Starting phenix.real_space_refine on Mon Nov 17 15:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmz_47021/11_2025/9dmz_47021.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmz_47021/11_2025/9dmz_47021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dmz_47021/11_2025/9dmz_47021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmz_47021/11_2025/9dmz_47021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dmz_47021/11_2025/9dmz_47021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmz_47021/11_2025/9dmz_47021.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 1.146 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 45 5.16 5 C 3540 2.51 5 N 1000 2.21 5 O 1105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5690 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "C" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "E" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.64, per 1000 atoms: 0.29 Number of scatterers: 5690 At special positions: 0 Unit cell: (137.514, 70.414, 46.3904, 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 45 16.00 O 1105 8.00 N 1000 7.00 C 3540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 184 " " NAG A 302 " - " ASN A 200 " " NAG B 301 " - " ASN B 184 " " NAG B 302 " - " ASN B 200 " " NAG C 301 " - " ASN C 184 " " NAG C 302 " - " ASN C 200 " " NAG D 301 " - " ASN D 184 " " NAG D 302 " - " ASN D 200 " " NAG E 301 " - " ASN E 184 " " NAG E 302 " - " ASN E 200 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 213.8 milliseconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1250 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 94 through 95 removed outlier: 6.646A pdb=" N GLY A 94 " --> pdb=" O GLN C 95 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY C 94 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 109 through 111 removed outlier: 6.473A pdb=" N LYS A 109 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS C 109 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 114 through 116 removed outlier: 6.423A pdb=" N HIS A 114 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS C 114 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.171A pdb=" N GLY B 130 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY A 130 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 134 through 138 removed outlier: 6.509A pdb=" N GLY A 134 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N MET C 137 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA A 136 " --> pdb=" O MET C 137 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C 134 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N MET E 137 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 136 " --> pdb=" O MET E 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 141 through 142 removed outlier: 6.483A pdb=" N LEU A 141 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU C 141 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 147 through 154 removed outlier: 6.566A pdb=" N ASP A 147 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASP C 150 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU A 149 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYR C 152 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG A 151 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ARG C 154 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 153 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP C 147 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASP E 150 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU C 149 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR E 152 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG C 151 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ARG E 154 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR C 153 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 157 through 159 removed outlier: 6.649A pdb=" N TYR A 158 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 158 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 164 through 166 removed outlier: 6.404A pdb=" N VAL A 164 " --> pdb=" O TYR C 165 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 164 " --> pdb=" O TYR E 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 171 removed outlier: 8.927A pdb=" N VAL B 169 