Starting phenix.real_space_refine on Thu Nov 14 10:21:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmz_47021/11_2024/9dmz_47021.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmz_47021/11_2024/9dmz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmz_47021/11_2024/9dmz_47021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmz_47021/11_2024/9dmz_47021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmz_47021/11_2024/9dmz_47021.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmz_47021/11_2024/9dmz_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.21, per 1000 atoms: 0.92 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: 1.21 Conformation dependent library (CDL) restraints added in 586.7 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: 0.91 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: 1.59 Time building geometry restraints manager: 1.42 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: 0.00 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: 2.310 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- 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 5830 Z= 0.202 Angle : 0.597 4.958 7890 Z= 0.318 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 *********************** 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 : 0.627 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: 1.0408 time to fit residues: 298.0058 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 : 0.619 ------------------------------------------------------------------------------- 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: 8.9990 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: 4.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 5830 Z= 0.186 Angle : 0.626 6.186 7890 Z= 0.319 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 *********************** 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 : 0.590 Fit side-chains REVERT: A 150 ASP cc_start: 0.7289 (t0) cc_final: 0.6739 (t0) REVERT: A 196 THR cc_start: 0.7775 (m) cc_final: 0.7450 (p) REVERT: A 206 ILE cc_start: 0.8535 (mt) cc_final: 0.8326 (mt) REVERT: B 99 HIS cc_start: 0.7936 (m90) cc_final: 0.7661 (m-70) REVERT: B 150 ASP cc_start: 0.7338 (t0) cc_final: 0.7031 (t0) REVERT: B 196 THR cc_start: 0.7591 (m) cc_final: 0.7223 (p) REVERT: C 196 THR cc_start: 0.7570 (m) cc_final: 0.7344 (p) REVERT: D 98 THR cc_start: 0.8795 (t) cc_final: 0.8560 (m) REVERT: E 99 HIS cc_start: 0.7879 (m90) cc_final: 0.7674 (m-70) REVERT: E 139 ARG cc_start: 0.6334 (ttp80) cc_final: 0.5919 (ttp-170) REVERT: E 167 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.6798 (tpm170) REVERT: E 174 ASN cc_start: 0.6708 (m110) cc_final: 0.6062 (m-40) outliers start: 18 outliers final: 6 residues processed: 247 average time/residue: 1.0223 time to fit residues: 264.7857 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 : 0.676 ------------------------------------------------------------------------------- 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 32 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 220 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** 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** D 220 GLN E 180 HIS ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5830 Z= 0.331 Angle : 0.720 10.327 7890 Z= 0.375 Chirality : 0.061 0.352 825 Planarity : 0.005 0.081 1025 Dihedral : 7.176 43.308 990 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.76 % Allowed : 23.76 % Favored : 72.48 % 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: -3.83 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 93 HIS 0.010 0.002 HIS E 143 PHE 0.014 0.002 PHE A 201 TYR 0.015 0.002 TYR E 131 ARG 0.007 0.001 ARG B 154 *********************** 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 254 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.709 Fit side-chains REVERT: A 132 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7940 (mmm) REVERT: A 150 ASP cc_start: 0.7464 (t0) cc_final: 0.6836 (t70) REVERT: A 196 THR cc_start: 0.7776 (m) cc_final: 0.7474 (p) REVERT: B 150 ASP cc_start: 0.7380 (t0) cc_final: 0.7069 (t70) REVERT: B 196 THR cc_start: 0.7892 (m) cc_final: 0.7498 (p) REVERT: C 196 THR cc_start: 0.7638 (m) cc_final: 0.7360 (p) REVERT: C 223 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7898 (ttm-80) REVERT: D 196 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7188 (p) REVERT: D 223 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5313 (tpt170) REVERT: E 107 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7999 (mtmm) REVERT: E 154 ARG cc_start: 0.5838 (mmt-90) cc_final: 0.4339 (ttt-90) REVERT: E 167 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.6772 (tpm170) REVERT: E 210 