238 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.85 % Allowed : 18.55 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.96 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 247 TYR 0.022 0.002 TYR D 236 PHE 0.010 0.002 PHE D 237 HIS 0.006 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8824) covalent geometry : angle 0.58367 (11992) SS BOND : bond 0.00203 ( 8) SS BOND : angle 0.23881 ( 16) hydrogen bonds : bond 0.01736 ( 98) hydrogen bonds : angle 4.89606 ( 294) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 142 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6593 (pttp) REVERT: A 193 LYS cc_start: 0.8446 (tttt) cc_final: 0.8062 (ttmt) REVERT: A 206 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5326 (tm-30) REVERT: B 193 LYS cc_start: 0.8468 (tttt) cc_final: 0.8061 (mttt) REVERT: B 228 MET cc_start: 0.7700 (ttm) cc_final: 0.7384 (ttt) REVERT: D 228 MET cc_start: 0.7551 (ttm) cc_final: 0.7073 (ttt) REVERT: D 236 TYR cc_start: 0.8514 (t80) cc_final: 0.8310 (t80) REVERT: E 192 MET cc_start: 0.7996 (mtt) cc_final: 0.7574 (mtt) REVERT: E 193 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8160 (mtpt) REVERT: E 210 MET cc_start: 0.8656 (ttt) cc_final: 0.8373 (ttm) REVERT: F 129 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6951 (pttp) REVERT: F 193 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8211 (mtpt) REVERT: F 210 MET cc_start: 0.8681 (ttt) cc_final: 0.8254 (ttm) REVERT: G 129 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7120 (ptmt) REVERT: G 190 LEU cc_start: 0.9095 (mp) cc_final: 0.8794 (mp) REVERT: G 193 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8289 (mtmt) REVERT: G 206 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: G 228 MET cc_start: 0.7665 (ttt) cc_final: 0.7313 (ttt) REVERT: H 129 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7102 (ptmt) REVERT: H 193 LYS cc_start: 0.8918 (mttt) cc_final: 0.8669 (mttt) REVERT: H 228 MET cc_start: 0.7691 (ttt) cc_final: 0.7262 (ttt) REVERT: H 236 TYR cc_start: 0.8666 (t80) cc_final: 0.8433 (t80) outliers start: 59 outliers final: 47 residues processed: 192 average time/residue: 0.0802 time to fit residues: 22.0635 Evaluate side-chains 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 194 GLN B 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.121083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.107530 restraints weight = 15730.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.109771 restraints weight = 6892.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.111391 restraints weight = 4035.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.112399 restraints weight = 2739.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.113091 restraints weight = 2114.024| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8832 Z= 0.248 Angle : 0.694 4.595 12008 Z= 0.395 Chirality : 0.055 0.138 1440 Planarity : 0.003 0.024 1488 Dihedral : 7.745 54.720 1228 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 6.65 % Allowed : 20.83 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.09 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 247 TYR 0.031 0.004 TYR C 236 PHE 0.013 0.003 PHE D 237 HIS 0.004 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 8824) covalent geometry : angle 0.69460 (11992) SS BOND : bond 0.00208 ( 8) SS BOND : angle 0.39381 ( 16) hydrogen bonds : bond 0.02047 ( 98) hydrogen bonds : angle 5.21728 ( 294) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6607 (pttp) REVERT: A 193 LYS cc_start: 0.8570 (tttt) cc_final: 0.8237 (ttmt) REVERT: B 193 LYS cc_start: 0.8575 (tttt) cc_final: 0.8238 (ttmt) REVERT: C 129 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7266 (ptmt) REVERT: D 124 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7484 (mttm) REVERT: D 129 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7235 (ptmt) REVERT: E 129 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6940 (pttp) REVERT: E 192 MET cc_start: 0.8099 (mtt) cc_final: 0.7680 (mtt) REVERT: E 193 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8646 (mttp) REVERT: E 210 MET cc_start: 0.8604 (ttt) cc_final: 0.8329 (ttm) REVERT: F 129 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7031 (pttp) REVERT: F 138 GLN cc_start: 0.7737 (mt0) cc_final: 0.7484 (mt0) REVERT: F 210 MET cc_start: 0.8614 (ttt) cc_final: 0.8204 (ttm) REVERT: G 124 LYS cc_start: 0.8287 (ptpt) cc_final: 0.6559 (mmmt) REVERT: G 129 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6886 (ptmt) REVERT: G 228 MET cc_start: 0.7841 (ttt) cc_final: 0.7502 (ttt) REVERT: H 124 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.6456 (mmmt) REVERT: H 129 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6866 (ptmt) REVERT: H 193 LYS cc_start: 0.9050 (mttt) cc_final: 0.8370 (mttm) REVERT: H 228 MET cc_start: 0.7901 (ttt) cc_final: 0.7522 (ttt) REVERT: H 236 TYR cc_start: 0.8776 (t80) cc_final: 0.8555 (t80) outliers start: 67 outliers final: 49 residues processed: 196 average time/residue: 0.0810 time to fit residues: 22.4523 Evaluate side-chains 196 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 253 CYS Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.124011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.110361 restraints weight = 15483.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.112745 restraints weight = 6856.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.114385 restraints weight = 3978.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.115464 restraints weight = 2695.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.116156 restraints weight = 2057.816| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8832 Z= 0.180 Angle : 0.650 8.003 12008 Z= 0.364 Chirality : 0.053 0.141 1440 Planarity : 0.003 0.019 1488 Dihedral : 7.175 48.023 1224 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 6.94 % Allowed : 21.43 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.08 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 247 TYR 0.027 0.003 TYR D 236 PHE 0.013 0.002 PHE C 237 HIS 0.003 0.001 HIS H 239 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8824) covalent geometry : angle 0.65029 (11992) SS BOND : bond 0.00218 ( 8) SS BOND : angle 0.34354 ( 16) hydrogen bonds : bond 0.01995 ( 98) hydrogen bonds : angle 5.09543 ( 294) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 135 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7284 (mttp) REVERT: A 129 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6642 (pttp) REVERT: A 193 LYS cc_start: 0.8552 (tttt) cc_final: 0.8231 (ttmt) REVERT: B 193 LYS cc_start: 0.8569 (tttt) cc_final: 0.8240 (ttmt) REVERT: C 124 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7365 (mttm) REVERT: C 129 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7324 (ptmt) REVERT: D 124 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7407 (mttm) REVERT: D 129 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7306 (ptmt) REVERT: D 207 MET cc_start: 0.5854 (ttt) cc_final: 0.5437 (mtp) REVERT: E 129 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6950 (pttp) REVERT: E 138 GLN cc_start: 0.7741 (mt0) cc_final: 0.7472 (mt0) REVERT: E 193 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8236 (mtpt) REVERT: E 210 MET cc_start: 0.8560 (ttt) cc_final: 0.8297 (ttm) REVERT: F 129 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6370 (pttp) REVERT: F 193 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8258 (mtpt) REVERT: F 210 MET cc_start: 0.8608 (ttt) cc_final: 0.8208 (ttm) REVERT: G 124 LYS cc_start: 0.8121 (ptpt) cc_final: 0.6397 (mmmt) REVERT: G 129 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7233 (ptmt) REVERT: G 228 MET cc_start: 0.7800 (ttt) cc_final: 0.7443 (ttt) REVERT: H 129 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7219 (ptmt) REVERT: H 193 LYS cc_start: 0.9002 (mttt) cc_final: 0.8323 (mttm) REVERT: H 228 MET cc_start: 0.7870 (ttt) cc_final: 0.7481 (ttt) REVERT: H 236 TYR cc_start: 0.8774 (t80) cc_final: 0.8486 (t80) outliers start: 70 outliers final: 47 residues processed: 194 average time/residue: 0.0728 time to fit residues: 19.7439 Evaluate side-chains 192 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 253 CYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 194 GLN G 170 GLN H 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.121444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.108109 restraints weight = 15844.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.110447 restraints weight = 6931.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.111990 restraints weight = 3984.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.112977 restraints weight = 2731.