Starting phenix.real_space_refine on Sat May 10 08:42:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmz_47021/05_2025/9dmz_47021.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmz_47021/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dmz_47021/05_2025/9dmz_47021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmz_47021/05_2025/9dmz_47021.map" model { file = "/net/cci-nas-00/data/ceres_data/9dmz_47021/05_2025/9dmz_47021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmz_47021/05_2025/9dmz_47021.cif" } resolution = 2.8 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= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.38, per 1000 atoms: 0.77 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: 1.29 Conformation dependent library (CDL) restraints added in 653.0 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: 0.84 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: 1.46 Time building geometry restraints manager: 1.53 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: 0.03 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: 3.650 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.420 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- 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 : 10.79 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 (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: -3.51 (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 TRP 0.002 0.000 TRP B 93 HIS 0.005 0.001 HIS A 143 PHE 0.009 0.001 PHE C 201 TYR 0.006 0.001 TYR C 172 ARG 0.001 0.000 ARG C 159 Details of bonding type rmsd link_NAG-ASN : bond 0.01028 ( 10) link_NAG-ASN : angle 9.25234 ( 30) hydrogen bonds : bond 0.15347 ( 92) hydrogen bonds : angle 9.71251 ( 276) SS BOND : bond 0.00358 ( 5) SS BOND : angle 0.34016 ( 10) covalent geometry : bond 0.00315 ( 5830) covalent geometry : angle 0.59705 ( 7890) *********************** 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 : 0.576 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: 0.9722 time to fit residues: 278.4471 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 : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.182769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.166733 restraints weight = 5685.549| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.24 r_work: 0.3998 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5845 Z= 0.124 Angle : 0.725 11.651 7930 Z= 0.341 Chirality : 0.061 0.421 825 Planarity : 0.003 0.048 1025 Dihedral : 5.899 35.220 990 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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 (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: -3.52 (0.27), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 93 HIS 0.005 0.001 HIS A 143 PHE 0.012 0.001 PHE A 201 TYR 0.007 0.001 TYR B 131 ARG 0.009 0.001 ARG D 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 10) link_NAG-ASN : angle 5.97510 ( 30) hydrogen bonds : bond 0.02531 ( 92) hydrogen bonds : angle 6.74890 ( 276) SS BOND : bond 0.00562 ( 5) SS BOND : angle 0.70327 ( 10) covalent geometry : bond 0.00278 ( 5830) covalent geometry : angle 0.62625 ( 7890) *********************** 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 262 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.588 Fit side-chains REVERT: A 150 ASP cc_start: 0.7395 (t0) cc_final: 0.6842 (t0) REVERT: A 196 THR cc_start: 0.7748 (m) cc_final: 0.7394 (p) REVERT: A 206 ILE cc_start: 0.8509 (mt) cc_final: 0.8304 (mt) REVERT: B 99 HIS cc_start: 0.7876 (m90) cc_final: 0.7622 (m-70) REVERT: B 150 ASP cc_start: 0.7426 (t0) cc_final: 0.7116 (t0) REVERT: B 196 THR cc_start: 0.7589 (m) cc_final: 0.7203 (p) REVERT: B 208 MET cc_start: 0.7590 (mtt) cc_final: 0.7371 (mtt) REVERT: C 196 THR cc_start: 0.7557 (m) cc_final: 0.7297 (p) REVERT: D 98 THR cc_start: 0.8630 (t) cc_final: 0.8310 (m) REVERT: E 139 ARG cc_start: 0.6415 (ttp80) cc_final: 0.5935 (ttp-170) REVERT: E 167 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.6886 (tpm170) REVERT: E 174 ASN cc_start: 0.6608 (m110) cc_final: 0.5994 (m-40) REVERT: E 196 THR cc_start: 0.7601 (m) cc_final: 0.7374 (p) outliers start: 18 outliers final: 6 residues processed: 247 average time/residue: 1.0653 time to fit residues: 276.1743 Evaluate side-chains 237 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 231 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 