Starting phenix.real_space_refine on Fri May 16 00:00:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj5_36340/05_2025/8jj5_36340_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj5_36340/05_2025/8jj5_36340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jj5_36340/05_2025/8jj5_36340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj5_36340/05_2025/8jj5_36340.map" model { file = "/net/cci-nas-00/data/ceres_data/8jj5_36340/05_2025/8jj5_36340_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj5_36340/05_2025/8jj5_36340_trim.cif" } resolution = 3.5 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= -0.005 sd= 0.124 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 4460 2.51 5 N 1108 2.21 5 O 1290 1.98 5 H 6679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13594 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3893 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "B" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2224 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain breaks: 1 Chain: "C" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3253 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 15, 'TRANS': 202} Chain: "D" Number of atoms: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 4040 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 243} 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 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.00, per 1000 atoms: 0.51 Number of scatterers: 13594 At special positions: 0 Unit cell: (94.5, 78.3, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1290 8.00 N 1108 7.00 C 4460 6.00 H 6679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS A 217 " distance=2.02 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 189 " distance=2.02 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 204 " distance=2.02 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 110 " distance=2.04 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 152 " distance=2.05 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 218 " distance=2.01 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 205 " distance=2.02 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 201 " - " ASN B 28 " " NAG D 301 " - " ASN D 131 " " NAG E 1 " - " ASN A 169 " " NAG F 1 " - " ASN B 57 " " NAG G 1 " - " ASN C 139 " " NAG H 1 " - " ASN C 170 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 57.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 12 through 42 removed outlier: 3.504A pdb=" N LEU A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.677A pdb=" N GLY A 52 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 87 removed outlier: 4.061A pdb=" N ALA A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE A 68 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 122 removed outlier: 5.670A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.855A pdb=" N GLN A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 157 removed outlier: 3.564A pdb=" N LEU A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 172 through 178 removed outlier: 4.109A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 217 through 257 removed outlier: 3.623A pdb=" N ILE A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'B' and resid 50 through 54 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 153 through 182 removed outlier: 3.705A pdb=" N VAL B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 75 removed outlier: 3.921A pdb=" N ARG C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 4.023A pdb=" N ARG C 120 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 132 Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.525A pdb=" N ILE C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 236 Proline residue: C 219 - end of helix Processing helix chain 'D' and resid 8 through 38 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 53 through 83 Processing helix chain 'D' and resid 84 through 114 removed outlier: 4.611A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.784A pdb=" N TYR D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 157 removed outlier: 3.802A pdb=" N GLY D 