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N VAL A 169 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN C 171 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN E 171 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 177 through 181 removed outlier: 6.176A pdb=" N THR A 177 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS C 180 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 179 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR C 177 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HIS E 180 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 179 " --> pdb=" O HIS E 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 196 removed outlier: 6.423A pdb=" N THR B 186 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLN D 189 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS B 188 " --> pdb=" O GLN D 189 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR D 191 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS B 190 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N THR D 193 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 192 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR D 195 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 194 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR A 186 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLN B 189 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS A 188 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR B 191 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS A 190 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR B 193 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 192 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR B 195 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR A 194 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 202 through 206 removed outlier: 6.254A pdb=" N GLU A 203 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE C 206 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP A 205 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C 203 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE E 206 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP C 205 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 220 through 223 removed outlier: 6.092A pdb=" N TYR A 221 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR C 221 " --> pdb=" O GLN E 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 226 through 228 removed outlier: 6.505A pdb=" N ALA B 227 " --> pdb=" O TYR D 228 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 227 " --> pdb=" O TYR B 228 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 276 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: 0.85 Time building geometry restraints manager: 0.59 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: 1864 1.34 - 1.46: 1009 1.46 - 1.57: 2877 1.57 - 1.69: 0 1.69 - 1.80: 80 Bond restraints: 5830 Sorted by residual: bond pdb=" C5 NAG E 302 " pdb=" O5 NAG E 302 " ideal model delta sigma weight residual 1.413 1.443 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C5 NAG D 302 " pdb=" O5 NAG D 302 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C5 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C5 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C5 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 5825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 7389 0.99 - 1.98: 363 1.98 - 2.97: 68 2.97 - 3.97: 54 3.97 - 4.96: 16 Bond angle restraints: 7890 Sorted by residual: angle pdb=" C ASN A 200 " pdb=" CA ASN A 200 " pdb=" CB ASN A 200 " ideal model delta sigma weight residual 111.73 106.77 4.96 1.42e+00 4.96e-01 1.22e+01 angle pdb=" C ASN C 200 " pdb=" CA ASN C 200 " pdb=" CB ASN C 200 " ideal model delta sigma weight residual 111.73 106.78 4.95 1.42e+00 4.96e-01 1.22e+01 angle pdb=" C ASN D 200 " pdb=" CA ASN D 200 " pdb=" CB ASN D 200 " ideal model delta sigma weight residual 111.73 106.78 4.95 1.42e+00 4.96e-01 1.22e+01 angle pdb=" C ASN E 200 " pdb=" CA ASN E 200 " pdb=" CB ASN E 200 " ideal model delta sigma weight residual 111.73 106.83 4.90 1.42e+00 4.96e-01 1.19e+01 angle pdb=" C ASN B 200 " pdb=" CA ASN B 200 " pdb=" CB ASN B 200 " ideal model delta sigma weight residual 111.73 106.83 4.90 1.42e+00 4.96e-01 1.19e+01 ... (remaining 7885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.89: 3091 12.89 - 25.79: 274 25.79 - 38.68: 160 38.68 - 51.58: 25 51.58 - 64.47: 10 Dihedral angle restraints: 3560 sinusoidal: 1565 harmonic: 1995 Sorted by residual: dihedral pdb=" CB CYS B 182 " pdb=" SG CYS B 182 " pdb=" SG CYS B 217 " pdb=" CB CYS B 217 " ideal model delta sinusoidal sigma weight residual -86.00 -119.09 33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CB CYS D 182 " pdb=" SG CYS D 182 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual -86.00 -119.08 33.08 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CB CYS C 182 " pdb=" SG CYS C 182 " pdb=" SG CYS C 217 " pdb=" CB CYS C 217 " ideal model delta sinusoidal sigma weight residual -86.00 -119.05 33.05 1 1.00e+01 1.00e-02 1.55e+01 ... (remaining 3557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 758 0.105 - 0.209: 62 0.209 - 0.314: 0 0.314 - 0.418: 0 0.418 - 0.523: 5 Chirality restraints: 825 Sorted by residual: chirality pdb=" C1 NAG D 302 " pdb=" ND2 ASN D 200 " pdb=" C2 NAG D 302 " pdb=" O5 NAG D 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 200 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" C1 NAG A 302 " pdb=" ND2 ASN A 200 " pdb=" C2 NAG A 302 " pdb=" O5 NAG A 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 822 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 200 " -0.022 2.00e-02 2.50e+03 2.24e-02 6.26e+00 pdb=" CG ASN E 200 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN E 200 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN E 200 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG E 302 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 200 " -0.022 2.00e-02 2.50e+03 2.24e-02 6.26e+00 pdb=" CG ASN D 200 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN D 200 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN D 200 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG D 302 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 200 " -0.022 2.00e-02 2.50e+03 2.22e-02 6.17e+00 pdb=" CG ASN C 200 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 200 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 200 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C 302 " -0.022 2.00e-02 2.50e+03 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1174 2.80 - 3.33: 5174 3.33 - 3.85: 10397 3.85 - 4.38: 12432 4.38 - 4.90: 23300 Nonbonded interactions: 52477 Sorted by model distance: nonbonded pdb=" O GLY B 117 " pdb=" OH TYR C 131 " model vdw 2.275 3.040 nonbonded pdb=" O GLY A 117 " pdb=" OH TYR E 131 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 131 " pdb=" O GLY D 117 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR B 221 " pdb=" O MET D 112 " model vdw 2.346 3.040 nonbonded pdb=" OH TYR A 221 " pdb=" O MET B 112 " model vdw 2.378 3.040 ... (remaining 52472 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 individual isotropic 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: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.420 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:9.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5845 Z= 0.146 Angle : 0.824 16.767 7930 Z= 0.370 Chirality : 0.064 0.523 825 Planarity : 0.002 0.018 1025 Dihedral : 13.013 64.474 2295 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.27), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 159 TYR 0.006 0.001 TYR C 172 PHE 0.009 0.001 PHE C 201 TRP 0.002 0.000 TRP B 93 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5830) covalent geometry : angle 0.59705 ( 7890) SS BOND : bond 0.00358 ( 5) SS BOND : angle 0.34016 ( 10) hydrogen bonds : bond 0.15347 ( 92) hydrogen bonds : angle 9.71251 ( 276) link_NAG-ASN : bond 0.01028 ( 10) link_NAG-ASN : angle 9.25234 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8578 (t0) cc_final: 0.8334 (t70) REVERT: A 150 ASP cc_start: 0.7231 (t0) cc_final: 0.6669 (t0) REVERT: A 196 THR cc_start: 0.7626 (m) cc_final: 0.7311 (p) REVERT: A 206 ILE cc_start: 0.8565 (mt) cc_final: 0.8326 (mt) REVERT: B 196 THR cc_start: 0.7594 (m) cc_final: 0.7218 (p) REVERT: C 147 ASP cc_start: 0.8713 (t0) cc_final: 0.8487 (t70) REVERT: C 196 THR cc_start: 0.7573 (m) cc_final: 0.7290 (p) REVERT: D 229 TYR cc_start: 0.7897 (m-80) cc_final: 0.7682 (m-80) REVERT: E 99 