194 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 0.0010 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- 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 220 GLN A 222 GLN ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 215 GLN C 220 GLN D 143 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN E 215 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145935 restraints weight = 5750.739| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.13 r_work: 0.3785 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 5845 Z= 0.326 Angle : 0.880 11.301 7930 Z= 0.439 Chirality : 0.064 0.363 825 Planarity : 0.006 0.075 1025 Dihedral : 7.781 43.418 990 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.27 % Allowed : 23.76 % Favored : 71.97 % 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: -3.89 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 93 HIS 0.010 0.003 HIS E 143 PHE 0.014 0.002 PHE A 201 TYR 0.015 0.003 TYR E 131 ARG 0.005 0.001 ARG C 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 10) link_NAG-ASN : angle 5.67731 ( 30) hydrogen bonds : bond 0.03273 ( 92) hydrogen bonds : angle 6.83377 ( 276) SS BOND : bond 0.00621 ( 5) SS BOND : angle 1.65599 ( 10) covalent geometry : bond 0.00704 ( 5830) covalent geometry : angle 0.80788 ( 7890) *********************** 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 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: A 150 ASP cc_start: 0.7639 (t0) cc_final: 0.6997 (t70) REVERT: A 172 TYR cc_start: 0.6918 (m-80) cc_final: 0.6621 (m-80) REVERT: A 196 THR cc_start: 0.7863 (m) cc_final: 0.7562 (p) REVERT: B 150 ASP cc_start: 0.7606 (t0) cc_final: 0.7286 (t70) REVERT: B 196 THR cc_start: 0.7908 (m) cc_final: 0.7507 (p) REVERT: C 196 THR cc_start: 0.7573 (m) cc_final: 0.7218 (t) REVERT: D 150 ASP cc_start: 0.7581 (t0) cc_final: 0.7276 (t0) REVERT: D 196 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7373 (t) REVERT: E 150 ASP cc_start: 0.7589 (t0) cc_final: 0.7269 (t70) REVERT: E 223 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7164 (ttp-170) outliers start: 25 outliers final: 7 residues processed: 238 average time/residue: 1.0562 time to fit residues: 262.9112 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 : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 194 THR 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 163 GLN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 215 GLN E 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.163042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.146248 restraints weight = 5838.169| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.27 r_work: 0.3806 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3581 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= 0.252 Angle : 0.791 10.160 7930 Z= 0.390 Chirality : 0.061 0.339 825 Planarity : 0.004 0.038 1025 Dihedral : 7.471 46.182 990 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.74 % Allowed : 24.96 % Favored : 72.31 % 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 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 93 HIS 0.010 0.002 HIS C 143 PHE 0.016 0.002 PHE A 201 TYR 0.019 0.002 TYR A 131 ARG 0.004 0.001 ARG C 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 10) link_NAG-ASN : angle 4.98884 ( 30) hydrogen bonds : bond 0.02776 ( 92) hydrogen bonds : angle 6.60106 ( 276) SS BOND : bond 0.00656 ( 5) SS BOND : angle 1.43070 ( 10) covalent geometry : bond 0.00542 ( 5830) covalent geometry : angle 0.72937 ( 7890) *********************** 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 241 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7642 (t0) cc_final: 0.7036 (t70) REVERT: A 196 THR cc_start: 0.7834 (m) cc_final: 0.7507 (t) REVERT: A 223 ARG cc_start: 0.8311 (tpt90) cc_final: 0.8045 (tpt90) REVERT: B 150 ASP cc_start: 0.7500 (t0) cc_final: 0.7200 (t70) REVERT: B 196 THR cc_start: 0.7902 (m) cc_final: 0.7589 (p) REVERT: C 196 THR cc_start: 0.7605 (m) cc_final: 0.7202 (t) REVERT: D 139 ARG cc_start: 0.6547 (ttm170) cc_final: 0.6195 (mmt-90) REVERT: D 196 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7400 (t) REVERT: D 216 MET cc_start: 0.8066 (ttm) cc_final: 0.7847 (ttt) REVERT: E 150 ASP cc_start: 0.7559 (t0) cc_final: 0.7238 (t70) REVERT: E 154 ARG cc_start: 0.6154 (mmt-90) cc_final: 0.4364 (ttm-80) REVERT: E 223 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7106 (ttp-170) outliers start: 16 outliers final: 3 residues processed: 228 average time/residue: 1.0285 time to fit residues: 245.5138 Evaluate side-chains 227 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 222 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 163 GLN 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 10 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 0.0570 chunk 60 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 1.8102 ------------------------------------------------------------------------------- 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 215 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 = 0.4095 r_free = 0.4095 target = 0.165286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.148485 restraints weight = 5739.349| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.27 r_work: 0.3835 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5845 Z= 0.186 Angle : 0.722 10.552 7930 Z= 0.355 Chirality : 0.058 0.319 825 Planarity : 0.003 0.030 1025 Dihedral : 7.134 48.349 990 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.76 % Allowed : 24.27 % Favored : 71.97 % 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 (0.24), 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 TRP 0.006 0.001 TRP B 93 HIS 0.008 0.001 HIS C 143 PHE 0.017 0.002 PHE A 201 TYR 0.020 0.002 TYR A 131 ARG 0.005 0.001 ARG C 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 10) link_NAG-ASN : angle 4.27354 ( 30) hydrogen bonds : bond 0.02404 ( 92) hydrogen bonds : angle 6.32078 ( 276) SS BOND : bond 0.00576 ( 5) SS BOND : angle 1.16788 ( 10) covalent geometry : bond 0.00405 ( 5830) covalent geometry : angle 0.67285 ( 7890) *********************** 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 244 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7614 (t0) cc_final: 0.7138 (t0) REVERT: A 196 THR cc_start: 0.7801 (m) cc_final: 0.7480 (t) REVERT: A 223 ARG cc_start: 0.8332 (tpt90) cc_final: 0.8090 (tpt90) REVERT: B 98 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (m) REVERT: B 139 ARG cc_start: 0.7292 (tpt170) cc_final: 0.7044 (tpt170) REVERT: B 150 ASP cc_start: 0.7505 (t0) cc_final: 0.7202 (t70) REVERT: B 196 THR cc_start: 0.7952 (m) cc_final: 0.7635 (p) REVERT: C 196 THR cc_start: 0.7584 (m) cc_final: 0.7176 (t) REVERT: D 139 ARG cc_start: 0.6582 (ttm170) cc_final: 0.6245 (mmt-90) REVERT: D 196 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7461 (t) REVERT: D 223 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6271 (ttm-80) REVERT: E 150 ASP cc_start: 0.7501 (t0) cc_final: 0.7178 (t70) REVERT: E 223 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7174 (ttp-170) outliers start: 22 outliers final: 8 residues processed: 228 average time/residue: 1.0172 time to fit residues: 243.0802 Evaluate side-chains 230 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 106 SER Chi-restraints excluded: chain C residue 106 SER 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 106 SER Chi-restraints excluded: chain E residue 163 GLN 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 64 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.0050 overall best weight: 1.1856 ------------------------------------------------------------------------------- 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 222 GLN ** B 143 HIS ** 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 180 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 = 0.4138 r_free = 0.4138 target = 0.168390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151606 restraints weight = 5717.093| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.26 r_work: 0.3875 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5845 Z= 0.147 Angle : 0.679 10.258 7930 Z= 0.335 Chirality : 0.056 0.308 825 Planarity : 0.003 0.023 1025 Dihedral : 6.847 49.248 990 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.25 % Allowed : 24.62 % 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 (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: -4.04 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.007 0.001 HIS E 143 PHE 0.017 0.002 PHE A 201 TYR 0.019 0.001 TYR A 131 ARG 0.004 0.001 ARG E 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 10) link_NAG-ASN : angle 3.69896 ( 30) hydrogen bonds : bond 0.02146 ( 92) hydrogen bonds : angle 6.05628 ( 276) SS BOND : bond 0.00232 ( 5) SS BOND : angle 