145 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 218 through 257 Proline residue: D 225 - end of helix removed outlier: 3.606A pdb=" N ALA D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.549A pdb=" N SER B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 76 Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 43 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 106 removed outlier: 5.948A pdb=" N LYS C 101 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL C 65 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 103 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 60 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR C 166 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLN C 179 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 168 " --> pdb=" O GLN C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 106 removed outlier: 5.948A pdb=" N LYS C 101 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL C 65 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 103 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 60 " --> pdb=" O VAL C 169 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1164 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: 4.68 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 1444 1.04 - 1.23: 6047 1.23 - 1.43: 2326 1.43 - 1.63: 3865 1.63 - 1.82: 84 Bond restraints: 13766 Sorted by residual: bond pdb=" N ARG D 9 " pdb=" H ARG D 9 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" CZ ARG D 9 " pdb=" NH2 ARG D 9 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.75e+01 bond pdb=" N TRP D 246 " pdb=" H TRP D 246 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N GLY C 225 " pdb=" H GLY C 225 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CD2 PHE C 220 " pdb=" HD2 PHE C 220 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 13761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 19364 2.53 - 5.07: 4088 5.07 - 7.60: 1145 7.60 - 10.13: 152 10.13 - 12.67: 18 Bond angle restraints: 24767 Sorted by residual: angle pdb=" CA PHE D 11 " pdb=" CB PHE D 11 " pdb=" CG PHE D 11 " ideal model delta sigma weight residual 113.80 121.20 -7.40 1.00e+00 1.00e+00 5.47e+01 angle pdb=" CA PHE D 92 " pdb=" CB PHE D 92 " pdb=" CG PHE D 92 " ideal model delta sigma weight residual 113.80 121.09 -7.29 1.00e+00 1.00e+00 5.31e+01 angle pdb=" CA PHE D 253 " pdb=" CB PHE D 253 " pdb=" CG PHE D 253 " ideal model delta sigma weight residual 113.80 120.90 -7.10 1.00e+00 1.00e+00 5.04e+01 angle pdb=" CA ASN D 19 " pdb=" CB ASN D 19 " pdb=" CG ASN D 19 " ideal model delta sigma weight residual 112.60 119.63 -7.03 1.00e+00 1.00e+00 4.94e+01 angle pdb=" CA ASN D 84 " pdb=" CB ASN D 84 " pdb=" CG ASN D 84 " ideal model delta sigma weight residual 112.60 119.62 -7.02 1.00e+00 1.00e+00 4.92e+01 ... (remaining 24762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 6150 21.65 - 43.31: 377 43.31 - 64.96: 185 64.96 - 86.62: 44 86.62 - 108.27: 10 Dihedral angle restraints: 6766 sinusoidal: 3739 harmonic: 3027 Sorted by residual: dihedral pdb=" C SER D 42 " pdb=" N SER D 42 " pdb=" CA SER D 42 " pdb=" CB SER D 42 " ideal model delta harmonic sigma weight residual -122.60 -138.41 15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" CA ASP D 39 " pdb=" C ASP D 39 " pdb=" N GLN D 40 " pdb=" CA GLN D 40 " ideal model delta harmonic sigma weight residual -180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA TYR D 41 " pdb=" C TYR D 41 " pdb=" N SER D 42 " pdb=" CA SER D 42 " ideal model delta harmonic sigma weight residual 180.00 -151.16 -28.84 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 6763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 877 0.154 - 0.308: 156 0.308 - 0.462: 33 0.462 - 0.617: 55 0.617 - 0.771: 22 Chirality restraints: 1143 Sorted by residual: chirality pdb=" C1 MAN G 5 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 2.09 0.31 2.00e-02 2.50e+03 2.33e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.43e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.27e+01 ... (remaining 1140 not shown) Planarity restraints: 2014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 