Starting phenix.real_space_refine on Thu Feb 13 05:11:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ote_17176/02_2025/8ote_17176.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ote_17176/02_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_17176/02_2025/8ote_17176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ote_17176/02_2025/8ote_17176.map" model { file = "/net/cci-nas-00/data/ceres_data/8ote_17176/02_2025/8ote_17176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ote_17176/02_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-5592/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: 5.83, per 1000 atoms: 0.67 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: 2.14 Conformation dependent library (CDL) restraints added in 987.3 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: 1.12 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: 2.24 Time building geometry restraints manager: 2.50 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: 0.08 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: 3.210 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: 22.070 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- 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 : 0.888 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: 0.2434 time to fit residues: 67.9198 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 : 0.901 ------------------------------------------------------------------------------- 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: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.132359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.117392 restraints weight = 13832.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.120047 restraints weight = 6086.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.121959 restraints weight = 3499.900| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2747 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= 0.199 Angle : 0.624 3.753 11992 Z= 0.358 Chirality : 0.053 0.133 1440 Planarity : 0.003 0.034 1488 Dihedral : 11.661 59.081 1317 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 5.56 % Allowed : 10.71 % Favored : 83.73 % 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 H 222 PHE 0.014 0.003 PHE D 237 TYR 0.024 0.002 TYR D 236 ARG 0.002 0.001 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6552 (pttp) REVERT: A 193 LYS cc_start: 0.8405 (tttt) cc_final: 0.7992 (ttmt) REVERT: B 193 LYS cc_start: 0.8450 (tttt) cc_final: 0.8025 (ttmt) REVERT: B 206 GLU cc_start: 0.5669 (pt0) cc_final: 0.5175 (tm-30) REVERT: C 129 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6464 (pttp) REVERT: D 129 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.6369 (pttp) REVERT: D 206 GLU cc_start: 0.5896 (pt0) cc_final: 0.5382 (tm-30) REVERT: E 129 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6106 (pttp) REVERT: E 153 THR cc_start: 0.7102 (OUTLIER) cc_final: 0.6783 (p) REVERT: E 182 ASN cc_start: 0.8039 (t0) cc_final: 0.7706 (t0) REVERT: E 193 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8257 (mttt) REVERT: E 206 GLU cc_start: 0.6344 (pt0) cc_final: 0.5545 (tm-30) REVERT: E 244 SER cc_start: 0.9046 (t) cc_final: 0.8788 (t) REVERT: F 122 ASP cc_start: 0.7315 (t0) cc_final: 0.7052 (t0) REVERT: F 124 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6902 (mttm) REVERT: F 129 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6127 (pttp) REVERT: F 153 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6801 (p) REVERT: F 182 ASN cc_start: 0.8032 (t0) cc_final: 0.7785 (t0) REVERT: F 193 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8138 (mtpt) REVERT: F 206 GLU cc_start: 0.6272 (pt0) cc_final: 0.5491 (tm-30) REVERT: F 244 SER cc_start: 0.9046 (t) cc_final: 0.8792 (t) REVERT: G 129 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7264 (ptmt) REVERT: G 193 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8302 (mttt) REVERT: H 129 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7274 (ptmt) REVERT: H 193 LYS cc_start: 0.8942 (mttt) cc_final: 0.8599 (mttt) outliers start: 56 outliers final: 37 residues processed: 196 average time/residue: 0.2226 time to fit residues: 59.2339 Evaluate side-chains 186 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain 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 153 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 149 THR Chi-restraints excluded: chain F residue 153 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 234 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 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: 2.9990 chunk 88 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN C 156 ASN G 156 ASN G 229 GLN H 156 ASN H 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.128299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.114085 restraints weight = 14451.