1.17879 ( 10) covalent geometry : bond 0.00329 ( 5830) covalent geometry : angle 0.63969 ( 7890) *********************** 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: 19 poor density : 226 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7606 (t0) cc_final: 0.7144 (t0) REVERT: A 196 THR cc_start: 0.7809 (m) cc_final: 0.7493 (t) REVERT: B 98 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8448 (m) REVERT: B 150 ASP cc_start: 0.7491 (t0) cc_final: 0.7192 (t70) REVERT: B 196 THR cc_start: 0.7936 (m) cc_final: 0.7628 (p) REVERT: C 196 THR cc_start: 0.7602 (m) cc_final: 0.7191 (t) REVERT: D 139 ARG cc_start: 0.6593 (ttm170) cc_final: 0.6171 (mmt-90) REVERT: D 196 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7426 (t) REVERT: D 223 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6564 (tpm170) REVERT: E 150 ASP cc_start: 0.7521 (t0) cc_final: 0.7186 (t70) REVERT: E 223 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.7147 (ttp-170) outliers start: 19 outliers final: 7 residues processed: 230 average time/residue: 1.0993 time to fit residues: 264.6063 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 : 0.626 ------------------------------------------------------------------------------- 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 106 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 overall best weight: 1.0500 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.170119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.153304 restraints weight = 5769.999| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.26 r_work: 0.3903 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5845 Z= 0.136 Angle : 0.660 11.097 7930 Z= 0.328 Chirality : 0.056 0.302 825 Planarity : 0.002 0.019 1025 Dihedral : 6.686 49.367 990 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.76 % Allowed : 23.25 % 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 (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: -4.08 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.006 0.001 HIS A 143 PHE 0.017 0.002 PHE A 201 TYR 0.019 0.001 TYR A 131 ARG 0.004 0.001 ARG A 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 10) link_NAG-ASN : angle 3.35669 ( 30) hydrogen bonds : bond 0.02050 ( 92) hydrogen bonds : angle 5.88425 ( 276) SS BOND : bond 0.00360 ( 5) SS BOND : angle 1.04739 ( 10) covalent geometry : bond 0.00309 ( 5830) covalent geometry : angle 0.62781 ( 7890) *********************** 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 248 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.586 Fit side-chains REVERT: A 150 ASP cc_start: 0.7568 (t0) cc_final: 0.7119 (t0) REVERT: A 196 THR cc_start: 0.7798 (m) cc_final: 0.7476 (t) REVERT: B 98 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8416 (m) REVERT: B 150 ASP cc_start: 0.7466 (t0) cc_final: 0.7161 (t70) REVERT: B 181 ASP cc_start: 0.7906 (t70) cc_final: 0.7652 (t70) REVERT: B 196 THR cc_start: 0.7916 (m) cc_final: 0.7608 (p) REVERT: C 196 THR cc_start: 0.7594 (m) cc_final: 0.7174 (t) REVERT: D 139 ARG cc_start: 0.6582 (ttm170) cc_final: 0.6221 (mmt-90) REVERT: D 196 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7460 (p) REVERT: D 223 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6524 (tpm170) REVERT: E 150 ASP cc_start: 0.7478 (t0) cc_final: 0.7134 (t70) REVERT: E 154 ARG cc_start: 0.6187 (mmt-90) cc_final: 0.3802 (ttm-80) REVERT: E 223 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7090 (ttp-170) outliers start: 22 outliers final: 8 residues processed: 231 average time/residue: 1.0706 time to fit residues: 259.0608 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 : 0.584 ------------------------------------------------------------------------------- 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 106 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 106 SER 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 194 THR 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 40 optimal weight: 0.0170 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 57 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.166995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149389 restraints weight = 5699.824| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.17 r_work: 0.3864 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5845 Z= 0.184 Angle : 0.707 10.844 7930 Z= 0.354 Chirality : 0.056 0.297 825 