230 " 0.199 2.00e-02 2.50e+03 1.35e-01 7.34e+02 pdb=" CG TRP A 230 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A 230 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 230 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP A 230 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TRP A 230 " 0.051 2.00e-02 2.50e+03 pdb=" CE3 TRP A 230 " -0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 230 " 0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 230 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 230 " 0.117 2.00e-02 2.50e+03 pdb=" HD1 TRP A 230 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP A 230 " -0.340 2.00e-02 2.50e+03 pdb=" HE3 TRP A 230 " -0.253 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 230 " 0.046 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 230 " -0.124 2.00e-02 2.50e+03 pdb=" HH2 TRP A 230 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 113 " 0.909 9.50e-02 1.11e+02 3.41e-01 6.41e+02 pdb=" NE ARG D 113 " 0.133 2.00e-02 2.50e+03 pdb=" CZ ARG D 113 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG D 113 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG D 113 " -0.093 2.00e-02 2.50e+03 pdb="HH11 ARG D 113 " -0.265 2.00e-02 2.50e+03 pdb="HH12 ARG D 113 " 0.333 2.00e-02 2.50e+03 pdb="HH21 ARG D 113 " 0.022 2.00e-02 2.50e+03 pdb="HH22 ARG D 113 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 48 " 0.326 2.00e-02 2.50e+03 1.24e-01 4.60e+02 pdb=" CG TYR A 48 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 TYR A 48 " -0.108 2.00e-02 2.50e+03 pdb=" CD2 TYR A 48 " -0.121 2.00e-02 2.50e+03 pdb=" CE1 TYR A 48 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR A 48 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 48 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR A 48 " 0.166 2.00e-02 2.50e+03 pdb=" HD1 TYR A 48 " -0.055 2.00e-02 2.50e+03 pdb=" HD2 TYR A 48 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TYR A 48 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 48 " 0.027 2.00e-02 2.50e+03 ... (remaining 2011 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 867 2.18 - 2.78: 23757 2.78 - 3.39: 38509 3.39 - 3.99: 49776 3.99 - 4.60: 72615 Nonbonded interactions: 185524 Sorted by model distance: nonbonded pdb=" HG SER A 162 " pdb=" OD1 ASP A 166 " model vdw 1.572 2.450 nonbonded pdb=" HH TYR D 129 " pdb=" OD1 ASP D 151 " model vdw 1.600 2.450 nonbonded pdb=" OE2 GLU C 43 " pdb=" HH TYR C 132 " model vdw 1.601 2.450 nonbonded pdb=" HH TYR A 135 " pdb=" OD1 ASP A 150 " model vdw 1.607 2.450 nonbonded pdb=" O PHE D 35 " pdb=" HG SER D 38 " model vdw 1.611 2.450 ... (remaining 185519 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 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.250 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.380 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 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 : 0.021 0.170 7110 Z= 1.153 Angle : 2.212 14.724 9717 Z= 1.447 Chirality : 0.194 0.771 1143 Planarity : 0.021 0.278 1192 Dihedral : 17.067 108.270 2725 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.88 % Favored : 91.00 % Rotamer: Outliers : 1.22 % Allowed : 8.53 % Favored : 90.26 % Cbeta Deviations : 4.87 % 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: -2.93 (0.25), residues: 856 helix: -1.78 (0.20), residues: 452 sheet: -0.70 (0.66), residues: 47 loop : -2.19 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.148 0.032 TRP A 185 HIS 0.014 0.004 HIS B 52 PHE 0.054 0.012 PHE A 68 TYR 0.289 0.036 TYR A 48 ARG 0.013 0.002 ARG D 228 Details of bonding type rmsd link_NAG-ASN : bond 0.01119 ( 6) link_NAG-ASN : angle 4.09686 ( 18) link_ALPHA1-6 : bond 0.02693 ( 1) link_ALPHA1-6 : angle 8.98225 ( 3) link_BETA1-4 : bond 0.02700 ( 6) link_BETA1-4 : angle 7.42702 ( 18) link_ALPHA1-3 : bond 0.01942 ( 1) link_ALPHA1-3 : angle 2.07816 ( 3) hydrogen bonds : bond 0.17562 ( 386) hydrogen bonds : angle 7.63530 ( 1164) SS BOND : bond 0.01332 ( 9) SS BOND : angle 1.80835 ( 18) covalent geometry : bond 0.02098 ( 7087) covalent geometry : angle 2.18056 ( 9657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 276 