Starting phenix.real_space_refine on Thu Mar 13 06:58:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ote_17176/03_2025/8ote_17176.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ote_17176/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ote_17176/03_2025/8ote_17176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ote_17176/03_2025/8ote_17176.map" model { file = "/net/cci-nas-00/data/ceres_data/8ote_17176/03_2025/8ote_17176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ote_17176/03_2025/8ote_17176.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.23, per 1000 atoms: 0.72 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: 2.07 Conformation dependent library (CDL) restraints added in 977.5 milliseconds 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: 1.13 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: 1.98 Time building geometry restraints manager: 2.44 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.460 Find NCS groups from input model: 0.170 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- 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 8824 Z= 0.581 Angle : 1.701 8.060 11992 Z= 1.088 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.008 0.005 HIS G 239 PHE 0.011 0.004 PHE C 237 TYR 0.046 0.008 TYR C 143 ARG 0.017 0.005 ARG D 180 *********************** 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 : 0.982 Fit side-chains REVERT: A 129 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8025 (ptmt) REVERT: A 157 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.5896 (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: 0.8706 (pt0) REVERT: B 157 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.5883 (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: 0.8190 (ptmt) REVERT: C 138 GLN cc_start: 0.8378 (mt0) cc_final: 0.8070 (tt0) REVERT: C 157 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.5502 (m-80) REVERT: C 246 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8627 (pt0) REVERT: D 129 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8204 (ptmt) REVERT: D 157 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.5479 (m-80) REVERT: D 246 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8673 (pt0) REVERT: E 129 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7939 (pttp) REVERT: E 246 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: F 129 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7912 (pttp) REVERT: F 246 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8443 (pt0) REVERT: G 124 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8241 (mtpp) REVERT: G 129 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8057 (ptmt) REVERT: G 157 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: G 210 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7750 (ttm) REVERT: H 124 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8250 (mtpp) 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: 0.6440 (m-80) outliers start: 64 outliers final: 32 residues processed: 211 average time/residue: 0.2353 time to fit residues: 65.9363 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 : 0.977 ------------------------------------------------------------------------------- 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 87 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.133186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.118164 restraints weight = 13736.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.120941 restraints weight = 6032.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.122842 restraints weight = 3397.709| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8824 Z= 0.191 Angle : 0.615 3.757 11992 Z= 0.353 Chirality : 0.053 0.133 1440 Planarity : 0.003 0.034 1488 Dihedral : 11.570 59.830 1317 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.06 % Allowed : 11.01 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.19), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.14), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 239 PHE 0.013 0.003 PHE D 237 TYR 0.024 0.002 TYR D 236 ARG 0.003 0.001 ARG G 180 *********************** 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 205 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 1.001 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: 0.7601 (OUTLIER) cc_final: 0.6620 (pttp) REVERT: A 193 LYS cc_start: 0.8421 (tttt) cc_final: 0.8006 (ttmt) REVERT: A 206 GLU cc_start: 0.5566 (pt0) cc_final: 0.5147 (tm-30) REVERT: B 193 LYS cc_start: 0.8454 (tttt) cc_final: 0.8037 (ttmt) REVERT: B 206 GLU cc_start: 0.5659 (pt0) cc_final: 0.5187 (tm-30) REVERT: C 129 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6478 (pttp) REVERT: D 129 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6506 (pttp) REVERT: D 206 GLU cc_start: 0.5897 (pt0) cc_final: 0.5397 (tm-30) REVERT: E 129 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6118 (pttp) REVERT: E 153 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6789 (p) REVERT: E 182 ASN cc_start: 0.8061 (t0) cc_final: 0.7722 (t0) REVERT: E 193 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8280 (mttt) REVERT: E 206 GLU cc_start: 0.6332 (pt0) cc_final: 0.5502 (tm-30) REVERT: E 