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6569 (mm-30) outliers start: 22 outliers final: 6 residues processed: 234 average time/residue: 1.0973 time to fit residues: 268.5217 Evaluate side-chains 228 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET 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 D residue 223 ARG Chi-restraints excluded: chain E residue 163 GLN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 210 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN C 215 GLN C 220 GLN C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 215 GLN E 220 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 5830 Z= 0.601 Angle : 0.863 11.261 7890 Z= 0.453 Chirality : 0.066 0.339 825 Planarity : 0.005 0.051 1025 Dihedral : 8.130 47.086 990 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.62 % Allowed : 22.74 % Favored : 72.65 % 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 0.008 0.002 TRP B 93 HIS 0.014 0.003 HIS C 143 PHE 0.015 0.003 PHE A 201 TYR 0.019 0.003 TYR B 131 ARG 0.005 0.001 ARG B 223 *********************** 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: 27 poor density : 219 time to evaluate : 0.597 Fit side-chains REVERT: A 139 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7412 (ttm170) REVERT: A 150 ASP cc_start: 0.7599 (t0) cc_final: 0.6932 (t70) REVERT: A 172 TYR cc_start: 0.6951 (m-80) cc_final: 0.6668 (m-80) REVERT: A 196 THR cc_start: 0.7848 (m) cc_final: 0.7550 (t) REVERT: B 150 ASP cc_start: 0.7516 (t0) cc_final: 0.7185 (t70) REVERT: B 196 THR cc_start: 0.7912 (m) cc_final: 0.7602 (p) REVERT: C 132 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7904 (mmm) REVERT: C 196 THR cc_start: 0.7662 (m) cc_final: 0.7279 (t) REVERT: D 150 ASP cc_start: 0.7492 (t0) cc_final: 0.7162 (t0) REVERT: D 196 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7399 (t) REVERT: D 223 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6456 (tpm170) REVERT: E 154 ARG cc_start: 0.5824 (mmt-90) cc_final: 0.4270 (ttm-80) REVERT: E 223 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6821 (ttp-170) outliers start: 27 outliers final: 9 residues processed: 227 average time/residue: 1.1347 time to fit residues: 269.2070 Evaluate side-chains 229 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 139 ARG 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 138 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN E 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5830 Z= 0.217 Angle : 0.661 10.700 7890 Z= 0.335 Chirality : 0.058 0.322 825 Planarity : 0.003 0.030 1025 Dihedral : 7.078 47.768 990 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.08 % Allowed : 26.15 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 93 HIS 0.007 0.001 HIS A 143 PHE 0.017 0.002 PHE A 201 TYR 0.020 0.001 TYR A 131 ARG 0.009 0.001 ARG A 154 *********************** 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 242 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7465 (t0) cc_final: 0.6980 (t0) REVERT: A 196 THR cc_start: 0.7815 (m) cc_final: 0.7516 (t) REVERT: A 206 ILE cc_start: 0.8627 (mt) cc_final: 0.8418 (mt) REVERT: B 132 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7994 (mmm) REVERT: B 150 ASP cc_start: 0.7362 (t0) cc_final: 0.7060 (t70) REVERT: B 196 THR cc_start: 0.7906 (m) cc_final: 0.7609 (p) REVERT: C 172 TYR cc_start: 0.6983 (m-80) cc_final: 0.6782 (m-80) REVERT: C 196 THR cc_start: 0.7634 (m) cc_final: 0.7232 (t) REVERT: C 223 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7968 (ttm-80) REVERT: D 196 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7423 (t) REVERT: D 223 ARG cc_start: 0.6593 (tpp-160) cc_final: 0.6293 (tpm170) REVERT: E 223 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6900 (ttp-170) outliers start: 18 outliers final: 5 residues processed: 228 average time/residue: 1.0764 time to fit residues: 256.9314 Evaluate side-chains 225 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 106 SER 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 56 optimal weight: 0.0770 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 0.0670 overall best weight: 3.2282 ------------------------------------------------------------------------------- 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 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN E 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5830 Z= 0.416 Angle : 0.759 11.936 7890 Z= 0.394 Chirality : 0.061 0.311 825 Planarity : 0.004 0.037 1025 Dihedral : 7.518 49.321 990 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.59 % Allowed : 24.96 % 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: -4.13 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 93 HIS 0.011 0.002 HIS