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.116732 restraints weight = 6210.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.118476 restraints weight = 3482.036| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8824 Z= 0.215 Angle : 0.602 4.738 11992 Z= 0.344 Chirality : 0.053 0.131 1440 Planarity : 0.003 0.030 1488 Dihedral : 9.542 59.542 1278 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.85 % Allowed : 12.20 % Favored : 80.95 % 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: -4.09 (0.19), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.14), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 239 PHE 0.011 0.002 PHE B 237 TYR 0.026 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 222 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 0.937 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: 0.7517 (OUTLIER) cc_final: 0.6573 (pttp) REVERT: A 193 LYS cc_start: 0.8389 (tttt) cc_final: 0.7981 (mttt) REVERT: A 206 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5208 (tm-30) REVERT: B 193 LYS cc_start: 0.8410 (tttt) cc_final: 0.7988 (mttt) REVERT: C 206 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5183 (tm-30) REVERT: E 129 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6249 (pttp) REVERT: E 193 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8217 (mtpt) REVERT: F 129 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6286 (pttp) REVERT: F 193 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8186 (mtpt) REVERT: G 129 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7250 (ptmt) REVERT: G 193 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8235 (mttt) REVERT: G 206 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6366 (pm20) REVERT: G 234 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8319 (m) REVERT: G 236 TYR cc_start: 0.8598 (t80) cc_final: 0.8261 (t80) REVERT: H 193 LYS cc_start: 0.8923 (mttt) cc_final: 0.8660 (mttt) REVERT: H 234 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8302 (m) REVERT: H 236 TYR cc_start: 0.8620 (t80) cc_final: 0.8213 (t80) outliers start: 69 outliers final: 42 residues processed: 207 average time/residue: 0.1954 time to fit residues: 56.4622 Evaluate side-chains 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 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 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 206 GLU 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: 10.0000 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 88 optimal weight: 0.0570 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: 2.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.131184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.116771 restraints weight = 14326.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.119504 restraints weight = 6150.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.121357 restraints weight = 3448.277| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8824 Z= 0.176 Angle : 0.560 4.407 11992 Z= 0.318 Chirality : 0.051 0.129 1440 Planarity : 0.002 0.024 1488 Dihedral : 8.189 59.890 1260 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.85 % Allowed : 15.48 % Favored : 78.67 % 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: -3.96 (0.19), 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 H 222 PHE 0.010 0.002 PHE D 237 TYR 0.023 0.002 TYR D 236 ARG 0.001 0.000 ARG A 247 *********************** 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 200 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8387 (tttt) cc_final: 0.7991 (mttt) REVERT: A 206 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5230 (tm-30) REVERT: B 193 LYS cc_start: 0.8432 (tttt) cc_final: 0.8040 (mttt) REVERT: B 206 GLU cc_start: 0.5864 (pt0) cc_final: 0.5193 (tm-30) REVERT: C 206 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.5044 (tm-30) REVERT: D 207 MET cc_start: 0.5471 (ttt) cc_final: 0.4904 (mtp) REVERT: D 228 MET cc_start: 0.7671 (ttm) cc_final: 0.7268 (ttt) REVERT: E 182 ASN cc_start: 0.8255 (t0) cc_final: 0.7945 (t0) REVERT: E 193 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8268 (mtpt) REVERT: F 182 ASN cc_start: 0.8249 (t0) cc_final: 0.7941 (t0) REVERT: F 193 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8280 (mtpt) REVERT: G 138 GLN cc_start: 0.8004 (mt0) cc_final: 0.7518 (tt0) REVERT: G 193 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8215 (mttt) REVERT: G 206 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: G 228 MET cc_start: 0.7753 (ttt) cc_final: 0.7488 (ttt) REVERT: G 236 TYR cc_start: 0.8581 (t80) cc_final: 0.8325 (t80) REVERT: H 129 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7148 (ptmt) REVERT: H 138 GLN cc_start: 0.7993 (mt0) cc_final: 0.7504 (tt0) REVERT: H 193 LYS cc_start: 0.8883 (mttt) cc_final: 0.8489 (mttt) REVERT: H 227 MET cc_start: 0.7531 (mtm) cc_final: 0.6843 (mpp) REVERT: H 228 MET cc_start: 0.7763 (ttt) cc_final: 0.7417 (ttt) REVERT: H 236 TYR cc_start: 0.8656 (t80) cc_final: 0.8332 (t80) outliers start: 59 outliers final: 45 residues processed: 190 average time/residue: 0.1865 time to fit residues: 50.0479 Evaluate side-chains 180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 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 214 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain 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 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain 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 246 GLU 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: 5.9990 chunk 90 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 245 GLN B 156 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN E 156 ASN F 156 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.124005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.110196 restraints weight = 15143.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.112534 restraints weight = 6676.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.114204 restraints weight = 3926.947| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8824 Z= 0.296 Angle : 0.639 4.558 11992 Z= 0.363 Chirality : 0.053 0.134 1440 Planarity : 0.003 0.024 1488 Dihedral : 8.055 59.625 1242 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 6.75 % Allowed : 19.54 % Favored : 73.71 % 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: -4.00 (0.19), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 239 PHE 0.012 0.002 PHE B 237 TYR 0.023 0.003 TYR D 236 ARG 0.001 0.000 ARG H 180 *********************** 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 208 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 140 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8495 (tttt) cc_final: 0.8136 (ttmt) REVERT: A 206 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5314 (tm-30) REVERT: B 193 LYS cc_start: 0.8499 (tttt) cc_final: 0.8142 (ttmt) REVERT: B 246 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8079 (pt0) REVERT: C 129 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7345 (ptmt) REVERT: D 129 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7330 (ptmt) REVERT: D 207 MET cc_start: 0.5701 (ttt) cc_final: 0.5388 (mtp) REVERT: D 228 MET cc_start: 0.7690 (ttm) cc_final: 0.7337 (ttt) REVERT: E 138 GLN cc_start: 0.7723 (mt0) cc_final: 0.7486 (mt0) REVERT: E 182 ASN cc_start: 0.8281 (t0) cc_final: 0.7925 (t0) REVERT: E 193 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8224 (mtpt) REVERT: F 182 ASN cc_start: 0.8272 (t0) cc_final: 0.7916 (t0) REVERT: F 193 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8229 (mtpt) REVERT: G 190 LEU cc_start: 0.9136 (mp) cc_final: 0.8831 (mp) REVERT: G 193 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8345 (mtmt) REVERT: G 228 MET cc_start: 0.7812 (ttt) cc_final: 0.7417 (ttt) REVERT: G 236 TYR cc_start: 0.8684 (t80) cc_final: 0.8476 (t80) REVERT: H 129 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7239 (ptmt) REVERT: H 193 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8625 (mttp) REVERT: H 228 MET cc_start: 0.7847 (ttt) cc_final: 0.7418 (ttt) REVERT: H 236 TYR cc_start: 0.8699 (t80) cc_final: 0.8450 (t80) outliers start: 68 outliers final: 55 residues processed: 197 average time/residue: 0.1877 time to fit residues: 51.9974 Evaluate side-chains 196 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 234 THR 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 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 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 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 210 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 124 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: 4.9990 chunk 58 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.125172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.111460 restraints weight = 15044.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.113832 restraints weight = 6633.