HIS cc_start: 0.7871 (m90) cc_final: 0.7650 (m-70) REVERT: E 139 ARG cc_start: 0.6320 (ttp80) cc_final: 0.5815 (ttp-170) REVERT: E 174 ASN cc_start: 0.6700 (m110) cc_final: 0.6077 (m-40) REVERT: E 196 THR cc_start: 0.7635 (m) cc_final: 0.7415 (p) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.4929 time to fit residues: 140.8496 Evaluate side-chains 234 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 174 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN C 156 ASN C 173 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 173 ASN E 215 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.183297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.166921 restraints weight = 5791.457| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.26 r_work: 0.3997 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5845 Z= 0.115 Angle : 0.718 11.617 7930 Z= 0.338 Chirality : 0.061 0.433 825 Planarity : 0.003 0.042 1025 Dihedral : 5.842 34.817 990 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.08 % Allowed : 23.93 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.27), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 154 TYR 0.007 0.001 TYR B 172 PHE 0.012 0.001 PHE A 201 TRP 0.003 0.001 TRP B 93 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5830) covalent geometry : angle 0.61646 ( 7890) SS BOND : bond 0.00252 ( 5) SS BOND : angle 0.62722 ( 10) hydrogen bonds : bond 0.02711 ( 92) hydrogen bonds : angle 6.79983 ( 276) link_NAG-ASN : bond 0.00539 ( 10) link_NAG-ASN : angle 6.02120 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.235 Fit side-chains REVERT: A 150 ASP cc_start: 0.7392 (t0) cc_final: 0.6899 (t0) REVERT: A 196 THR cc_start: 0.7749 (m) cc_final: 0.7396 (p) REVERT: A 206 ILE cc_start: 0.8505 (mt) cc_final: 0.8303 (mt) REVERT: B 99 HIS cc_start: 0.7839 (m90) cc_final: 0.7583 (m-70) REVERT: B 196 THR cc_start: 0.7634 (m) cc_final: 0.7249 (p) REVERT: B 208 MET cc_start: 0.7616 (mtt) cc_final: 0.7416 (mtt) REVERT: C 196 THR cc_start: 0.7565 (m) cc_final: 0.7302 (p) REVERT: E 139 ARG cc_start: 0.6391 (ttp80) cc_final: 0.6001 (ttp-170) REVERT: E 167 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.6886 (tpm170) REVERT: E 174 ASN cc_start: 0.6607 (m110) cc_final: 0.6010 (m-40) REVERT: E 196 THR cc_start: 0.7616 (m) cc_final: 0.7387 (p) outliers start: 18 outliers final: 4 residues processed: 242 average time/residue: 0.4895 time to fit residues: 123.9655 Evaluate side-chains 233 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 229 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain D residue 196 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN D 143 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 180 HIS E 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.175540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.158322 restraints weight = 5705.791| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.10 r_work: 0.3920 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5845 Z= 0.152 Angle : 0.702 9.698 7930 Z= 0.343 Chirality : 0.057 0.340 825 Planarity : 0.004 0.072 1025 Dihedral : 6.505 42.873 990 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.25 % Allowed : 22.74 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.26), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 167 TYR 0.015 0.001 TYR E 152 PHE 0.014 0.002 PHE A 201 TRP 0.006 0.001 TRP B 93 HIS 0.006 0.002 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 5830) covalent geometry : angle 0.63957 ( 7890) SS BOND : bond 0.00916 ( 5) SS BOND : angle 1.01220 ( 10) hydrogen bonds : bond 0.02537 ( 92) hydrogen bonds : angle 6.19175 ( 276) link_NAG-ASN : bond 0.00515 ( 10) link_NAG-ASN : angle 4.73315 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.225 Fit side-chains REVERT: A 150 ASP cc_start: 0.7426 (t0) cc_final: 0.6846 (t0) REVERT: A 170 ASP cc_start: 0.8230 (m-30) cc_final: 0.8029 (m-30) REVERT: A 196 THR cc_start: 0.7795 (m) cc_final: 0.7479 (p) REVERT: B 150 ASP cc_start: 0.7470 (t0) cc_final: 0.7158 (t0) REVERT: B 196 THR cc_start: 0.7838 (m) cc_final: 0.7440 (p) REVERT: C 196 THR cc_start: 0.7528 (m) cc_final: 0.7292 (p) REVERT: C 223 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8045 (ttm-80) REVERT: D 98 THR cc_start: 0.8682 (t) cc_final: 0.8409 (m) REVERT: E 139 ARG cc_start: 0.6792 (ttp80) cc_final: 0.6181 (ttp-170) REVERT: E 154 ARG cc_start: 0.5905 (mmt-90) cc_final: 0.4560 (ttt-90) REVERT: E 167 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.6879 (tpm170) REVERT: E 196 THR cc_start: 0.7584 (m) cc_final: 0.7367 (p) outliers start: 19 outliers final: 6 residues processed: 239 average time/residue: 0.4896 time to fit residues: 122.7388 Evaluate side-chains 230 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 210 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN A 215 GLN A 220 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 176 ASN C 215 GLN C 220 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN E 99 HIS E 215 GLN E 220 GLN E 226 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.161789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145213 restraints weight = 5801.785| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.26 r_work: 0.3787 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5845 Z= 0.292 Angle : 0.824 10.494 7930 Z= 0.414 Chirality : 0.061 0.330 825 Planarity : 0.004 0.039 1025 Dihedral : 7.499 48.100 990 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.91 % Allowed : 23.59 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 154 TYR 0.018 0.003 TYR E 131 PHE 0.015 0.002 PHE A 201 TRP 0.007 0.002 TRP B 93 HIS 0.011 0.002 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 5830) covalent geometry : angle 0.76915 ( 7890) SS BOND : bond 0.00540 ( 5) SS BOND : angle 1.81789 ( 10) hydrogen bonds : bond 0.02978 ( 92) hydrogen bonds : angle 6.57020 ( 276) link_NAG-ASN : bond 0.00240 ( 10) link_NAG-ASN : angle 4.75561 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7662 (t0) cc_final: 0.7024 (t70) REVERT: A 172 TYR cc_start: 0.6914 (m-80) cc_final: 0.6629 (m-80) REVERT: A 196 THR cc_start: 0.7790 (m) cc_final: 0.7455 (t) REVERT: B 132 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7782 (mmm) REVERT: B 150 ASP cc_start: 0.7526 (t0) cc_final: 0.7182 (t70) REVERT: B 196 THR cc_start: 0.7890 (m) cc_final: 0.7566 (p) REVERT: C 132 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7695 (mmm) REVERT: C 196 THR cc_start: 0.7557 (m) cc_final: 0.7164 (t) REVERT: D 150 ASP cc_start: 0.7560 (t0) cc_final: 0.7257 (t0) REVERT: D 196 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7380 (t) REVERT: D 216 MET cc_start: 0.8013 (ttm) cc_final: 0.7775 (ttt) REVERT: D 223 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6592 (tpm170) REVERT: E 139 ARG cc_start: 0.7220 (ttp80) cc_final: 0.6199 (ttp-170) REVERT: E 223 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7064 (ttp-170) outliers start: 17 outliers final: 2 residues processed: 235 average time/residue: 0.4916 time to fit residues: 121.0571 Evaluate side-chains 230 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 223 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.164291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147484 restraints weight = 5871.595| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.29 r_work: 0.3824 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5845 Z= 0.209 Angle : 0.740 11.253 7930 Z= 0.367 Chirality : 0.058 0.315 825 Planarity : 0.003 0.024 1025 Dihedral : 7.181 48.448 990 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.42 % Allowed : 24.44 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 167 TYR 0.018 0.002 TYR A 131 PHE 0.016 0.002 PHE A 201 TRP 0.006 0.002 TRP B 93 HIS 0.009 0.002 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 5830) covalent geometry : angle 0.69198 ( 7890) SS BOND : bond 0.00243 ( 5) SS BOND : angle 1.39855 ( 10) hydrogen bonds : bond 0.02478 ( 92) hydrogen bonds : angle 6.29268 ( 276) link_NAG-ASN : bond 0.00308 ( 10) link_NAG-ASN : angle 4.25242 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7632 (t0) cc_final: 0.7044 (t70) REVERT: A 196 THR cc_start: 0.7812 (m) cc_final: 0.7482 (t) REVERT: B 98 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8507 (m) REVERT: B 150 ASP cc_start: 0.7518 (t0) cc_final: 0.7215 (t70) REVERT: B 196 THR cc_start: 0.7913 (m) cc_final: 0.7616 (p) REVERT: C 154 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7262 (ttt-90) REVERT: C 196 THR cc_start: 0.7608 (m) cc_final: 0.7202 (t) REVERT: C 223 