C 143 PHE 0.016 0.002 PHE A 201 TYR 0.023 0.002 TYR A 131 ARG 0.005 0.001 ARG C 167 *********************** 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 240 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7525 (t0) cc_final: 0.6908 (t70) REVERT: A 196 THR cc_start: 0.7855 (m) cc_final: 0.7554 (t) REVERT: A 216 MET cc_start: 0.8172 (tpp) cc_final: 0.7943 (ttm) REVERT: B 150 ASP cc_start: 0.7460 (t0) cc_final: 0.7179 (t70) REVERT: B 196 THR cc_start: 0.7895 (m) cc_final: 0.7632 (p) REVERT: C 132 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7856 (mmm) REVERT: C 163 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: C 196 THR cc_start: 0.7702 (m) cc_final: 0.7318 (t) REVERT: D 196 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7415 (t) REVERT: D 223 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6441 (tpm170) REVERT: E 223 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6905 (ttp-170) outliers start: 21 outliers final: 6 residues processed: 225 average time/residue: 1.1613 time to fit residues: 272.8393 Evaluate side-chains 227 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 194 THR 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 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5830 Z= 0.310 Angle : 0.707 11.649 7890 Z= 0.363 Chirality : 0.059 0.306 825 Planarity : 0.003 0.028 1025 Dihedral : 7.257 49.383 990 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.76 % Allowed : 24.62 % 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: -4.17 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 93 HIS 0.010 0.002 HIS E 143 PHE 0.017 0.002 PHE A 201 TYR 0.021 0.002 TYR A 131 ARG 0.006 0.001 ARG C 167 *********************** 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 : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7504 (t0) cc_final: 0.6886 (t70) REVERT: A 196 THR cc_start: 0.7845 (m) cc_final: 0.7561 (t) REVERT: A 216 MET cc_start: 0.8170 (tpp) cc_final: 0.7905 (ttm) REVERT: B 150 ASP cc_start: 0.7370 (t0) cc_final: 0.7068 (t70) REVERT: B 154 ARG cc_start: 0.7274 (ttm-80) cc_final: 0.6973 (ttt180) REVERT: B 196 THR cc_start: 0.7859 (m) cc_final: 0.7622 (p) REVERT: C 132 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7784 (mmm) REVERT: C 196 THR cc_start: 0.7714 (m) cc_final: 0.7337 (t) REVERT: D 196 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7496 (p) REVERT: E 223 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6884 (ttp-170) outliers start: 22 outliers final: 7 residues processed: 234 average time/residue: 1.1536 time to fit residues: 282.0881 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 : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 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 132 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 106 SER 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 12 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 56 optimal weight: 0.0010 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- 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 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.004 0.038 5830 Z= 0.256 Angle : 0.692 11.653 7890 Z= 0.354 Chirality : 0.058 0.302 825 Planarity : 0.004 0.053 1025 Dihedral : 7.009 49.340 990 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.91 % Allowed : 25.13 % 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: -4.18 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (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 A 201 TYR 0.021 0.002 TYR A 131 ARG 0.011 0.001 ARG A 154 *********************** 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 244 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8961 (t) cc_final: 0.8732 (m) REVERT: A 150 ASP cc_start: 0.7486 (t0) cc_final: 0.6890 (t70) REVERT: A 196 THR cc_start: 0.7823 (m) cc_final: 0.7540 (t) REVERT: A 216 MET cc_start: 0.8169 (tpp) cc_final: 0.7866 (ttm) REVERT: B 132 MET cc_start: 0.8258 (mmm) cc_final: 0.7804 (mmp) REVERT: B 150 ASP cc_start: 0.7358 (t0) cc_final: 0.7073 (t70) REVERT: B 196 THR cc_start: 0.7852 (m) cc_final: 0.7624 (p) REVERT: B 209 MET cc_start: 0.7934 (mmm) cc_final: 0.7731 (tpt) REVERT: B 223 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7650 (ttm-80) REVERT: C 132 MET cc_start: 0.8044 (mmm) cc_final: 0.7644 (mtm) REVERT: C 157 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7521 (tmt) REVERT: C 196 THR cc_start: 0.7710 (m) cc_final: 0.7325 (t) REVERT: D 154 ARG cc_start: 0.6906 (tpt170) cc_final: 0.6695 (ttt-90) REVERT: D 196 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7491 (p) REVERT: D 223 ARG cc_start: 0.6802 (tpm170) cc_final: 0.6359 (tpm-80) REVERT: E 223 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6856 (ttp-170) outliers start: 17 outliers final: 10 residues processed: 232 average time/residue: 1.0953 time to fit residues: 266.3778 Evaluate side-chains 231 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 106 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 0.0050 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5830 Z= 0.322 Angle : 0.723 12.035 7890 Z= 0.373 Chirality : 0.058 0.298 825 Planarity : 0.004 0.026 1025 Dihedral : 7.103 48.994 990 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % 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: -4.22 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 93 HIS 0.010 0.002 HIS E 143 PHE 0.017 0.002 PHE A 201 TYR 0.022 0.002 TYR A 131 ARG 0.009 0.001 ARG A 154 *********************** 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 242 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 98 THR cc_start: 0.8953 (t) cc_final: 0.8713 (m) REVERT: A 150 ASP cc_start: 0.7507 (t0) cc_final: 0.6894 (t70) REVERT: A 196 THR cc_start: 0.7775 (m) cc_final: 0.7474 (t) REVERT: B 150 ASP cc_start: 0.7373 (t0) cc_final: 0.7083 (t70) REVERT: C 132 MET cc_start: 0.8071 (mmm) cc_final: 0.7585 (mtm) REVERT: C 196 THR cc_start: 0.7671 (m) cc_final: 0.7296 (t) REVERT: C 223 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7863 (ttm-80) REVERT: D 196 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7503 (p) REVERT: D 223 ARG cc_start: 0.6931 (tpm170) cc_final: 0.5842 (ttm170) REVERT: E 223 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6859 (ttp-170) outliers start: 19 outliers final: 11 residues processed: 231 average time/residue: 1.1400 time to fit residues: 275.1090 Evaluate side-chains 237 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 106 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 216 MET 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 64 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5830 Z= 0.222 Angle : 0.677 11.605 7890 Z= 0.347 Chirality : 0.056 0.295 825 Planarity : 0.003 0.054 1025 Dihedral : 6.719 47.862 990 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.22 % Allowed : 27.01 % Favored : 70.77 % 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: -4.19 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 93 HIS 0.007 0.001 HIS E 143 PHE 0.018 0.002 PHE A 201 TYR 0.021 0.001 TYR A 131 ARG 0.007 0.001 ARG B 159 ********************** 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 239 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 226 time to evaluate : 0.666 Fit side-chains REVERT: A 98 THR cc_start: 0.8914 (t) cc_final: 0.8682 (m) REVERT: A 147 ASP cc_start: 0.8826 (t0) cc_final: 0.8558 (t70) REVERT: A 150 ASP cc_start: 0.7459 (t0) cc_final: 0.6994 (t0) REVERT: A 196 THR cc_start: 0.7778 (m) cc_final: 0.7490 (t) REVERT: B 150 ASP cc_start: 0.7366 (t0) cc_final: 0.7076 (t70) REVERT: B 196 THR cc_start: 0.7890 (m) cc_final: 0.7665 (p) REVERT: C 132 MET cc_start: 0.7907 (mmm) cc_final: 0.7545 (mtm) REVERT: C 154 ARG cc_start: 0.7251 (ttt180) cc_final: 0.7009 (ttt-90) REVERT: C 196 THR cc_start: 0.7664 (m) cc_final: 0.7284 (t) REVERT: C 223 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7500 (tpt90) REVERT: D 196 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7495 (p) REVERT: D 223 ARG cc_start: 0.6878 (tpm170) cc_final: 0.6412 (tpm-80) REVERT: E 154 ARG cc_start: 0.5853 (mmt-90) cc_final: 0.3746 (ttm-80) REVERT: E 223 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6902 (ttp-170) outliers start: 13 outliers final: 9 residues processed: 230 average time/residue: 1.0851 time to fit residues: 261.5101 Evaluate side-chains 225 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 106 SER Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 196 THR 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 14 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 180 HIS C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.172579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.156011 restraints weight = 5604.354| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.30 r_work: 0.3958 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5830 Z= 0.199 Angle : 0.658 11.191 7890 Z= 0.338 Chirality : 0.056 0.292 825 Planarity : 0.003 0.040 1025 Dihedral : 6.503 47.057 990 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.05 % Allowed : 27.18 % Favored : 70.77 % 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: -4.17 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 93 HIS 0.006 0.001 HIS E 143 PHE 0.018 0.002 PHE A 201 TYR 0.018 0.001 TYR A 131 ARG 0.006 0.001 ARG B 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4058.31 seconds wall clock time: 72 minutes 56.53 seconds (4376.53 seconds total)