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.115556 restraints weight = 3896.593| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4191 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= 0.264 Angle : 0.629 5.370 11992 Z= 0.355 Chirality : 0.053 0.137 1440 Planarity : 0.003 0.020 1488 Dihedral : 7.367 50.173 1236 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 6.94 % Allowed : 20.83 % Favored : 72.22 % 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 0.004 0.001 HIS F 239 PHE 0.012 0.002 PHE D 237 TYR 0.022 0.003 TYR D 236 ARG 0.002 0.000 ARG F 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 212 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 142 time to evaluate : 0.979 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 161 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 193 LYS cc_start: 0.8479 (tttt) cc_final: 0.8134 (ttmt) REVERT: A 206 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5310 (tm-30) REVERT: A 246 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7996 (pt0) REVERT: B 193 LYS cc_start: 0.8519 (tttt) cc_final: 0.8190 (ttmt) REVERT: B 246 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: C 129 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6549 (pttp) REVERT: D 129 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6553 (pttp) REVERT: D 207 MET cc_start: 0.5707 (ttt) cc_final: 0.5297 (mtp) REVERT: E 182 ASN cc_start: 0.8272 (t0) cc_final: 0.7900 (t0) REVERT: E 193 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8338 (mtpt) REVERT: F 182 ASN cc_start: 0.8272 (t0) cc_final: 0.7899 (t0) REVERT: F 193 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8259 (mtpt) REVERT: G 193 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8314 (mtmt) REVERT: G 228 MET cc_start: 0.7820 (ttt) cc_final: 0.7414 (ttt) REVERT: G 236 TYR cc_start: 0.8686 (t80) cc_final: 0.8482 (t80) REVERT: H 129 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7259 (ptmt) REVERT: H 193 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8619 (mttp) REVERT: H 227 MET cc_start: 0.7630 (mtm) cc_final: 0.7022 (mpp) REVERT: H 228 MET cc_start: 0.7881 (ttt) cc_final: 0.7503 (ttt) REVERT: H 236 TYR cc_start: 0.8722 (t80) cc_final: 0.8511 (t80) outliers start: 70 outliers final: 59 residues processed: 194 average time/residue: 0.1768 time to fit residues: 48.4191 Evaluate side-chains 206 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 246 GLU 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 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 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 LEU 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 190 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 253 CYS Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.123747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.110098 restraints weight = 15442.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.112437 restraints weight = 6804.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.114061 restraints weight = 3991.011| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8824 Z= 0.287 Angle : 0.651 7.233 11992 Z= 0.365 Chirality : 0.053 0.138 1440 Planarity : 0.003 0.021 1488 Dihedral : 7.314 42.776 1236 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 7.04 % Allowed : 21.73 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.99 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 239 PHE 0.012 0.002 PHE D 237 TYR 0.031 0.003 TYR C 236 ARG 0.001 0.000 ARG E 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 213 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 0.938 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: 0.8536 (tttt) cc_final: 0.8225 (ttmt) REVERT: A 246 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8064 (pt0) REVERT: B 193 LYS cc_start: 0.8538 (tttt) cc_final: 0.8230 (ttmt) REVERT: B 246 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: C 129 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6542 (pttp) REVERT: D 129 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6548 (pttp) REVERT: D 207 MET cc_start: 0.5804 (ttt) cc_final: 0.5496 (mtp) REVERT: E 138 GLN cc_start: 0.7733 (mt0) cc_final: 0.7484 (mt0) REVERT: E 182 ASN cc_start: 0.8297 (t0) cc_final: 0.7914 (t0) REVERT: E 193 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8317 (mtpt) REVERT: F 138 GLN cc_start: 0.7748 (mt0) cc_final: 0.7485 (mt0) REVERT: F 182 ASN cc_start: 0.8282 (t0) cc_final: 0.7897 (t0) REVERT: F 193 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8351 (mtpt) REVERT: G 124 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.6519 (mmmt) REVERT: G 227 MET cc_start: 0.7536 (mpt) cc_final: 0.7067 (mpt) REVERT: G 228 MET cc_start: 0.7896 (ttt) cc_final: 0.7496 (ttt) REVERT: G 236 TYR cc_start: 0.8784 (t80) cc_final: 0.8473 (t80) REVERT: H 129 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7283 (ptmt) REVERT: H 193 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8527 (mttp) REVERT: H 228 MET cc_start: 0.7959 (ttt) cc_final: 0.7588 (ttt) outliers start: 71 outliers final: 61 residues processed: 196 average time/residue: 0.1868 time to fit residues: 51.5912 Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 246 GLU 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 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 137 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 LEU 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 190 LEU Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 124 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.129306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.114987 restraints weight = 14895.