244 SER cc_start: 0.9029 (t) cc_final: 0.8769 (t) REVERT: F 129 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6117 (pttp) REVERT: F 153 THR cc_start: 0.7113 (OUTLIER) cc_final: 0.6817 (p) REVERT: F 182 ASN cc_start: 0.8053 (t0) cc_final: 0.7720 (t0) REVERT: F 193 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8213 (mtpt) REVERT: F 206 GLU cc_start: 0.6264 (pt0) cc_final: 0.5528 (tm-30) REVERT: F 244 SER cc_start: 0.9030 (t) cc_final: 0.8773 (t) REVERT: G 129 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7403 (ptmt) REVERT: G 193 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8317 (mttt) REVERT: H 129 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7258 (ptmt) REVERT: H 193 LYS cc_start: 0.8949 (mttt) cc_final: 0.8622 (mttt) outliers start: 51 outliers final: 33 residues processed: 194 average time/residue: 0.2218 time to fit residues: 58.8012 Evaluate side-chains 178 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 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 234 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 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 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 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 45 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 = 0.4488 r_free = 0.4488 target = 0.129766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.115316 restraints weight = 14176.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.118019 restraints weight = 6134.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.119773 restraints weight = 3445.238| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8824 Z= 0.200 Angle : 0.592 4.454 11992 Z= 0.337 Chirality : 0.052 0.130 1440 Planarity : 0.003 0.033 1488 Dihedral : 9.375 59.655 1275 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.45 % Allowed : 11.81 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.19), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.14), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 239 PHE 0.012 0.002 PHE A 213 TYR 0.024 0.003 TYR D 236 ARG 0.001 0.000 ARG G 180 *********************** 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 202 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 137 time to evaluate : 1.072 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: 0.7556 (OUTLIER) cc_final: 0.6580 (pttp) REVERT: A 193 LYS cc_start: 0.8381 (tttt) cc_final: 0.7969 (ttmt) REVERT: A 206 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5501 (tm-30) REVERT: B 193 LYS cc_start: 0.8407 (tttt) cc_final: 0.8000 (ttmt) REVERT: B 206 GLU cc_start: 0.5836 (OUTLIER) cc_final: 0.5277 (tm-30) REVERT: D 206 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5377 (tm-30) REVERT: D 228 MET cc_start: 0.7744 (ttm) cc_final: 0.7334 (ttt) REVERT: E 193 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8227 (mtpt) REVERT: F 193 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8263 (mtpt) REVERT: F 244 SER cc_start: 0.9075 (t) cc_final: 0.8860 (t) REVERT: G 129 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7265 (ptmt) REVERT: G 193 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8236 (mttt) REVERT: G 206 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6316 (pm20) REVERT: G 234 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8272 (m) REVERT: G 236 TYR cc_start: 0.8592 (t80) cc_final: 0.8308 (t80) REVERT: H 193 LYS cc_start: 0.8926 (mttt) cc_final: 0.8673 (mttt) REVERT: H 234 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8306 (m) REVERT: H 236 TYR cc_start: 0.8644 (t80) cc_final: 0.8267 (t80) outliers start: 65 outliers final: 43 residues processed: 190 average time/residue: 0.2305 time to fit residues: 62.3533 Evaluate side-chains 181 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 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 193 LYS Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 234 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 137 VAL Chi-restraints excluded: chain E residue 149 THR 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 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 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 Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.123005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.109246 restraints weight = 15377.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.111697 restraints weight = 6699.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.113320 restraints weight = 3807.025| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8824 Z= 0.333 Angle : 0.671 4.787 11992 Z= 0.382 Chirality : 0.054 0.136 1440 Planarity : 0.003 0.031 1488 Dihedral : 9.346 58.703 1255 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 6.75 % Allowed : 16.47 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.19), 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 HIS 0.002 0.001 HIS H 222 PHE 0.012 0.003 PHE D 237 TYR 0.023 0.004 TYR D 236 ARG 0.002 0.000 ARG F 180 *********************** 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 217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 149 time to evaluate : 1.089 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: 0.7524 (OUTLIER) cc_final: 