Planarity : 0.003 0.045 1025 Dihedral : 6.836 49.121 990 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.25 % Allowed : 24.79 % Favored : 71.97 % 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: -4.10 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.009 0.001 HIS E 143 PHE 0.016 0.002 PHE A 201 TYR 0.021 0.002 TYR A 131 ARG 0.004 0.001 ARG A 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 10) link_NAG-ASN : angle 3.36211 ( 30) hydrogen bonds : bond 0.02291 ( 92) hydrogen bonds : angle 5.96808 ( 276) SS BOND : bond 0.00321 ( 5) SS BOND : angle 1.29986 ( 10) covalent geometry : bond 0.00407 ( 5830) covalent geometry : angle 0.67628 ( 7890) *********************** 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 242 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.628 Fit side-chains REVERT: A 150 ASP cc_start: 0.7598 (t0) cc_final: 0.7106 (t0) REVERT: A 196 THR cc_start: 0.7812 (m) cc_final: 0.7489 (t) REVERT: B 98 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8429 (m) REVERT: B 150 ASP cc_start: 0.7479 (t0) cc_final: 0.7177 (t70) REVERT: B 196 THR cc_start: 0.7887 (m) cc_final: 0.7595 (p) REVERT: C 163 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: C 196 THR cc_start: 0.7584 (m) cc_final: 0.7178 (t) REVERT: D 139 ARG cc_start: 0.6529 (ttm170) cc_final: 0.6165 (mmt-90) REVERT: D 154 ARG cc_start: 0.7182 (tpt170) cc_final: 0.6606 (tpt170) REVERT: D 196 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7394 (t) REVERT: D 223 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6625 (tpm170) REVERT: E 150 ASP cc_start: 0.7501 (t0) cc_final: 0.7165 (t70) REVERT: E 154 ARG cc_start: 0.6127 (mmt-90) cc_final: 0.3819 (ttm-80) REVERT: E 223 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7099 (ttp-170) outliers start: 19 outliers final: 9 residues processed: 229 average time/residue: 1.0323 time to fit residues: 248.0006 Evaluate side-chains 234 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 106 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 163 GLN 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 194 THR 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 6 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 215 GLN ** D 114 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146963 restraints weight = 5735.711| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.21 r_work: 0.3831 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5845 Z= 0.214 Angle : 0.738 11.211 7930 Z= 0.371 Chirality : 0.058 0.291 825 Planarity : 0.003 0.028 1025 Dihedral : 6.992 48.429 990 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.25 % Allowed : 25.30 % Favored : 71.45 % 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: -4.14 (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 TRP 0.006 0.001 TRP B 93 HIS 0.010 0.002 HIS E 143 PHE 0.016 0.002 PHE A 201 TYR 0.022 0.002 TYR A 131 ARG 0.005 0.001 ARG C 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 10) link_NAG-ASN : angle 3.49576 ( 30) hydrogen bonds : bond 0.02416 ( 92) hydrogen bonds : angle 6.03801 ( 276) SS BOND : bond 0.00365 ( 5) SS BOND : angle 1.56127 ( 10) covalent geometry : bond 0.00470 ( 5830) covalent geometry : angle 0.70546 ( 7890) *********************** 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 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7611 (t0) cc_final: 0.7154 (t0) REVERT: A 196 THR cc_start: 0.7819 (m) cc_final: 0.7511 (t) REVERT: B 98 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8425 (m) REVERT: B 150 ASP cc_start: 0.7491 (t0) cc_final: 0.7185 (t70) REVERT: B 196 THR cc_start: 0.7864 (m) cc_final: 0.7616 (p) REVERT: B 209 MET cc_start: 0.7917 (mmm) cc_final: 0.7714 (tpt) REVERT: C 163 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: C 196 THR cc_start: 0.7640 (m) cc_final: 0.7245 (t) REVERT: C 223 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.7862 (tpt90) REVERT: D 139 ARG cc_start: 0.6539 (tpm170) cc_final: 0.6285 (mmt-90) REVERT: D 196 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7410 (t) REVERT: D 223 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6645 (tpm170) REVERT: E 150 ASP cc_start: 0.7563 (t0) cc_final: 0.7248 (t70) REVERT: E 223 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7099 (ttp-170) outliers start: 19 outliers final: 12 residues processed: 229 average time/residue: 1.0414 time to fit residues: 249.7098 Evaluate