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.117659 restraints weight = 6446.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.119450 restraints weight = 3646.416| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8824 Z= 0.188 Angle : 0.590 6.930 11992 Z= 0.329 Chirality : 0.051 0.136 1440 Planarity : 0.002 0.019 1488 Dihedral : 6.478 32.416 1232 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 6.55 % Allowed : 22.62 % 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: -3.84 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.011 0.002 PHE D 237 TYR 0.037 0.002 TYR H 236 ARG 0.001 0.000 ARG B 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 200 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5245 (tm-30) REVERT: A 246 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: B 246 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7789 (pt0) REVERT: C 129 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6507 (pttp) REVERT: D 129 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6525 (pttp) REVERT: D 207 MET cc_start: 0.5645 (ttt) cc_final: 0.5256 (mtp) REVERT: E 182 ASN cc_start: 0.8250 (t0) cc_final: 0.7858 (t0) REVERT: E 193 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8319 (mtpt) REVERT: F 182 ASN cc_start: 0.8246 (t0) cc_final: 0.7850 (t0) REVERT: F 193 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8313 (mtpt) REVERT: F 210 MET cc_start: 0.8477 (ttt) cc_final: 0.8066 (ttm) REVERT: G 227 MET cc_start: 0.7371 (mpt) cc_final: 0.6811 (mpt) REVERT: G 228 MET cc_start: 0.7772 (ttt) cc_final: 0.7382 (ttt) REVERT: G 234 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8259 (m) REVERT: G 236 TYR cc_start: 0.8681 (t80) cc_final: 0.8303 (t80) REVERT: H 129 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7157 (ptmt) REVERT: H 138 GLN cc_start: 0.7898 (mt0) cc_final: 0.7469 (tt0) REVERT: H 193 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8461 (mttp) REVERT: H 227 MET cc_start: 0.7443 (mtm) cc_final: 0.7037 (mpp) REVERT: H 228 MET cc_start: 0.7832 (ttt) cc_final: 0.7443 (ttt) REVERT: H 234 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8303 (m) outliers start: 66 outliers final: 52 residues processed: 186 average time/residue: 0.1970 time to fit residues: 51.5239 Evaluate side-chains 190 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 130 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR 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 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 246 GLU 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 181 LEU Chi-restraints excluded: chain C residue 190 LEU 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 190 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 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 206 GLU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 0.0060 chunk 69 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 overall best weight: 5.2004 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.122244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.108906 restraints weight = 15815.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.111119 restraints weight = 6906.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.112715 restraints weight = 4065.804| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8824 Z= 0.349 Angle : 0.694 6.121 11992 Z= 0.389 Chirality : 0.054 0.137 1440 Planarity : 0.003 0.021 1488 Dihedral : 7.214 38.553 1227 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 6.45 % Allowed : 23.12 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.01 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 239 PHE 0.014 0.002 PHE D 237 TYR 0.036 0.004 TYR H 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 203 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: C 129 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7392 (ptmt) REVERT: D 129 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6535 (pttp) REVERT: D 207 MET cc_start: 0.6009 (ttt) cc_final: 0.5618 (mtp) REVERT: E 182 ASN cc_start: 0.8302 (t0) cc_final: 0.7927 (t0) REVERT: E 193 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8202 (mtpt) REVERT: F 138 GLN cc_start: 0.7757 (mt0) cc_final: 0.7528 (mt0) REVERT: F 182 ASN cc_start: 0.8305 (t0) cc_final: 0.7904 (t0) REVERT: F 193 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8237 (mtpt) REVERT: G 124 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.6348 (mmmt) REVERT: G 227 MET cc_start: 0.7646 (mpt) cc_final: 0.7131 (mpt) REVERT: G 228 MET cc_start: 0.7976 (ttt) cc_final: 0.7585 (ttt) REVERT: G 236 TYR cc_start: 0.8774 (t80) cc_final: 0.8490 (t80) REVERT: H 124 LYS cc_start: 0.8203 (ptpt) cc_final: 0.6402 (mmmt) REVERT: H 129 