0.6646 (pttp) REVERT: A 193 LYS cc_start: 0.8490 (tttt) cc_final: 0.8097 (ttmt) REVERT: B 193 LYS cc_start: 0.8518 (tttt) cc_final: 0.8141 (ttmt) REVERT: C 124 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7320 (mttm) REVERT: D 124 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7320 (mttm) REVERT: E 129 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6267 (pttp) REVERT: E 193 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8253 (mtpt) REVERT: F 129 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6331 (pttp) REVERT: F 193 LYS cc_start: 0.8877 (ttmt) cc_final: 0.8250 (mtpt) REVERT: F 210 MET cc_start: 0.8566 (ttt) cc_final: 0.8217 (ttm) REVERT: G 129 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7308 (ptmt) REVERT: G 192 MET cc_start: 0.7604 (mtt) cc_final: 0.7340 (ttm) REVERT: G 193 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8397 (mtmt) REVERT: G 206 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6539 (pm20) REVERT: G 228 MET cc_start: 0.7905 (ttt) cc_final: 0.7522 (ttt) REVERT: G 236 TYR cc_start: 0.8691 (t80) cc_final: 0.8395 (t80) REVERT: H 129 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7234 (ptmt) REVERT: H 193 LYS cc_start: 0.9012 (mttt) cc_final: 0.8641 (mttp) REVERT: H 228 MET cc_start: 0.7937 (ttt) cc_final: 0.7555 (ttt) outliers start: 68 outliers final: 52 residues processed: 205 average time/residue: 0.2163 time to fit residues: 62.0322 Evaluate side-chains 199 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 210 MET 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 193 LYS 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 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 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 210 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 57 optimal weight: 0.3980 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.121571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.108072 restraints weight = 15650.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.110302 restraints weight = 6839.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.111945 restraints weight = 4016.149| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8824 Z= 0.367 Angle : 0.708 4.367 11992 Z= 0.401 Chirality : 0.055 0.140 1440 Planarity : 0.003 0.025 1488 Dihedral : 8.449 52.409 1243 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 7.04 % Allowed : 20.54 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.19), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 239 PHE 0.012 0.003 PHE C 237 TYR 0.028 0.004 TYR C 236 ARG 0.002 0.001 ARG F 247 *********************** 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 219 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 148 time to evaluate : 0.902 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 193 LYS cc_start: 0.8562 (tttt) cc_final: 0.8222 (ttmt) REVERT: B 193 LYS cc_start: 0.8587 (tttt) cc_final: 0.8265 (ttmt) REVERT: C 124 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7420 (mttm) REVERT: C 129 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7418 (ptmt) REVERT: D 129 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7357 (ptmt) REVERT: D 207 MET cc_start: 0.5949 (ttt) cc_final: 0.5624 (mtp) REVERT: E 129 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7165 (pttp) REVERT: E 138 GLN cc_start: 0.7741 (mt0) cc_final: 0.7492 (mt0) REVERT: E 182 ASN cc_start: 0.8320 (t0) cc_final: 0.7976 (t0) REVERT: E 193 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8277 (mtpt) REVERT: F 129 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7126 (pttp) REVERT: F 138 GLN cc_start: 0.7728 (mt0) cc_final: 0.7484 (mt0) REVERT: F 182 ASN cc_start: 0.8327 (t0) cc_final: 0.7971 (t0) REVERT: F 193 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8290 (mtpt) REVERT: F 210 MET cc_start: 0.8559 (ttt) cc_final: 0.8143 (ttm) REVERT: F 244 SER cc_start: 0.9142 (t) cc_final: 0.8923 (t) REVERT: G 192 MET cc_start: 0.7764 (mtt) cc_final: 0.7527 (ttm) REVERT: G 193 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8428 (mtmt) REVERT: G 228 MET cc_start: 0.7929 (ttt) cc_final: 0.7551 (ttt) REVERT: G 236 TYR cc_start: 0.8780 (t80) cc_final: 0.8432 (t80) REVERT: H 129 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7283 (ptmt) REVERT: H 193 LYS cc_start: 0.9089 (mtmt) cc_final: 0.8392 (mttm) REVERT: H 228 MET cc_start: 0.7990 (ttt) cc_final: 0.7598 (ttt) outliers start: 71 outliers final: 59 residues processed: 204 average time/residue: 0.1970 time to fit residues: 56.0553 Evaluate side-chains 208 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 143 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 210 MET 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 193 LYS Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 THR 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 231 THR 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 210 MET 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 56 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 78 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.127377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.113512 restraints weight = 14840.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.116049 restraints weight = 6552.