side-chains 237 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 106 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 155 GLU 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 194 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 12 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 4 optimal weight: 0.0050 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 180 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 220 GLN E 99 HIS E 215 GLN E 220 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.175235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.158030 restraints weight = 5734.839| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.13 r_work: 0.3980 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3909 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= 0.119 Angle : 0.662 10.934 7930 Z= 0.331 Chirality : 0.056 0.291 825 Planarity : 0.003 0.033 1025 Dihedral : 6.394 46.734 990 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.88 % Allowed : 27.18 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.006 0.001 HIS A 143 PHE 0.018 0.002 PHE A 201 TYR 0.020 0.001 TYR A 131 ARG 0.004 0.001 ARG E 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 10) link_NAG-ASN : angle 2.92857 ( 30) hydrogen bonds : bond 0.01994 ( 92) hydrogen bonds : angle 5.58745 ( 276) SS BOND : bond 0.00165 ( 5) SS BOND : angle 0.64481 ( 10) covalent geometry : bond 0.00268 ( 5830) covalent geometry : angle 0.63836 ( 7890) ********************** 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 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 232 time to evaluate : 0.605 Fit side-chains REVERT: A 147 ASP cc_start: 0.8570 (t0) cc_final: 0.8324 (t70) REVERT: A 150 ASP cc_start: 0.7544 (t0) cc_final: 0.7085 (t0) REVERT: A 196 THR cc_start: 0.7778 (m) cc_final: 0.7450 (t) REVERT: A 223 ARG cc_start: 0.8206 (tpt90) cc_final: 0.7961 (ttt90) REVERT: B 98 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8395 (m) REVERT: B 150 ASP cc_start: 0.7459 (t0) cc_final: 0.7156 (t70) REVERT: B 181 ASP cc_start: 0.7979 (t70) cc_final: 0.7712 (t70) REVERT: B 196 THR cc_start: 0.7859 (m) cc_final: 0.7580 (p) REVERT: C 196 THR cc_start: 0.7605 (m) cc_final: 0.7190 (t) REVERT: C 223 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7924 (tpt90) REVERT: D 196 THR cc_start: 0.7692 (m) cc_final: 0.7438 (p) REVERT: D 223 ARG cc_start: 0.6826 (tpp-160) cc_final: 0.6432 (tpm170) REVERT: E 132 MET cc_start: 0.6923 (mpp) cc_final: 0.5011 (tpt) REVERT: E 150 ASP cc_start: 0.7469 (t0) cc_final: 0.7113 (t70) REVERT: E 154 ARG cc_start: 0.6129 (mmt-90) cc_final: 0.3743 (ttm-80) REVERT: E 194 THR cc_start: 0.8022 (m) cc_final: 0.7773 (m) REVERT: E 223 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7030 (ttp-170) outliers start: 11 outliers final: 5 residues processed: 236 average time/residue: 0.9499 time to fit residues: 235.5831 Evaluate side-chains 231 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 106 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 183 VAL 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 9 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 173 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 173 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.173802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.157299 restraints weight = 5691.069| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 1.24 r_work: 0.3962 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5845 Z= 0.127 Angle : 0.659 9.388 7930 Z= 0.333 Chirality : 0.055 0.288 825 Planarity : 0.003 0.023 1025 Dihedral : 6.317 46.535 990 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.03 % Allowed : 28.38 % 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 (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: -4.11 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 93 HIS 0.006 0.001 HIS E 143 PHE 0.017 0.002 PHE A 201 TYR 0.016 0.001 TYR A 131 ARG 0.006 0.001 ARG A 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 10) link_NAG-ASN : angle 2.77383 ( 30) hydrogen bonds : bond 0.01933 ( 92) hydrogen bonds : angle 5.50912 ( 276) SS BOND : bond 0.00299 ( 5) SS BOND : angle 1.01756 ( 10) covalent geometry : bond 0.00290 ( 5830) covalent geometry : angle 0.63742 ( 7890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5516.81 seconds wall clock time: 95 minutes 53.37 seconds (5753.37 seconds total)