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.113589 restraints weight = 2110.052| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8832 Z= 0.222 Angle : 0.693 6.972 12008 Z= 0.389 Chirality : 0.054 0.141 1440 Planarity : 0.003 0.020 1488 Dihedral : 7.410 49.441 1220 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 7.24 % Allowed : 21.43 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.16 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 247 TYR 0.026 0.004 TYR D 236 PHE 0.021 0.003 PHE A 213 HIS 0.004 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 8824) covalent geometry : angle 0.69369 (11992) SS BOND : bond 0.00192 ( 8) SS BOND : angle 0.40409 ( 16) hydrogen bonds : bond 0.02020 ( 98) hydrogen bonds : angle 5.19286 ( 294) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 144 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6600 (pttp) REVERT: C 124 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7429 (mttm) REVERT: C 129 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7251 (ptmt) REVERT: C 239 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6521 (t70) REVERT: D 129 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7220 (ptmt) REVERT: D 207 MET cc_start: 0.5812 (ttt) cc_final: 0.5517 (mtp) REVERT: E 129 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6945 (pttp) REVERT: E 138 GLN cc_start: 0.7871 (mt0) cc_final: 0.7602 (mt0) REVERT: E 182 ASN cc_start: 0.8324 (t0) cc_final: 0.8030 (t0) REVERT: F 129 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6517 (pttp) REVERT: F 138 GLN cc_start: 0.7866 (mt0) cc_final: 0.7568 (mt0) REVERT: F 182 ASN cc_start: 0.8321 (t0) cc_final: 0.8028 (t0) REVERT: G 124 LYS cc_start: 0.8269 (ptpt) cc_final: 0.7907 (ptpp) REVERT: G 129 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6877 (ptmt) REVERT: G 228 MET cc_start: 0.7915 (ttt) cc_final: 0.7558 (ttt) REVERT: H 124 LYS cc_start: 0.7990 (ptpp) cc_final: 0.6188 (mmmt) REVERT: H 129 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7200 (ptmt) REVERT: H 193 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8326 (mttm) REVERT: H 228 MET cc_start: 0.7970 (ttt) cc_final: 0.7570 (ttt) REVERT: H 236 TYR cc_start: 0.8771 (t80) cc_final: 0.8536 (t80) outliers start: 73 outliers final: 58 residues processed: 204 average time/residue: 0.0743 time to fit residues: 21.6132 Evaluate side-chains 209 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 142 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 253 CYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.126361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.112501 restraints weight = 15212.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.114905 restraints weight = 6711.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.116612 restraints weight = 3941.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.117740 restraints weight = 2666.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.118465 restraints weight = 2027.849| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8832 Z= 0.133 Angle : 0.626 7.495 12008 Z= 0.347 Chirality : 0.052 0.139 1440 Planarity : 0.002 0.019 1488 Dihedral : 6.636 43.843 1216 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.36 % Allowed : 23.81 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.95 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 247 TYR 0.024 0.002 TYR D 236 PHE 0.022 0.002 PHE A 213 HIS 0.002 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8824) covalent geometry : angle 0.62624 (11992) SS BOND : bond 0.00272 ( 8) SS BOND : angle 0.32000 ( 16) hydrogen bonds : bond 0.01857 ( 98) hydrogen bonds : angle 5.00612 ( 294) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6639 (pttp) REVERT: B 124 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7149 (mttp) REVERT: C 124 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7337 (mttm) REVERT: D 129 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.6305 (pttp) REVERT: D 207 MET cc_start: 0.5766 (ttt) cc_final: 0.5384 (mtp) REVERT: E 182 ASN cc_start: 0.8364 (t0) cc_final: 0.8056 (t0) REVERT: F 138 GLN cc_start: 0.7721 (mt0) cc_final: 0.7439 (mt0) REVERT: F 182 ASN cc_start: 0.8388 (t0) cc_final: 0.8083 (t0) REVERT: F 193 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8210 (mtpt) REVERT: F 210 MET cc_start: 0.8606 (ttt) cc_final: 0.8141 (ttm) REVERT: G 124 LYS cc_start: 0.7945 (ptpt) cc_final: 0.6215 (mmmt) REVERT: G 193 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8255 (mtmt) REVERT: G 228 MET cc_start: 0.7775 (ttt) cc_final: 0.7379 (ttt) REVERT: H 122 ASP cc_start: 0.8148 (t0) cc_final: 0.7848 (t0) REVERT: H 124 LYS cc_start: 0.7915 (ptpp) cc_final: 0.6020 (mmmt) REVERT: H 193 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8266 (mttm) REVERT: H 228 MET cc_start: 0.7815 (ttt) cc_final: 0.7428 (ttt) REVERT: H 236 TYR cc_start: 0.8734 (t80) cc_final: 0.8523 (t80) outliers start: 54 outliers final: 48 residues processed: 190 average time/residue: 0.0783 time to fit residues: 21.3270 Evaluate side-chains 191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 9.9990 chunk 52 optimal weight: 0.0070 chunk 26 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.125894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.112142 restraints weight = 15240.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.114566 restraints weight = 6683.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.116266 restraints weight = 3890.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.117335 restraints weight = 2628.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.118040 restraints weight = 2009.352| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8832 Z= 0.147 Angle : 0.632 7.644 12008 Z= 0.350 Chirality : 0.052 0.137 1440 Planarity : 0.003 0.020 1488 Dihedral : 6.474 36.757 1216 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.65 % Allowed : 23.91 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.89 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 247 TYR 0.025 0.003 TYR D 236 PHE 0.022 0.002 PHE A 213 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8824) covalent geometry : angle 0.63279 (11992) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.29259 ( 16) hydrogen bonds : bond 0.01769 ( 98) hydrogen bonds : angle 4.88165 ( 294) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7361 (mttp) REVERT: A 129 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6651 (pttp) REVERT: C 124 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7330 (mttm) REVERT: D 129 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6304 (pttp) REVERT: D 207 MET cc_start: 0.5862 (ttt) cc_final: 0.5526 (mtp) REVERT: E 129 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6968 (pttp) REVERT: E 182 ASN cc_start: 0.8348 (t0) cc_final: 0.8041 (t0) REVERT: F 182 ASN cc_start: 0.8386 (t0) cc_final: 0.8084 (t0) REVERT: F 193 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8663 (mttp) REVERT: G 124 LYS cc_start: 0.7952 (ptpt) cc_final: 0.6271 (mmmt) REVERT: G 193 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8253 (mtmt) REVERT: G 228 MET cc_start: 0.7757 (ttt) cc_final: 0.7391 (ttt) REVERT: H 122 ASP cc_start: 0.8179 (t0) cc_final: 0.7873 (t0) REVERT: H 124 LYS cc_start: 0.7962 (ptpp) cc_final: 0.6075 (mmmt) REVERT: H 193 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8409 (mtpt) REVERT: H 228 MET cc_start: 0.7842 (ttt) cc_final: 0.7462 (ttt) outliers start: 57 outliers final: 50 residues processed: 189 average time/residue: 0.0824 time to fit residues: 22.1332 Evaluate side-chains 196 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.120531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.107411 restraints weight = 16251.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.109655 restraints weight = 7091.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.111150 restraints weight = 4104.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.112084 restraints weight = 2821.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.112698 restraints weight = 2195.251| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8832 Z= 0.271 Angle : 0.759 7.695 12008 Z= 0.424 Chirality : 0.056 0.141 1440 Planarity : 0.004 0.021 1488 Dihedral : 7.393 43.838 1216 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 6.15 % Allowed : 23.81 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.12 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 180 TYR 0.040 0.005 TYR H 236 PHE 0.016 0.003 PHE C 237 HIS 0.005 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 8824) covalent geometry : angle 0.75958 (11992) SS BOND : bond 0.00241 ( 8) SS BOND : angle 0.43050 ( 16) hydrogen bonds : bond 0.02243 ( 98) hydrogen bonds : angle 5.22562 ( 294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1557.83 seconds wall clock time: 27 minutes 46.94 seconds (1666.94 seconds total)