Starting phenix.real_space_refine on Sun Apr 27 12:38:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmz_47021/04_2025/9dmz_47021.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmz_47021/04_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_47021/04_2025/9dmz_47021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmz_47021/04_2025/9dmz_47021.map" model { file = "/net/cci-nas-00/data/ceres_data/9dmz_47021/04_2025/9dmz_47021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmz_47021/04_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-5669/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: 4.81, per 1000 atoms: 0.85 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: 1.15 Conformation dependent library (CDL) restraints added in 646.8 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: 0.87 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: 1.65 Time building geometry restraints manager: 1.38 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: 0.04 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.260 Find NCS groups from input model: 0.340 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:17.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- 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 : 0.614 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: 0.9956 time to fit residues: 285.2056 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 : 0.643 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.9186 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.181317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.165265 restraints weight = 5689.736| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.23 r_work: 0.3982 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5845 Z= 0.132 Angle : 0.735 11.570 7930 Z= 0.346 Chirality : 0.061 0.433 825 Planarity : 0.003 0.051 1025 Dihedral : 5.984 35.326 990 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -3.54 (0.27), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.20), 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 0.002 PHE A 201 TYR 0.007 0.001 TYR B 131 ARG 0.013 0.001 ARG D 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 10) link_NAG-ASN : angle 6.02895 ( 30) hydrogen bonds : bond 0.02473 ( 92) hydrogen bonds : angle 6.75617 ( 276) SS BOND : bond 0.00710 ( 5) SS BOND : angle 0.79007 ( 10) covalent geometry : bond 0.00291 ( 5830) covalent geometry : angle 0.63554 ( 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 261 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 0.624 Fit side-chains REVERT: A 150 ASP cc_start: 0.7387 (t0) cc_final: 0.6834 (t0) REVERT: A 196 THR cc_start: 0.7739 (m) cc_final: 0.7383 (p) REVERT: A 206 ILE cc_start: 0.8543 (mt) cc_final: 0.8339 (mt) REVERT: B 150 ASP cc_start: 0.7427 (t0) cc_final: 0.7124 (t0) REVERT: B 196 THR cc_start: 0.7592 (m) cc_final: 0.7204 (p) REVERT: B 208 MET cc_start: 0.7599 (mtt) cc_final: 0.7370 (mtt) REVERT: C 196 THR cc_start: 0.7547 (m) cc_final: 0.7284 (p) REVERT: E 139 ARG cc_start: 0.6450 (ttp80) cc_final: 0.5986 (ttp-170) REVERT: E 167 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.6877 (tpm170) REVERT: E 174 ASN cc_start: 0.6626 (m110) cc_final: 0.6007 (m-40) REVERT: E 196 THR cc_start: 0.7597 (m) cc_final: 0.7363 (p) outliers start: 18 outliers final: 5 residues processed: 246 average time/residue: 1.0210 time to fit residues: 263.3440 Evaluate side-chains 234 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 229 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 58 optimal weight: 0.0070 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.0170 chunk 9 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 0.0970 chunk 56 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.2034 ------------------------------------------------------------------------------- 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 162 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.185219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.168209 restraints weight = 5765.204| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.14 r_work: 0.4041 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5845 Z= 0.097 Angle : 0.642 9.444 7930 Z= 0.307 Chirality : 0.056 0.363 825 Planarity : 0.003 0.062 1025 Dihedral : 5.847 40.829 990 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.54 % Allowed : 25.64 % Favored : 72.82 % 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: -3.63 (0.26), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 93 HIS 0.003 0.001 HIS B 114 PHE 0.014 0.001 PHE A 201 TYR 0.014 0.001 TYR E 152 ARG 0.005 0.000 ARG C 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 10) link_NAG-ASN : angle 4.65507 ( 30) hydrogen bonds : bond 0.02161 ( 92) hydrogen bonds : angle 6.11861 ( 276) SS BOND : bond 0.00532 ( 5) SS BOND : angle 0.45281 ( 10) covalent geometry : bond 0.00232 ( 