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.117761 restraints weight = 3747.312| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8824 Z= 0.207 Angle : 0.610 5.674 11992 Z= 0.342 Chirality : 0.052 0.137 1440 Planarity : 0.002 0.019 1488 Dihedral : 7.288 46.260 1243 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.95 % Allowed : 22.92 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.011 0.002 PHE C 237 TYR 0.021 0.002 TYR D 236 ARG 0.001 0.000 ARG E 247 *********************** 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 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 137 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8470 (tttt) cc_final: 0.8123 (ttmt) REVERT: A 228 MET cc_start: 0.7690 (ttm) cc_final: 0.7364 (ttt) REVERT: C 129 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6507 (pttp) REVERT: D 129 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.6496 (pttp) REVERT: D 207 MET cc_start: 0.5595 (ttt) cc_final: 0.5183 (mtp) REVERT: E 182 ASN cc_start: 0.8255 (t0) cc_final: 0.7907 (t0) REVERT: E 193 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8338 (mtpt) REVERT: F 129 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7012 (pttp) REVERT: F 182 ASN cc_start: 0.8294 (t0) cc_final: 0.7926 (t0) REVERT: F 193 LYS cc_start: 0.8903 (ttmt) cc_final: 0.8364 (mtpt) REVERT: F 210 MET cc_start: 0.8549 (ttt) cc_final: 0.8164 (ttm) REVERT: F 244 SER cc_start: 0.9114 (t) cc_final: 0.8871 (t) REVERT: G 138 GLN cc_start: 0.8022 (mt0) cc_final: 0.7591 (tt0) REVERT: G 192 MET cc_start: 0.7624 (mtt) cc_final: 0.7333 (ttm) REVERT: G 193 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8356 (mtmt) REVERT: G 228 MET cc_start: 0.7815 (ttt) cc_final: 0.7417 (ttt) REVERT: G 236 TYR cc_start: 0.8671 (t80) cc_final: 0.8378 (t80) REVERT: H 129 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7141 (ptmt) REVERT: H 138 GLN cc_start: 0.8006 (mt0) cc_final: 0.7576 (tt0) REVERT: H 193 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8637 (mttp) REVERT: H 228 MET cc_start: 0.7874 (ttt) cc_final: 0.7478 (ttt) REVERT: H 234 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8322 (m) REVERT: H 236 TYR cc_start: 0.8704 (t80) cc_final: 0.8284 (t80) outliers start: 60 outliers final: 44 residues processed: 184 average time/residue: 0.2210 time to fit residues: 56.4132 Evaluate side-chains 182 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 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 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 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 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 214 CYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 chunk 88 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN H 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.127128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.112890 restraints weight = 14966.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.115446 restraints weight = 6496.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.117202 restraints weight = 3750.201| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8824 Z= 0.216 Angle : 0.609 7.684 11992 Z= 0.339 Chirality : 0.052 0.135 1440 Planarity : 0.002 0.018 1488 Dihedral : 6.963 40.467 1235 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.35 % Allowed : 22.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 239 PHE 0.010 0.002 PHE C 237 TYR 0.026 0.002 TYR D 236 ARG 0.001 0.000 ARG G 247 *********************** 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 198 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 134 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8447 (tttt) cc_final: 0.8093 (ttmt) REVERT: C 129 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.6471 (pttp) REVERT: D 129 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.6341 (pttp) REVERT: D 207 MET cc_start: 0.5609 (ttt) cc_final: 0.5190 (mtp) REVERT: D 228 MET cc_start: 0.7548 (ttm) cc_final: 0.7116 (ttt) REVERT: E 129 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6300 (pttp) REVERT: E 182 ASN cc_start: 0.8206 (t0) cc_final: 0.7846 (t0) REVERT: E 193 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8311 (mtpt) REVERT: F 129 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6298 (pttp) REVERT: F 182 ASN cc_start: 0.8213 (t0) cc_final: 0.7839 (t0) REVERT: F 193 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8291 (mtpt) REVERT: F 210 MET cc_start: 0.8567 (ttt) cc_final: 0.8193 (ttm) REVERT: F 244 SER cc_start: 0.9101 (t) cc_final: 0.8860 (t) REVERT: G 124 LYS cc_start: 0.8049 (ptpt) cc_final: 0.6499 (mmmt) REVERT: G 138 GLN cc_start: 0.7968 (mt0) cc_final: 0.7544 (tt0) REVERT: G 193 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8576 (mttt) REVERT: G 207 MET cc_start: 0.6222 (mtp) cc_final: 0.6010 (mtp) REVERT: G 228 MET cc_start: 0.7777 (ttt) cc_final: 0.7350 (ttt) REVERT: G 236 TYR cc_start: 0.8635 (t80) cc_final: 0.8403 (t80) REVERT: H 124 LYS cc_start: 0.8041 (ptpt) cc_final: 0.6474 (mmmt) REVERT: H 129 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7160 (ptmt) REVERT: H 138 GLN cc_start: 0.7993 (mt0) cc_final: 0.7558 (tt0) REVERT: H 193 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8476 (mttp) REVERT: H 228 MET cc_start: 0.7840 (ttt) cc_final: 0.7327 (ttt) REVERT: H 236 TYR cc_start: 0.8654 (t80) cc_final: 0.8338 (t80) outliers start: 64 outliers final: 52 residues processed: 186 average time/residue: 0.2011 time to fit residues: 51.9513 Evaluate side-chains 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 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 181 LEU 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 190 LEU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.124156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.110329 restraints weight = 15508.