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.6820 (m100) cc_final: 0.6429 (m100) REVERT: A 85 LEU cc_start: 0.8291 (mm) cc_final: 0.8021 (mm) REVERT: A 90 SER cc_start: 0.8737 (p) cc_final: 0.8276 (p) REVERT: A 211 TYR cc_start: 0.6570 (m-80) cc_final: 0.6128 (m-10) REVERT: A 247 MET cc_start: 0.5128 (mtp) cc_final: 0.4469 (mtp) REVERT: C 91 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5271 (tm-30) REVERT: D 24 MET cc_start: 0.7650 (mtt) cc_final: 0.7104 (mmt) outliers start: 9 outliers final: 2 residues processed: 281 average time/residue: 0.4115 time to fit residues: 150.8290 Evaluate side-chains 196 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 GLN D 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.190593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.175634 restraints weight = 36907.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.180445 restraints weight = 16117.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.183394 restraints weight = 8628.994| |-----------------------------------------------------------------------------| r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 7110 Z= 0.263 Angle : 0.935 9.992 9717 Z= 0.487 Chirality : 0.049 0.315 1143 Planarity : 0.007 0.076 1192 Dihedral : 13.062 86.516 1230 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.03 % Allowed : 16.51 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.88 (0.27), residues: 856 helix: -0.66 (0.23), residues: 460 sheet: -1.13 (0.54), residues: 61 loop : -1.99 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 39 HIS 0.010 0.002 HIS A 116 PHE 0.022 0.002 PHE A 71 TYR 0.042 0.003 TYR A 48 ARG 0.007 0.001 ARG D 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 6) link_NAG-ASN : angle 3.86071 ( 18) link_ALPHA1-6 : bond 0.02195 ( 1) link_ALPHA1-6 : angle 3.70889 ( 3) link_BETA1-4 : bond 0.01178 ( 6) link_BETA1-4 : angle 4.21317 ( 18) link_ALPHA1-3 : bond 0.00479 ( 1) link_ALPHA1-3 : angle 3.87906 ( 3) hydrogen bonds : bond 0.07402 ( 386) hydrogen bonds : angle 5.61724 ( 1164) SS BOND : bond 0.00721 ( 9) SS BOND : angle 3.19366 ( 18) covalent geometry : bond 0.00578 ( 7087) covalent geometry : angle 0.88957 ( 9657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6303 (mmm) cc_final: 0.5766 (mmm) REVERT: A 85 LEU cc_start: 0.7978 (mm) cc_final: 0.7743 (mm) REVERT: A 175 ARG cc_start: 0.7163 (mtm180) cc_final: 0.6851 (mtm180) REVERT: B 157 VAL cc_start: 0.4254 (t) cc_final: 0.3978 (t) REVERT: C 91 GLU cc_start: 0.6176 (mt-10) cc_final: 0.5557 (tm-30) REVERT: D 255 TRP cc_start: 0.7370 (t60) cc_final: 0.6866 (t60) outliers start: 15 outliers final: 11 residues processed: 209 average time/residue: 0.3775 time to fit residues: 105.3828 Evaluate side-chains 191 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 137 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 8.9990 chunk 35 optimal weight: 0.0570 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 177 GLN D 19 ASN D 40 GLN ** D 130 GLN ** 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 = 0.4725 r_free = 0.4725 target = 0.191885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.177001 restraints weight = 36362.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.181884 restraints weight = 15625.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.184784 restraints weight = 8256.210| |-----------------------------------------------------------------------------| r_work (final): 0.4670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7110 Z= 0.171 Angle : 0.791 8.123 9717 Z= 0.406 Chirality : 0.044 0.242 1143 Planarity : 0.005 0.061 1192 Dihedral : 11.217 76.132 1225 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.89 % Allowed : 18.00 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.34 (0.27), residues: 856 helix: -0.19 (0.24), residues: 451 sheet: -0.86 (0.58), residues: 60 loop : -1.77 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 230 HIS 0.004 0.001 HIS A 116 PHE 0.022 0.002 PHE A 34 TYR 0.028 0.002 TYR A 48 ARG 0.004 0.001 ARG B 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 6) link_NAG-ASN : angle 2.88269 ( 18) link_ALPHA1-6 : bond 0.01637 ( 1) link_ALPHA1-6 : angle 3.24364 ( 3) link_BETA1-4 : bond 0.00900 ( 6) link_BETA1-4 : angle 3.70810 ( 18) link_ALPHA1-3 : bond 0.00633 ( 1) link_ALPHA1-3 : angle 2.82306 ( 3) hydrogen bonds : bond 0.06419 ( 386) hydrogen bonds : angle 5.20686 ( 1164) SS BOND : bond 0.00279 ( 9) SS BOND : angle 1.58780 ( 18) covalent geometry : bond 0.00357 ( 7087) covalent geometry : angle 0.76037 ( 9657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5023 (t80) REVERT: A 51 MET cc_start: 0.6291 (mmm) cc_final: 0.5877 (mmm) REVERT: A 85 LEU cc_start: 0.7930 (mm) cc_final: 0.7686 (mm) REVERT: C 91 GLU cc_start: 0.6323 (mt-10) cc_final: 0.5512 (tm-30) REVERT: D 32 GLU cc_start: 0.0689 (mm-30) cc_final: 0.0184 (mt-10) REVERT: D 246 TRP cc_start: 0.6517 (m-10) cc_final: 0.6188 (m100) REVERT: D 254 TYR cc_start: 0.7686 (t80) cc_final: 0.7392 (t80) outliers start: 14 outliers final: 9 residues processed: 189 average time/residue: 0.3797 time to fit residues: 97.2948 Evaluate side-chains 176 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 41 TYR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 248 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.189366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.174475 restraints weight = 37018.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.179249 restraints weight = 16040.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.182098 restraints weight = 8584.653| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7110 Z= 0.198 Angle : 0.754 7.480 9717 Z= 0.389 Chirality : 0.043 0.270 1143 Planarity : 0.005 0.056 1192 Dihedral : 10.028 72.948 1225 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.98 % Allowed : 19.49 % Favored : 77.54 % 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: -1.18 (0.28), residues: 856 helix: -0.04 (0.24), residues: 446 sheet: -1.05 (0.59), residues: 64 loop : -1.65 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 230 HIS 0.004 0.001 HIS A 116 PHE 0.027 0.002 PHE A 34 TYR 0.024 0.002 TYR A 114 ARG 0.003 0.001 ARG A 88 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 6) link_NAG-ASN : angle 2.50412 ( 18) link_ALPHA1-6 : bond 0.01000 ( 1) link_ALPHA1-6 : angle 2.23830 ( 3) link_BETA1-4 : bond 0.00644 ( 6) link_BETA1-4 : angle 3.35372 ( 18) link_ALPHA1-3 : bond 0.00660 ( 1) link_ALPHA1-3 : angle 2.95058 ( 3) hydrogen bonds : bond 0.06179 ( 386) hydrogen bonds : angle 5.12762 ( 1164) SS BOND : bond 0.00306 ( 9) SS BOND : angle 1.65436 ( 18) covalent geometry : bond 0.00425 ( 7087) covalent geometry : angle 0.72770 ( 9657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5121 (t80) REVERT: A 50 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7110 (tt) REVERT: A 51 MET cc_start: 0.6432 (mmm) cc_final: 0.6021 (mmm) REVERT: A 87 ARG cc_start: 0.6398 (ptp-110) cc_final: 0.6190 (ttp-110) outliers start: 22 outliers final: 14 residues processed: 196 average time/residue: 0.3943 time to fit residues: 102.5965 Evaluate side-chains 187 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 119 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 248 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.191469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.176439 restraints weight = 36611.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.181288 restraints weight = 15749.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.184236 restraints weight = 8417.649| |-----------------------------------------------------------------------------| r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 7110 Z= 0.157 Angle : 0.702 7.224 9717 Z= 0.362 Chirality : 0.042 0.228 1143 Planarity : 0.004 0.055 1192 Dihedral : 9.027 69.537 1225 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.98 % Allowed : 20.57 % Favored : 76.45 % 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: -0.77 (0.28), residues: 856 helix: 0.33 (0.24), residues: 445 sheet: -0.93 (0.60), residues: 64 loop : -1.47 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 39 HIS 0.004 0.001 HIS A 116 PHE 0.017 0.001 PHE D 64 TYR 0.020 0.002 TYR A 114 ARG 0.003 0.000 ARG D 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 