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8195 (ttm-80) REVERT: D 196 THR cc_start: 0.7715 (m) cc_final: 0.7412 (t) REVERT: D 216 MET cc_start: 0.7993 (ttm) cc_final: 0.7772 (ttt) REVERT: D 223 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6552 (tpm170) REVERT: E 139 ARG cc_start: 0.7170 (ttp80) cc_final: 0.6160 (ttp-170) REVERT: E 223 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7118 (ttp-170) outliers start: 20 outliers final: 7 residues processed: 228 average time/residue: 0.5110 time to fit residues: 121.9615 Evaluate side-chains 229 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 28 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN C 215 GLN C 226 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.164070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147240 restraints weight = 5796.224| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.29 r_work: 0.3822 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5845 Z= 0.219 Angle : 0.746 11.706 7930 Z= 0.371 Chirality : 0.058 0.308 825 Planarity : 0.003 0.026 1025 Dihedral : 7.177 49.254 990 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.93 % Allowed : 24.44 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 139 TYR 0.020 0.002 TYR A 131 PHE 0.016 0.002 PHE A 201 TRP 0.006 0.002 TRP B 93 HIS 0.010 0.002 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 5830) covalent geometry : angle 0.70438 ( 7890) SS BOND : bond 0.00409 ( 5) SS BOND : angle 1.34456 ( 10) hydrogen bonds : bond 0.02502 ( 92) hydrogen bonds : angle 6.24423 ( 276) link_NAG-ASN : bond 0.00279 ( 10) link_NAG-ASN : angle 3.99588 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7639 (t0) cc_final: 0.7028 (t70) REVERT: A 196 THR cc_start: 0.7812 (m) cc_final: 0.7489 (t) REVERT: B 98 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8478 (m) REVERT: B 150 ASP cc_start: 0.7507 (t0) cc_final: 0.7198 (t70) REVERT: B 196 THR cc_start: 0.7907 (m) cc_final: 0.7596 (p) REVERT: C 132 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7668 (mmm) REVERT: C 154 ARG cc_start: 0.7423 (ttt180) cc_final: 0.7162 (ttt-90) REVERT: C 157 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7617 (tmt) REVERT: C 196 THR cc_start: 0.7578 (m) cc_final: 0.7169 (t) REVERT: D 196 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7437 (t) REVERT: D 223 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6584 (tpm170) REVERT: E 139 ARG cc_start: 0.7181 (ttp80) cc_final: 0.6200 (ttp-170) REVERT: E 223 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7196 (ttp-170) outliers start: 23 outliers final: 6 residues processed: 227 average time/residue: 0.5025 time to fit residues: 119.5943 Evaluate side-chains 229 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 11 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN E 99 HIS E 215 GLN E 220 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.171166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.155022 restraints weight = 5781.475| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.29 r_work: 0.3938 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5845 Z= 0.126 Angle : 0.673 11.283 7930 Z= 0.332 Chirality : 0.056 0.302 825 Planarity : 0.002 0.031 1025 Dihedral : 6.658 49.193 990 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.22 % Allowed : 25.64 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 139 TYR 0.019 0.001 TYR A 131 PHE 0.017 0.002 PHE A 201 TRP 0.004 0.001 TRP B 93 HIS 0.006 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5830) covalent geometry : angle 0.64213 ( 7890) SS BOND : bond 0.00486 ( 5) SS BOND : angle 0.92371 ( 10) hydrogen bonds : bond 0.02035 ( 92) hydrogen bonds : angle 5.83860 ( 276) link_NAG-ASN : bond 0.00410 ( 10) link_NAG-ASN : angle 3.31940 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7573 (t0) cc_final: 0.7100 (t0) REVERT: A 196 THR cc_start: 0.7809 (m) cc_final: 0.7485 (t) REVERT: B 98 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8465 (m) REVERT: B 132 MET cc_start: 0.8133 (mmm) cc_final: 0.7787 (mmp) REVERT: B 150 ASP cc_start: 0.7482 (t0) cc_final: 0.7174 (t70) REVERT: B 196 THR cc_start: 0.7946 (m) cc_final: 0.7648 (p) REVERT: B 204 THR cc_start: 0.8454 (m) cc_final: 0.8235 (p) REVERT: B 223 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7838 (ttm-80) REVERT: C 132 MET cc_start: 0.7858 (mmm) cc_final: 0.7411 (mtm) REVERT: C 196 THR cc_start: 0.7602 (m) cc_final: 0.7184 (t) REVERT: D 196 THR cc_start: 0.7754 (m) cc_final: 0.7458 (t) REVERT: E 139 ARG cc_start: 0.7019 (ttp80) cc_final: 0.6030 (ttp-170) REVERT: E 223 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7175 (ttp-170) outliers start: 13 outliers final: 6 residues processed: 227 average time/residue: 0.5011 time to fit residues: 119.0029 Evaluate side-chains 227 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 26 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.154026 restraints weight = 5708.739| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.26 r_work: 0.3925 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5845 Z= 0.139 Angle : 0.681 10.570 7930 Z= 0.338 Chirality : 0.056 0.298 825 Planarity : 0.003 0.033 1025 Dihedral : 6.592 48.900 990 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.91 % Allowed : 25.98 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 167 TYR 0.018 0.002 TYR A 131 PHE 0.016 0.002 PHE B 201 TRP 0.005 0.001 TRP B 93 HIS 0.007 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5830) covalent geometry : angle 0.65291 ( 7890) SS BOND : bond 0.00234 ( 5) SS BOND : angle 1.12752 ( 10) hydrogen bonds : bond 0.02112 ( 92) hydrogen bonds : angle 5.84540 ( 276) link_NAG-ASN : bond 0.00356 ( 10) link_NAG-ASN : angle 3.15616 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.256 Fit side-chains REVERT: A 147 ASP cc_start: 0.8770 (t0) cc_final: 0.8397 (t70) REVERT: A 150 ASP cc_start: 0.7554 (t0) cc_final: 0.7095 (t0) REVERT: A 196 THR cc_start: 0.7797 (m) cc_final: 0.7477 (t) REVERT: B 98 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8430 (m) REVERT: B 132 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7902 (mmp) REVERT: B 150 ASP cc_start: 0.7488 (t0) cc_final: 0.7194 (t0) REVERT: B 196 THR cc_start: 0.7915 (m) cc_final: 0.7617 (p) REVERT: B 209 MET cc_start: 0.7837 (mmm) cc_final: 0.7586 (tpt) REVERT: C 132 MET cc_start: 0.7780 (mmm) cc_final: 0.7385 (mtm) REVERT: C 196 THR cc_start: 0.7614 (m) cc_final: 0.7200 (t) REVERT: D 196 THR cc_start: 0.7749 (m) cc_final: 0.7442 (t) REVERT: E 107 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7826 (mtmm) REVERT: E 139 ARG cc_start: 0.7058 (ttp80) cc_final: 0.6063 (ttp-170) REVERT: E 154 ARG cc_start: 0.6175 (mmt-90) cc_final: 0.3810 (ttm-80) REVERT: E 167 ARG cc_start: 0.8087 (ttt-90) cc_final: 0.6934 (tpm170) REVERT: E 223 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7139 (ttp-170) outliers start: 17 outliers final: 6 residues processed: 229 average time/residue: 0.5090 time to fit residues: 122.0694 Evaluate side-chains 232 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 35 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 overall best weight: 3.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN E 99 HIS E 220 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145197 restraints weight = 5812.381| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.28 r_work: 0.3797 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5845 Z= 0.280 Angle : 0.809 10.890 7930 Z= 0.412 Chirality : 0.060 0.291 825 Planarity : 0.004 0.053 1025 Dihedral : 7.218 48.522 990 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.42 % Allowed : 25.98 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 154 TYR 0.022 0.003 TYR C 131 PHE 0.016 0.002 PHE C 201 TRP 0.007 0.002 TRP B 93 HIS 0.012 0.002 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 5830) covalent geometry : angle 0.77578 ( 7890) SS BOND : bond 0.00297 ( 5) SS BOND : angle 1.91886 ( 10) hydrogen bonds : bond 0.02810 ( 92) hydrogen bonds : angle 6.19700 ( 276) link_NAG-ASN : bond 0.00260 ( 10) link_NAG-ASN : angle 3.67030 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8813 (t0) cc_final: 0.8442 (t70) REVERT: A 150 ASP cc_start: 0.7638 (t0) cc_final: 0.7045 (t70) REVERT: A 196 THR cc_start: 0.7805 (m) cc_final: 0.7498 (t) REVERT: B 98 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8471 (m) REVERT: B 132 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7872 (mmp) REVERT: B 150 ASP cc_start: 0.7509 (t0) cc_final: 0.7191 (t70) REVERT: B 154 ARG cc_start: 0.7474 (ttt-90) cc_final: 0.7173 (ttt180) REVERT: B 196 THR cc_start: 0.7909 (m) cc_final: 0.7661 (p) REVERT: C 132 MET cc_start: 0.7858 (mmm) cc_final: 0.7523 (mtm) REVERT: C 154 ARG cc_start: 0.7559 (ttt180) cc_final: 0.7225 (ttt-90) REVERT: C 163 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: C 196 THR cc_start: 0.7673 (m) cc_final: 0.7279 (t) REVERT: D 150 ASP cc_start: 0.7529 (t0) cc_final: 0.7191 (t0) REVERT: D 154 ARG cc_start: 0.7241 (tpt170) cc_final: 0.6751 (tpt170) REVERT: D 196 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7424 (t) REVERT: D 223 ARG cc_start: 0.7207 (tpm170) cc_final: 0.6134 (ttm170) REVERT: E 139 ARG cc_start: 0.7220 (ttp80) cc_final: 0.6257 (ttp-170) REVERT: E 223 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7187 (ttp-170) outliers start: 20 outliers final: 7 residues processed: 231 average time/residue: 0.5574 time to fit residues: 134.3199 Evaluate side-chains 233 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN D 146 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.166619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.149719 restraints weight = 5784.492| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.30 r_work: 0.3861 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5845 Z= 0.181 Angle : 0.732 10.562 7930 Z= 0.369 Chirality : 0.057 0.290 825 Planarity : 0.003 0.042 1025 Dihedral : 6.852 47.350 990 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.71 % Allowed : 28.03 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 139 TYR 0.022 0.002 TYR A 131 PHE 0.016 0.002 PHE A 201 TRP 0.005 0.001 TRP A 93 HIS 0.009 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5830) covalent geometry : angle 0.70204 ( 7890) SS BOND : bond 0.00238 ( 5) SS BOND : angle 1.28480 ( 10) hydrogen bonds : bond 0.02255 ( 92) hydrogen bonds : angle 5.92929 ( 276) link_NAG-ASN : bond 0.00314 ( 10) link_NAG-ASN : angle 3.40048 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8770 (t0) cc_final: 0.8402 (t70) REVERT: A 150 ASP cc_start: 0.7609 (t0) cc_final: 0.7041 (t70) REVERT: A 196 THR cc_start: 0.7764 (m) cc_final: 0.7445 (t) REVERT: B 98 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8449 (m) REVERT: B 132 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7843 (mmp) REVERT: B 150 ASP cc_start: 0.7498 (t0) cc_final: 0.7214 (t70) REVERT: B 196 THR cc_start: 0.7888 (m) cc_final: 0.7635 (p) REVERT: B 223 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8056 (ttm-80) REVERT: C 132 MET cc_start: 0.7735 (mmm) cc_final: 0.7471 (mtm) REVERT: C 154 ARG cc_start: 0.7465 (ttt180) cc_final: 0.7145 (ttt-90) REVERT: C 196 THR cc_start: 0.7623 (m) cc_final: 0.7236 (t) REVERT: C 223 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7889 (tpt90) REVERT: D 196 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7418 (t) REVERT: D 223 ARG cc_start: 0.7122 (tpm170) cc_final: 0.6105 (ttm-80) REVERT: E 139 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6123 (ttp-170) REVERT: E 223 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7166 (ttp-170) outliers start: 10 outliers final: 3 residues processed: 227 average time/residue: 0.5117 time to fit residues: 121.5814 Evaluate side-chains 227 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 0.0370 chunk 28 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.167867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151247 restraints weight = 5643.392| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.27 r_work: 0.3891 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5845 Z= 0.173 Angle : 0.728 11.197 7930 Z= 0.367 Chirality : 0.057 0.290 825 Planarity : 0.003 0.033 1025 Dihedral : 6.703 46.253 990 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.54 % Allowed : 28.55 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 139 TYR 0.021 0.002 TYR A 131 PHE 0.016 0.002 PHE A 201 TRP 0.005 0.001 TRP B 93 HIS 0.009 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5830) covalent geometry : angle 0.70093 ( 7890) SS BOND : bond 0.00292 ( 5) SS BOND : angle 1.32675 ( 10) hydrogen bonds : bond 0.02255 ( 92) hydrogen bonds : angle 5.85646 ( 276) link_NAG-ASN : bond 0.00330 ( 10) link_NAG-ASN : angle 3.23642 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2800.50 seconds wall clock time: 48 minutes 42.80 seconds (2922.80 seconds total)