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.112715 restraints weight = 6804.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.114390 restraints weight = 3950.605| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8824 Z= 0.272 Angle : 0.644 5.922 11992 Z= 0.362 Chirality : 0.053 0.136 1440 Planarity : 0.003 0.019 1488 Dihedral : 7.180 37.630 1235 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 6.55 % Allowed : 22.52 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 239 PHE 0.012 0.002 PHE C 237 TYR 0.024 0.003 TYR D 236 ARG 0.001 0.000 ARG F 247 *********************** 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 201 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 135 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8493 (tttt) cc_final: 0.8193 (ttmt) REVERT: C 124 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7432 (mttm) REVERT: C 129 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6490 (pttp) REVERT: D 129 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7354 (ptmt) REVERT: D 207 MET cc_start: 0.5746 (ttt) cc_final: 0.5454 (mtp) REVERT: E 129 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7147 (pttp) REVERT: E 138 GLN cc_start: 0.7775 (mt0) cc_final: 0.7481 (mt0) REVERT: E 182 ASN cc_start: 0.8233 (t0) cc_final: 0.7854 (t0) REVERT: E 193 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8309 (mtpt) REVERT: F 129 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6417 (pttp) REVERT: F 138 GLN cc_start: 0.7725 (mt0) cc_final: 0.7459 (mt0) REVERT: F 182 ASN cc_start: 0.8252 (t0) cc_final: 0.7877 (t0) REVERT: F 193 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8278 (mtpt) REVERT: F 244 SER cc_start: 0.9088 (t) cc_final: 0.8853 (t) REVERT: G 124 LYS cc_start: 0.8133 (ptpt) cc_final: 0.6398 (mmmt) REVERT: G 193 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8322 (mtmt) REVERT: G 228 MET cc_start: 0.7880 (ttt) cc_final: 0.7492 (ttt) REVERT: G 236 TYR cc_start: 0.8700 (t80) cc_final: 0.8419 (t80) REVERT: H 124 LYS cc_start: 0.8161 (ptpt) cc_final: 0.6503 (mmmt) REVERT: H 129 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7279 (ptmt) REVERT: H 193 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8507 (mttp) REVERT: H 228 MET cc_start: 0.7884 (ttt) cc_final: 0.7503 (ttt) REVERT: H 236 TYR cc_start: 0.8709 (t80) cc_final: 0.8418 (t80) outliers start: 66 outliers final: 55 residues processed: 189 average time/residue: 0.1958 time to fit residues: 51.2533 Evaluate side-chains 195 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 134 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 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 181 LEU 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 190 LEU Chi-restraints excluded: chain E residue 210 MET 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 214 CYS 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 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 103 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN G 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.120172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.106943 restraints weight = 16203.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.109111 restraints weight = 7151.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.110653 restraints weight = 4240.406| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8824 Z= 0.415 Angle : 0.750 7.416 11992 Z= 0.422 Chirality : 0.056 0.141 1440 Planarity : 0.004 0.020 1488 Dihedral : 8.036 45.440 1235 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 6.55 % Allowed : 23.71 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 222 PHE 0.014 0.002 PHE C 237 TYR 0.025 0.004 TYR D 236 ARG 0.002 0.000 ARG G 247 *********************** 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 218 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7399 (mttm) REVERT: C 129 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7463 (ptmt) REVERT: C 161 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7599 (mt-10) REVERT: D 124 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7405 (mttm) REVERT: D 129 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7390 (ptmt) REVERT: D 207 MET cc_start: 0.5991 (ttt) cc_final: 0.5764 (mtp) REVERT: D 246 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: E 129 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6804 (pttp) REVERT: E 138 GLN cc_start: 0.7882 (mt0) cc_final: 0.7620 (mt0) REVERT: E 182 ASN cc_start: 0.8301 (t0) cc_final: 0.7910 (t0) REVERT: E 193 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8303 (mtpt) REVERT: F 129 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7169 (pttp) REVERT: F 138 GLN cc_start: 0.7912 (mt0) cc_final: 0.7643 (mt0) REVERT: F 182 ASN cc_start: 0.8319 (t0) cc_final: 0.7927 (t0) REVERT: F 193 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8250 (mtpt) REVERT: F 210 MET cc_start: 0.8596 (ttt) cc_final: 0.8297 (ttm) REVERT: F 244 SER cc_start: 0.9104 (t) cc_final: 0.8903 (t) REVERT: G 124 LYS cc_start: 0.8259 (ptpt) cc_final: 0.6422 (mmmt) REVERT: G 193 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8332 (mtmt) REVERT: G 228 MET cc_start: 0.8035 (ttt) cc_final: 0.7671 (ttt) REVERT: G 236 TYR cc_start: 0.8788 (t80) cc_final: 0.8544 (t80) REVERT: H 124 LYS cc_start: 0.8279 (ptpt) cc_final: 0.6476 (mmmt) REVERT: H 129 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.6989 (ptmt) REVERT: H 193 LYS cc_start: 0.9100 (mtmt) cc_final: 0.8784 (mttp) REVERT: H 228 MET cc_start: 0.8048 (ttt) cc_final: 0.7686 (ttt) REVERT: H 236 TYR cc_start: 0.8827 (t80) cc_final: 0.8517 (t80) outliers start: 66 outliers final: 50 residues processed: 206 average time/residue: 0.1933 time to fit residues: 55.5670 Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 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 246 GLU 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.126638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.112824 restraints weight = 15177.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.115201 restraints weight = 6685.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.116928 restraints weight = 3933.318| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8824 Z= 0.208 Angle : 0.639 7.734 11992 Z= 0.355 Chirality : 0.052 0.140 1440 Planarity : 0.002 0.020 1488 Dihedral : 6.884 38.859 1227 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.95 % Allowed : 25.00 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (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 HIS 0.002 0.001 HIS F 239 PHE 0.011 0.002 PHE C 237 TYR 0.027 0.002 TYR D 236 ARG 0.001 0.000 ARG A 247 ********************** 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 194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 134 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7161 (mttp) REVERT: C 124 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7327 (mttm) REVERT: C 129 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6496 (pttp) REVERT: C 161 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 124 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7351 (mttm) REVERT: D 129 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6436 (pttp) REVERT: D 207 MET cc_start: 0.5800 (ttt) cc_final: 0.5442 (mtp) REVERT: E 138 GLN cc_start: 0.7741 (mt0) cc_final: 0.7439 (mt0) REVERT: E 182 ASN cc_start: 0.8223 (t0) cc_final: 0.7850 (t0) REVERT: E 193 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8326 (mtpt) REVERT: F 129 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7070 (pttp) REVERT: F 138 GLN cc_start: 0.7785 (mt0) cc_final: 0.7470 (mt0) REVERT: F 182 ASN cc_start: 0.8271 (t0) cc_final: 0.7882 (t0) REVERT: F 193 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8317 (mtpt) REVERT: F 210 MET cc_start: 0.8531 (ttt) cc_final: 0.8245 (ttm) REVERT: F 244 SER cc_start: 0.9094 (t) cc_final: 0.8852 (t) REVERT: G 138 GLN cc_start: 0.8012 (mt0) cc_final: 0.7613 (tt0) REVERT: G 193 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8631 (mttp) REVERT: G 228 MET cc_start: 0.7904 (ttt) cc_final: 0.7543 (ttt) REVERT: G 236 TYR cc_start: 0.8679 (t80) cc_final: 0.8419 (t80) REVERT: H 129 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7149 (ptmt) REVERT: H 193 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8290 (mttm) REVERT: H 228 MET cc_start: 0.7941 (ttt) cc_final: 0.7571 (ttt) REVERT: H 236 TYR cc_start: 0.8695 (t80) cc_final: 0.8398 (t80) outliers start: 60 outliers final: 48 residues processed: 186 average time/residue: 0.2425 time to fit residues: 62.9483 Evaluate side-chains 189 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 210 MET 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 129 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 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 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 245 GLN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 GLN H 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.121418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.108059 restraints weight = 15897.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.110294 restraints weight = 7013.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.111688 restraints weight = 4114.358| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8824 Z= 0.362 Angle : 0.726 7.526 11992 Z= 0.406 Chirality : 0.055 0.139 1440 Planarity : 0.003 0.021 1488 Dihedral : 7.589 42.385 1227 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 6.15 % Allowed : 24.80 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 239 PHE 0.015 0.002 PHE D 237 TYR 0.024 0.004 TYR D 236 ARG 0.001 0.000 ARG G 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.59 seconds wall clock time: 65 minutes 27.27 seconds (3927.27 seconds total)