5830) covalent geometry : angle 0.57592 ( 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 245 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 236 time to evaluate : 0.858 Fit side-chains REVERT: A 150 ASP cc_start: 0.7363 (t0) cc_final: 0.6898 (t0) REVERT: A 196 THR cc_start: 0.7789 (m) cc_final: 0.7462 (p) REVERT: B 99 HIS cc_start: 0.7796 (m90) cc_final: 0.7575 (m-70) REVERT: B 107 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7839 (mtmm) REVERT: B 196 THR cc_start: 0.7787 (m) cc_final: 0.7373 (p) REVERT: C 196 THR cc_start: 0.7603 (m) cc_final: 0.7346 (p) REVERT: D 98 THR cc_start: 0.8574 (t) cc_final: 0.8297 (m) REVERT: E 139 ARG cc_start: 0.6335 (ttp80) cc_final: 0.5966 (ttp-170) REVERT: E 154 ARG cc_start: 0.5599 (mmt-90) cc_final: 0.4399 (ttt-90) REVERT: E 174 ASN cc_start: 0.6499 (m110) cc_final: 0.5919 (m-40) REVERT: E 196 THR cc_start: 0.7591 (m) cc_final: 0.7377 (p) outliers start: 9 outliers final: 3 residues processed: 238 average time/residue: 1.0756 time to fit residues: 268.6493 Evaluate side-chains 226 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 0.0270 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** 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 162 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.185796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168935 restraints weight = 5770.364| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.37 r_work: 0.4054 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5845 Z= 0.100 Angle : 0.621 8.961 7930 Z= 0.299 Chirality : 0.055 0.329 825 Planarity : 0.002 0.032 1025 Dihedral : 5.915 46.346 990 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.56 % Allowed : 25.81 % 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 (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: -3.69 (0.26), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 93 HIS 0.003 0.001 HIS A 143 PHE 0.014 0.001 PHE A 201 TYR 0.010 0.001 TYR E 131 ARG 0.008 0.001 ARG D 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 10) link_NAG-ASN : angle 3.81687 ( 30) hydrogen bonds : bond 0.02003 ( 92) hydrogen bonds : angle 5.82666 ( 276) SS BOND : bond 0.00298 ( 5) SS BOND : angle 0.60848 ( 10) covalent geometry : bond 0.00234 ( 5830) covalent geometry : angle 0.57643 ( 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 246 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.610 Fit side-chains REVERT: A 150 ASP cc_start: 0.7415 (t0) cc_final: 0.6940 (t0) REVERT: A 170 ASP cc_start: 0.8186 (m-30) cc_final: 0.7984 (m-30) REVERT: A 196 THR cc_start: 0.7745 (m) cc_final: 0.7408 (p) REVERT: B 99 HIS cc_start: 0.7866 (m90) cc_final: 0.7606 (m-70) REVERT: B 196 THR cc_start: 0.7772 (m) cc_final: 0.7358 (p) REVERT: C 196 THR cc_start: 0.7578 (m) cc_final: 0.7316 (p) REVERT: D 98 THR cc_start: 0.8546 (t) cc_final: 0.8267 (m) REVERT: E 139 ARG cc_start: 0.6552 (ttp80) cc_final: 0.5929 (ttp-170) REVERT: E 154 ARG cc_start: 0.5905 (mmt-90) cc_final: 0.4708 (ttt-90) REVERT: E 163 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: E 174 ASN cc_start: 0.6550 (m110) cc_final: 0.5860 (m-40) REVERT: E 196 THR cc_start: 0.7549 (m) cc_final: 0.7322 (p) outliers start: 15 outliers final: 6 residues processed: 235 average time/residue: 1.2100 time to fit residues: 298.2182 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 : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR 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 196 THR Chi-restraints excluded: chain E residue 163 GLN 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: 4.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 162 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.170018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153502 restraints weight = 5706.217| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.22 r_work: 0.3899 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5845 Z= 0.174 Angle : 0.701 10.434 7930 Z= 0.351 Chirality : 0.056 0.309 825 Planarity : 0.003 0.040 1025 Dihedral : 6.670 49.417 990 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.59 % Allowed : 24.62 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 93 HIS 0.009 0.002 HIS E 143 PHE 0.019 0.002 PHE E 201 TYR 0.018 0.002 TYR E 131 ARG 0.006 0.001 ARG B 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 10) link_NAG-ASN : angle 3.56954 ( 30) hydrogen bonds : bond 0.02371 ( 92) hydrogen bonds : angle 5.89613 ( 276) SS BOND : bond 0.00260 ( 5) SS BOND : angle 1.48750 ( 10) covalent geometry : bond 0.00383 ( 5830) covalent geometry : angle 0.66550 ( 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 256 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.674 Fit side-chains REVERT: A 150 ASP cc_start: 0.7509 (t0) cc_final: 0.6941 (t70) REVERT: A 196 THR cc_start: 0.7773 (m) cc_final: 0.7437 (p) REVERT: B 150 ASP cc_start: 0.7497 (t0) cc_final: 