6) link_NAG-ASN : angle 2.20502 ( 18) link_ALPHA1-6 : bond 0.01056 ( 1) link_ALPHA1-6 : angle 1.30317 ( 3) link_BETA1-4 : bond 0.00629 ( 6) link_BETA1-4 : angle 3.07366 ( 18) link_ALPHA1-3 : bond 0.00869 ( 1) link_ALPHA1-3 : angle 2.57760 ( 3) hydrogen bonds : bond 0.05773 ( 386) hydrogen bonds : angle 4.87920 ( 1164) SS BOND : bond 0.00449 ( 9) SS BOND : angle 1.53674 ( 18) covalent geometry : bond 0.00335 ( 7087) covalent geometry : angle 0.67950 ( 9657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6252 (OUTLIER) cc_final: 0.4959 (t80) REVERT: A 51 MET cc_start: 0.6286 (mmm) cc_final: 0.5970 (mmm) REVERT: A 153 MET cc_start: 0.6402 (ttm) cc_final: 0.6152 (ttp) REVERT: D 246 TRP cc_start: 0.6591 (m-10) cc_final: 0.6296 (m100) outliers start: 22 outliers final: 15 residues processed: 194 average time/residue: 0.3801 time to fit residues: 99.6225 Evaluate side-chains 191 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 252 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 GLN D 40 GLN D 229 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.189592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.174704 restraints weight = 37288.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.179528 restraints weight = 16011.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.182409 restraints weight = 8470.099| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7110 Z= 0.186 Angle : 0.701 6.775 9717 Z= 0.364 Chirality : 0.043 0.240 1143 Planarity : 0.005 0.048 1192 Dihedral : 8.785 73.209 1225 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.38 % Allowed : 20.70 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.28), residues: 856 helix: 0.29 (0.24), residues: 446 sheet: -0.96 (0.59), residues: 64 loop : -1.51 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 168 HIS 0.006 0.001 HIS A 116 PHE 0.020 0.002 PHE D 64 TYR 0.020 0.002 TYR D 91 ARG 0.003 0.000 ARG A 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 2.13743 ( 18) link_ALPHA1-6 : bond 0.00557 ( 1) link_ALPHA1-6 : angle 1.38708 ( 3) link_BETA1-4 : bond 0.00557 ( 6) link_BETA1-4 : angle 2.86663 ( 18) link_ALPHA1-3 : bond 0.00630 ( 1) link_ALPHA1-3 : angle 2.63433 ( 3) hydrogen bonds : bond 0.05739 ( 386) hydrogen bonds : angle 4.90072 ( 1164) SS BOND : bond 0.00290 ( 9) SS BOND : angle 1.28667 ( 18) covalent geometry : bond 0.00398 ( 7087) covalent geometry : angle 0.68208 ( 9657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5037 (t80) REVERT: A 120 MET cc_start: 0.5740 (ptm) cc_final: 0.5377 (tpt) REVERT: D 88 LEU cc_start: 0.6434 (mt) cc_final: 0.6098 (mt) REVERT: D 246 TRP cc_start: 0.6480 (m-90) cc_final: 0.6239 (m100) REVERT: D 252 MET cc_start: 0.7676 (tpt) cc_final: 0.7309 (tpt) REVERT: D 257 ARG cc_start: 0.7402 (tpm170) cc_final: 0.6863 (tpm170) outliers start: 25 outliers final: 20 residues processed: 197 average time/residue: 0.3458 time to fit residues: 93.5205 Evaluate side-chains 190 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 119 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 248 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.193421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.178466 restraints weight = 36153.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.183448 restraints weight = 15459.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.186386 restraints weight = 8109.407| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7110 Z= 0.134 Angle : 0.663 6.283 9717 Z= 0.339 Chirality : 0.041 0.197 1143 Planarity : 0.004 0.051 1192 Dihedral : 8.362 71.590 1225 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.84 % Allowed : 22.06 % Favored : 75.10 % 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: -0.46 (0.28), residues: 856 helix: 0.58 (0.24), residues: 447 sheet: -0.73 (0.60), residues: 62 loop : -1.34 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.004 0.001 HIS D 229 PHE 0.014 0.001 PHE D 64 TYR 0.015 0.002 TYR A 114 ARG 0.003 0.000 ARG D 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 6) link_NAG-ASN : angle 1.97857 ( 18) link_ALPHA1-6 : bond 0.00496 ( 1) link_ALPHA1-6 : angle 1.38296 ( 3) link_BETA1-4 : bond 0.00543 ( 6) link_BETA1-4 : angle 2.68451 ( 18) link_ALPHA1-3 : bond 0.01133 ( 1) link_ALPHA1-3 : angle 2.35513 ( 3) hydrogen bonds : bond 0.05461 ( 386) hydrogen bonds : angle 4.70144 ( 1164) SS BOND : bond 0.00248 ( 9) SS BOND : angle 1.36650 ( 18) covalent geometry : bond 0.00277 ( 7087) covalent geometry : angle 0.64444 ( 9657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.5005 (t80) REVERT: A 120 MET cc_start: 0.5502 (ptm) cc_final: 0.5276 (tpt) REVERT: C 160 THR cc_start: 0.6503 (m) cc_final: 0.6276 (p) REVERT: D 252 MET cc_start: 0.7846 (tpt) cc_final: 0.7561 (tpt) REVERT: D 257 ARG cc_start: 0.7462 (tpm170) cc_final: 0.6940 (tpm170) outliers start: 21 outliers final: 15 residues processed: 199 average time/residue: 0.3320 time to fit residues: 90.4889 Evaluate side-chains 194 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 248 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 47 optimal weight: 0.0970 chunk 73 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.193543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.178478 restraints weight = 36640.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.183457 restraints weight = 15665.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.186410 restraints weight = 8263.598| |-----------------------------------------------------------------------------| r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7110 Z= 0.141 Angle : 0.657 6.278 9717 Z= 0.340 Chirality : 0.041 0.200 1143 Planarity : 0.004 0.047 1192 Dihedral : 8.091 68.633 1225 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.44 % Allowed : 22.73 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.28), residues: 856 helix: 0.58 (0.24), residues: 444 sheet: -0.95 (0.56), residues: 72 loop : -1.24 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 168 HIS 0.004 0.001 HIS D 229 PHE 0.015 0.001 PHE D 64 TYR 0.021 0.002 TYR A 114 ARG 0.002 0.000 ARG D 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 6) link_NAG-ASN : angle 1.87261 ( 18) link_ALPHA1-6 : bond 0.00376 ( 1) link_ALPHA1-6 : angle 1.51895 ( 3) link_BETA1-4 : bond 0.00506 ( 6) link_BETA1-4 : angle 2.57819 ( 18) link_ALPHA1-3 : bond 0.00561 ( 1) link_ALPHA1-3 : angle 2.13214 ( 3) hydrogen bonds : bond 0.05365 ( 386) hydrogen bonds : angle 4.70475 ( 1164) SS BOND : bond 0.00235 ( 9) SS BOND : angle 1.21812 ( 18) covalent geometry : bond 0.00303 ( 7087) covalent geometry : angle 0.64027 ( 9657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6355 (OUTLIER) cc_final: 0.5237 (t80) REVERT: A 51 MET cc_start: 0.6166 (mmm) cc_final: 0.5495 (tpp) REVERT: C 160 THR cc_start: 0.6486 (m) cc_final: 0.6251 (p) REVERT: D 252 MET cc_start: 0.7788 (tpt) cc_final: 0.7537 (tpt) REVERT: D 257 ARG cc_start: 0.7456 (tpm170) cc_final: 0.6885 (tpm170) outliers start: 18 outliers final: 13 residues processed: 194 average time/residue: 0.3483 time to fit residues: 92.5936 Evaluate side-chains 189 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 119 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 248 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.191883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.176743 restraints weight = 36690.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.181641 restraints weight = 15863.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.184578 restraints weight = 8436.751| |-----------------------------------------------------------------------------| r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7110 Z= 0.165 Angle : 0.667 6.244 9717 Z= 0.346 Chirality : 0.042 0.214 1143 Planarity : 0.004 0.047 1192 Dihedral : 8.044 64.894 1225 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.44 % Allowed : 22.73 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.28), residues: 856 helix: 0.64 (0.24), residues: 448 sheet: -0.68 (0.64), residues: 54 loop : -1.26 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.008 0.002 HIS A 116 PHE 0.018 0.001 PHE D 64 TYR 0.018 0.002 TYR D 91 ARG 0.004 0.000 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 1.85502 ( 18) link_ALPHA1-6 : bond 0.00237 ( 1) link_ALPHA1-6 : angle 1.70957 ( 3) link_BETA1-4 : bond 0.00438 ( 6) link_BETA1-4 : angle 2.48189 ( 18) link_ALPHA1-3 : bond 0.00487 ( 1) link_ALPHA1-3 : angle 2.23456 ( 3) hydrogen bonds : bond 0.05358 ( 386) hydrogen bonds : angle 4.72999 ( 1164) SS BOND : bond 0.00281 ( 9) SS BOND : angle 1.17521 ( 18) covalent geometry : bond 0.00362 ( 7087) covalent geometry : angle 0.65128 ( 9657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5212 (t80) REVERT: A 51 MET cc_start: 0.6343 (mmm) cc_final: 0.5483 (tpp) REVERT: C 25 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.5982 (tt) REVERT: D 193 MET cc_start: 0.4942 (mmt) cc_final: 0.3814 (pmm) outliers start: 18 outliers final: 13 residues processed: 194 average time/residue: 0.3529 time to fit residues: 93.3479 Evaluate side-chains 195 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.194078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.179009 restraints weight = 36650.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.183944 restraints weight = 15798.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.186882 restraints weight = 8382.574| |-----------------------------------------------------------------------------| r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7110 Z= 0.139 Angle : 0.658 6.982 9717 Z= 0.340 Chirality : 0.041 0.199 1143 Planarity : 0.004 0.047 1192 Dihedral : 7.834 61.990 1225 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.76 % Allowed : 23.95 % Favored : 74.29 % 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: -0.25 (0.28), residues: 856 helix: 0.70 (0.24), residues: 454 sheet: -0.78 (0.60), residues: 66 loop : -1.16 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 168 HIS 0.007 0.001 HIS A 116 PHE 0.014 0.001 PHE D 64 TYR 0.017 0.002 TYR A 228 ARG 0.005 0.000 ARG B 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 1.72987 ( 18) link_ALPHA1-6 : bond 0.00306 ( 1) link_ALPHA1-6 : angle 1.66401 ( 3) link_BETA1-4 : bond 0.00467 ( 6) link_BETA1-4 : angle 2.42430 ( 18) link_ALPHA1-3 : bond 0.00608 ( 1) link_ALPHA1-3 : angle 2.02846 ( 3) hydrogen bonds : bond 0.05191 ( 386) hydrogen bonds : angle 4.68533 ( 1164) SS BOND : bond 0.00217 ( 9) SS BOND : angle 1.11823 ( 18) covalent geometry : bond 0.00305 ( 7087) covalent geometry : angle 0.64433 ( 9657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5222 (t80) REVERT: A 51 MET cc_start: 0.6249 (mmm) cc_final: 0.5433 (tpp) REVERT: D 193 MET cc_start: 0.4673 (mmt) cc_final: 0.3634 (pmm) outliers start: 13 outliers final: 10 residues processed: 190 average time/residue: 0.3440 time to fit residues: 89.3198 Evaluate side-chains 189 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.193518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.179643 restraints weight = 36375.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.184281 restraints weight = 15688.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.187046 restraints weight = 8246.701| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7110 Z= 0.157 Angle : 0.667 6.422 9717 Z= 0.345 Chirality : 0.041 0.205 1143 Planarity : 0.004 0.045 1192 Dihedral : 7.749 59.660 1225 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.76 % Allowed : 23.95 % Favored : 74.29 % 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: -0.31 (0.28), residues: 856 helix: 0.60 (0.24), residues: 460 sheet: -0.82 (0.57), residues: 70 loop : -1.14 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.006 0.001 HIS A 116 PHE 0.016 0.001 PHE D 64 TYR 0.016 0.002 TYR A 228 ARG 0.004 0.000 ARG B 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 1.70369 ( 18) link_ALPHA1-6 : bond 0.00272 ( 1) link_ALPHA1-6 : angle 1.77046 ( 3) link_BETA1-4 : bond 0.00483 ( 6) link_BETA1-4 : angle 2.37474 ( 18) link_ALPHA1-3 : bond 0.00319 ( 1) link_ALPHA1-3 : angle 1.96203 ( 3) hydrogen bonds : bond 0.05180 ( 386) hydrogen bonds : angle 4.74367 ( 1164) SS BOND : bond 0.00236 ( 9) SS BOND : angle 1.12005 ( 18) covalent geometry : bond 0.00351 ( 7087) covalent geometry : angle 0.65363 ( 9657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4239.11 seconds wall clock time: 73 minutes 48.52 seconds (4428.52 seconds total)