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7326 (ptmt) REVERT: H 193 LYS cc_start: 0.9063 (mtmt) cc_final: 0.8383 (mttm) REVERT: H 228 MET cc_start: 0.8020 (ttt) cc_final: 0.7624 (ttt) outliers start: 65 outliers final: 56 residues processed: 191 average time/residue: 0.1910 time to fit residues: 51.2722 Evaluate side-chains 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR 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 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 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 190 LEU Chi-restraints excluded: chain C residue 193 LYS 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 190 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 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 206 GLU 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 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 253 CYS Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.127467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.113610 restraints weight = 15095.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.116068 restraints weight = 6650.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.117792 restraints weight = 3872.823| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8824 Z= 0.204 Angle : 0.618 8.092 11992 Z= 0.343 Chirality : 0.052 0.137 1440 Planarity : 0.002 0.019 1488 Dihedral : 6.477 30.968 1227 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.85 % Allowed : 24.40 % 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: -3.84 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 239 PHE 0.010 0.002 PHE D 237 TYR 0.032 0.002 TYR H 236 ARG 0.001 0.000 ARG F 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 195 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 136 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7983 (pt0) REVERT: C 129 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.6535 (pttp) REVERT: C 161 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7450 (mt-10) REVERT: D 129 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6549 (pttp) REVERT: D 207 MET cc_start: 0.5821 (ttt) cc_final: 0.5482 (mtp) REVERT: E 182 ASN cc_start: 0.8304 (t0) cc_final: 0.7906 (t0) REVERT: E 193 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8228 (mttt) REVERT: F 138 GLN cc_start: 0.7708 (mt0) cc_final: 0.7428 (mt0) REVERT: F 182 ASN cc_start: 0.8276 (t0) cc_final: 0.7881 (t0) REVERT: F 193 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8339 (mtpt) REVERT: F 210 MET cc_start: 0.8407 (ttt) cc_final: 0.7974 (ttm) REVERT: G 124 LYS cc_start: 0.7727 (ptpt) cc_final: 0.6139 (mmmt) REVERT: G 138 GLN cc_start: 0.7870 (mt0) cc_final: 0.7438 (tt0) REVERT: G 227 MET cc_start: 0.7484 (mpt) cc_final: 0.6956 (mpt) REVERT: G 228 MET cc_start: 0.7853 (ttt) cc_final: 0.7476 (ttt) REVERT: G 236 TYR cc_start: 0.8684 (t80) cc_final: 0.8422 (t80) REVERT: H 124 LYS cc_start: 0.7866 (ptpt) cc_final: 0.6323 (mmmt) REVERT: H 129 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7234 (ptmt) REVERT: H 138 GLN cc_start: 0.7963 (mt0) cc_final: 0.7533 (tt0) REVERT: H 193 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8483 (mttp) REVERT: H 227 MET cc_start: 0.7546 (mtm) cc_final: 0.7203 (mpp) REVERT: H 228 MET cc_start: 0.7930 (ttt) cc_final: 0.7533 (ttt) outliers start: 59 outliers final: 53 residues processed: 185 average time/residue: 0.1982 time to fit residues: 51.7991 Evaluate side-chains 192 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 234 THR 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 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 190 LEU 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 190 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 253 CYS Chi-restraints excluded: chain F residue 124 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain G residue 214 CYS Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 67 optimal weight: 0.1980 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.123932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.110445 restraints weight = 15530.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.112555 restraints weight = 6797.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.114319 restraints weight = 4089.379| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8824 Z= 0.286 Angle : 0.660 7.599 11992 Z= 0.369 Chirality : 0.053 0.137 1440 Planarity : 0.003 0.021 1488 Dihedral : 6.818 33.443 1227 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 5.95 % Allowed : 24.31 % 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: -3.88 (0.20), residues: 1064 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 239 PHE 0.012 0.002 PHE D 237 TYR 0.033 0.003 TYR H 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: 3065.84 seconds wall clock time: 55 minutes 59.84 seconds (3359.84 seconds total)