0.7188 (t0) REVERT: B 196 THR cc_start: 0.7841 (m) cc_final: 0.7456 (p) REVERT: C 196 THR cc_start: 0.7482 (m) cc_final: 0.7224 (p) REVERT: D 98 THR cc_start: 0.8614 (t) cc_final: 0.8412 (m) REVERT: D 167 ARG cc_start: 0.7826 (ttt-90) cc_final: 0.7625 (ttt-90) REVERT: D 196 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7134 (p) REVERT: E 139 ARG cc_start: 0.7107 (ttp80) cc_final: 0.6225 (ttp-170) REVERT: E 154 ARG cc_start: 0.6191 (mmt-90) cc_final: 0.4074 (ttm-80) REVERT: E 196 THR cc_start: 0.7756 (m) cc_final: 0.7537 (p) outliers start: 21 outliers final: 6 residues processed: 238 average time/residue: 1.2391 time to fit residues: 308.7254 Evaluate side-chains 232 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL 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 D residue 210 GLU Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 183 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 chunk 36 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** A 215 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 222 GLN C 226 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 215 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.176248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.159053 restraints weight = 5662.800| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.15 r_work: 0.3995 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5845 Z= 0.106 Angle : 0.634 10.387 7930 Z= 0.310 Chirality : 0.055 0.295 825 Planarity : 0.002 0.018 1025 Dihedral : 6.244 49.105 990 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.39 % Allowed : 26.32 % Favored : 71.28 % 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: -3.81 (0.26), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 93 HIS 0.005 0.001 HIS C 143 PHE 0.016 0.002 PHE E 201 TYR 0.016 0.001 TYR A 131 ARG 0.004 0.001 ARG B 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 10) link_NAG-ASN : angle 3.14515 ( 30) hydrogen bonds : bond 0.01892 ( 92) hydrogen bonds : angle 5.59689 ( 276) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.89052 ( 10) covalent geometry : bond 0.00249 ( 5830) covalent geometry : angle 0.60418 ( 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 250 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7419 (t0) cc_final: 0.6948 (t0) REVERT: A 196 THR cc_start: 0.7760 (m) cc_final: 0.7432 (p) REVERT: B 150 ASP cc_start: 0.7497 (t0) cc_final: 0.7182 (t0) REVERT: B 196 THR cc_start: 0.7861 (m) cc_final: 0.7441 (p) REVERT: C 196 THR cc_start: 0.7492 (m) cc_final: 0.7258 (p) REVERT: C 223 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7782 (tpt90) REVERT: D 196 THR cc_start: 0.7509 (m) cc_final: 0.7100 (p) REVERT: E 99 HIS cc_start: 0.7863 (m90) cc_final: 0.7643 (m-70) REVERT: E 139 ARG cc_start: 0.6875 (ttp80) cc_final: 0.6071 (ttp-170) REVERT: E 154 ARG cc_start: 0.6139 (mmt-90) cc_final: 0.3982 (ttm-80) REVERT: E 163 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: E 223 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6999 (ttp-170) outliers start: 14 outliers final: 4 residues processed: 239 average time/residue: 1.2694 time to fit residues: 317.8817 Evaluate side-chains 232 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain D residue 155 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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** B 215 GLN C 176 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.169189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152478 restraints weight = 5793.680| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.29 r_work: 0.3899 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5845 Z= 0.180 Angle : 0.701 10.813 7930 Z= 0.349 Chirality : 0.056 0.292 825 Planarity : 0.003 0.032 1025 Dihedral : 6.617 49.015 990 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.22 % Allowed : 28.38 % Favored : 69.40 % 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: -3.87 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.19), 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 0.018 0.002 PHE E 201 TYR 0.019 0.002 TYR A 131 ARG 0.004 0.001 ARG B 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 10) link_NAG-ASN : angle 3.22411 ( 30) hydrogen bonds : bond 0.02246 ( 92) hydrogen bonds : angle 5.75908 ( 276) SS BOND : bond 0.00323 ( 5) SS BOND : angle 1.46352 ( 10) covalent geometry : bond 0.00400 ( 5830) covalent geometry : angle 0.67194 ( 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 246 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.674 Fit side-chains REVERT: A 150 ASP cc_start: 0.7542 (t0) cc_final: 0.6980 (t70) REVERT: A 196 THR cc_start: 0.7731 (m) cc_final: 0.7459 (p) REVERT: B 150 ASP cc_start: 0.7517 (t0) cc_final: 0.7199 (t0) REVERT: B 181 ASP cc_start: 0.7965 (t70) cc_final: 0.7740 (t70) REVERT: B 196 THR cc_start: 0.7877 (m) cc_final: 0.7471 (p) REVERT: C 196 THR cc_start: 0.7558 (m) cc_final: 0.7223 (p) REVERT: D 196 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7273 (p) REVERT: D 223 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6536 (tpm170) REVERT: E 154 ARG cc_start: 0.6063 (mmt-90) cc_final: 0.3930 (ttm-80) REVERT: E 223 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7137 (ttp-170) outliers start: 13 outliers final: 5 residues processed: 234 average time/residue: 1.2266 time to fit residues: 300.5676 Evaluate side-chains 240 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 223 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 0.0870 chunk 54 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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 220 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 220 GLN C 215 GLN C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146060 restraints weight = 5710.455| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.26 r_work: 0.3802 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5845 Z= 0.284 Angle : 0.807 11.416 7930 Z= 0.409 Chirality : 0.060 0.290 825 Planarity : 0.004 0.048 1025 Dihedral : 7.289 48.782 990 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.71 % Allowed : 29.06 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 93 HIS 0.013 0.002 HIS E 143 PHE 0.016 0.003 PHE A 201 TYR 0.025 0.003 TYR A 131 ARG 0.007 0.001 ARG C 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 3.82516 ( 30) hydrogen bonds : bond 0.02784 ( 92) hydrogen bonds : angle 6.09342 ( 276) SS BOND : bond 0.00224 ( 5) SS BOND : angle 1.90118 ( 10) covalent geometry : bond 0.00620 ( 5830) covalent geometry : angle 0.77080 ( 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 231 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.622 Fit side-chains REVERT: A 150 ASP cc_start: 0.7659 (t0) cc_final: 0.7061 (t70) REVERT: A 172 TYR cc_start: 0.6917 (m-80) cc_final: 0.6642 (m-80) REVERT: A 196 THR cc_start: 0.7803 (m) cc_final: 0.7473 (t) REVERT: B 150 ASP cc_start: 0.7553 (t0) cc_final: 0.7212 (t70) REVERT: B 196 THR cc_start: 0.7906 (m) cc_final: 0.7586 (p) REVERT: C 196 THR cc_start: 0.7580 (m) cc_final: 0.7171 (t) REVERT: D 150 ASP cc_start: 0.7538 (t0) cc_final: 0.7199 (t70) REVERT: D 196 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7420 (t) REVERT: D 223 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6654 (tpm170) REVERT: E 150 ASP cc_start: 0.7579 (t0) cc_final: 0.7241 (t70) REVERT: E 154 ARG cc_start: 0.6264 (mmt-90) cc_final: 0.4110 (ttm-80) REVERT: E 223 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7211 (ttp-170) outliers start: 10 outliers final: 5 residues processed: 223 average time/residue: 1.1862 time to fit residues: 276.0196 Evaluate side-chains 222 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR 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 D residue 223 ARG Chi-restraints excluded: chain E residue 163 GLN 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: 3.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 220 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN E 99 HIS E 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.168109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151656 restraints weight = 5682.624| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.29 r_work: 0.3889 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5845 Z= 0.162 Angle : 0.708 10.803 7930 Z= 0.354 Chirality : 0.057 0.288 825 Planarity : 0.003 0.029 1025 Dihedral : 6.772 47.798 990 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.71 % Allowed : 29.23 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.008 0.001 HIS E 143 PHE 0.018 0.002 PHE E 201 TYR 0.021 0.002 TYR A 131 ARG 0.005 0.001 ARG C 159 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 10) link_NAG-ASN : angle 3.44223 ( 30) hydrogen bonds : bond 0.02144 ( 92) hydrogen bonds : angle 5.80582 ( 276) SS BOND : bond 0.00259 ( 5) SS BOND : angle 1.24484 ( 10) covalent geometry : bond 0.00361 ( 5830) covalent geometry : angle 0.67552 ( 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 233 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 0.634 Fit side-chains REVERT: A 150 ASP cc_start: 0.7597 (t0) cc_final: 0.7020 (t70) REVERT: A 196 THR cc_start: 0.7760 (m) cc_final: 0.7431 (t) REVERT: B 98 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8484 (m) REVERT: B 150 ASP cc_start: 0.7471 (t0) cc_final: 0.7160 (t70) REVERT: B 181 ASP cc_start: 0.7935 (t70) cc_final: 0.7708 (t70) REVERT: B 196 THR cc_start: 0.7861 (m) cc_final: 0.7544 (p) REVERT: C 196 THR cc_start: 0.7586 (m) cc_final: 0.7152 (t) REVERT: C 223 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7825 (tpt90) REVERT: D 132 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7034 (mmm) REVERT: D 154 ARG cc_start: 0.7200 (ttt-90) cc_final: 0.6921 (ttt180) REVERT: D 196 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7416 (t) REVERT: D 223 ARG cc_start: 0.6905 (tpp-160) cc_final: 0.6489 (tpm170) REVERT: E 139 ARG cc_start: 0.6302 (ttp-170) cc_final: 0.6074 (ttp-170) REVERT: E 154 ARG cc_start: 0.6156 (mmt-90) cc_final: 0.3971 (ttm-80) REVERT: E 223 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7140 (ttp-170) outliers start: 10 outliers final: 2 residues processed: 225 average time/residue: 1.0917 time to fit residues: 257.1931 Evaluate side-chains 222 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 216 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain D residue 132 MET 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 12 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.0040 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- 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** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.170410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.153947 restraints weight = 5739.201| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.29 r_work: 0.3926 rms_B_bonded: 1.50 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: 0.7808 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5845 Z= 0.148 Angle : 0.692 9.895 7930 Z= 0.347 Chirality : 0.056 0.289 825 Planarity : 0.003 0.024 1025 Dihedral : 6.562 46.626 990 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.37 % Allowed : 29.91 % Favored : 68.72 % 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: -4.03 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.008 0.001 HIS E 143 PHE 0.017 0.002 PHE E 201 TYR 0.021 0.002 TYR A 131 ARG 0.007 0.001 ARG B 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 10) link_NAG-ASN : angle 3.11941 ( 30) hydrogen bonds : bond 0.02072 ( 92) hydrogen bonds : angle 5.65041 ( 276) SS BOND : bond 0.00217 ( 5) SS BOND : angle 1.18114 ( 10) covalent geometry : bond 0.00333 ( 5830) covalent geometry : angle 0.66498 ( 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 237 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 229 time to evaluate : 0.599 Fit side-chains REVERT: A 139 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.7032 (ttm170) REVERT: A 150 ASP cc_start: 0.7576 (t0) cc_final: 0.7128 (t0) REVERT: A 196 THR cc_start: 0.7776 (m) cc_final: 0.7447 (t) REVERT: B 98 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8447 (m) REVERT: B 150 ASP cc_start: 0.7503 (t0) cc_final: 0.7189 (t70) REVERT: B 181 ASP cc_start: 0.7949 (t70) cc_final: 0.7732 (t70) REVERT: B 196 THR cc_start: 0.7890 (m) cc_final: 0.7571 (p) REVERT: B 209 MET cc_start: 0.7968 (mmm) cc_final: 0.7717 (tpt) REVERT: C 154 ARG cc_start: 0.7403 (ttt180) cc_final: 0.7182 (ttt-90) REVERT: C 196 THR cc_start: 0.7608 (m) cc_final: 0.7173 (t) REVERT: C 223 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7871 (tpt90) REVERT: D 132 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6837 (mmm) REVERT: D 196 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7480 (p) REVERT: D 223 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6491 (tpm170) REVERT: E 132 MET cc_start: 0.6947 (mpp) cc_final: 0.4951 (tpt) REVERT: E 154 ARG cc_start: 0.6133 (mmt-90) cc_final: 0.3957 (ttm-80) REVERT: E 223 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7155 (ttp-170) outliers start: 8 outliers final: 4 residues processed: 229 average time/residue: 1.0184 time to fit residues: 244.5486 Evaluate side-chains 228 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 146 ASN Chi-restraints excluded: chain D residue 132 MET 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 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: 5.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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** B 222 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 ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.172507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.155986 restraints weight = 5647.517| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.28 r_work: 0.3957 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5845 Z= 0.140 Angle : 0.684 10.031 7930 Z= 0.344 Chirality : 0.056 0.286 825 Planarity : 0.003 0.045 1025 Dihedral : 6.420 45.566 990 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.37 % Allowed : 29.91 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.006 0.001 HIS E 143 PHE 0.017 0.002 PHE E 201 TYR 0.020 0.001 TYR A 131 ARG 0.008 0.001 ARG D 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 10) link_NAG-ASN : angle 2.92717 ( 30) hydrogen bonds : bond 0.02013 ( 92) hydrogen bonds : angle 5.56080 ( 276) SS BOND : bond 0.00243 ( 5) SS BOND : angle 1.06867 ( 10) covalent geometry : bond 0.00318 ( 5830) covalent geometry : angle 0.66019 ( 7890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6094.60 seconds wall clock time: 106 minutes 38.76 seconds (6398.76 seconds total)