Starting phenix.real_space_refine on Sun Nov 17 13:04:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/11_2024/8jj5_36340_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/11_2024/8jj5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/11_2024/8jj5_36340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/11_2024/8jj5_36340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/11_2024/8jj5_36340_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/11_2024/8jj5_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-5513/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: 6.66, per 1000 atoms: 0.49 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: 3.79 Conformation dependent library (CDL) restraints added in 1.2 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: 0.84 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: 4.37 Time building geometry restraints manager: 4.47 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: 0.420 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: 0.200 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.680 ------------------------------------------------------------------------------- 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 7087 Z= 1.372 Angle : 2.181 11.766 9657 Z= 1.445 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 *********************** 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 : 1.125 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: 0.4280 time to fit residues: 156.2796 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 : 1.069 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 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 7087 Z= 0.380 Angle : 0.890 8.375 9657 Z= 0.475 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 *********************** 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 : 1.296 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: 0.6191 (mmm) cc_final: 0.5574 (mmm) REVERT: A 85 LEU cc_start: 0.8129 (mm) cc_final: 0.7829 (mm) REVERT: A 175 ARG cc_start: 0.7215 (mtm180) cc_final: 0.6893 (mtm180) REVERT: B 157 VAL cc_start: 0.4206 (t) cc_final: 0.3938 (t) REVERT: C 91 GLU cc_start: 0.6295 (mt-10) cc_final: 0.5513 (tm-30) REVERT: D 24 MET cc_start: 0.7899 (mtt) cc_final: 0.7430 (mmt) REVERT: D 255 TRP cc_start: 0.7748 (t60) cc_final: 0.7090 (t60) outliers start: 15 outliers final: 11 residues processed: 209 average time/residue: 0.3883 time to fit residues: 109.1935 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 : 0.952 ------------------------------------------------------------------------------- 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 42 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7087 Z= 0.230 Angle : 0.758 6.587 9657 Z= 0.398 Chirality : 0.044 0.230 1143 Planarity : 0.005 0.061 1192 Dihedral : 11.045 75.903 1225 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.76 % Allowed : 18.40 % Favored : 79.84 % 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: -1.28 (0.27), residues: 856 helix: -0.15 (0.24), residues: 451 sheet: -0.78 (0.59), residues: 60 loop : -1.73 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 230 HIS 0.005 0.001 HIS A 116 PHE 0.024 0.002 PHE A 34 TYR 0.027 0.002 TYR A 114 ARG 0.003 0.000 ARG A 46 *********************** 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 200 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 1.052 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: 0.6460 (OUTLIER) cc_final: 0.5122 (t80) REVERT: A 51 MET cc_start: 0.6183 (mmm) cc_final: 0.5722 (mmm) REVERT: A 85 LEU cc_start: 0.7981 (mm) cc_final: 0.7726 (mm) REVERT: A 106 GLU cc_start: 0.7380 (tp30) cc_final: 0.7122 (tp30) REVERT: C 91 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5459 (tm-30) REVERT: D 24 MET cc_start: 0.7745 (mtt) cc_final: 0.7344 (mmt) REVERT: D 32 GLU cc_start: 0.0619 (mm-30) cc_final: 0.0204 (mt-10) REVERT: D 246 TRP cc_start: 0.6917 (m-10) cc_final: 0.6414 (m100) outliers start: 13 outliers final: 9 residues processed: 192 average time/residue: 0.3931 time to fit residues: 101.7742 Evaluate side-chains 178 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 75 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN D 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7087 Z= 0.193 Angle : 0.680 6.010 9657 Z= 0.354 Chirality : 0.042 0.220 1143 Planarity : 0.004 0.058 1192 Dihedral : 9.461 72.637 1225 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.57 % Allowed : 19.35 % Favored : 78.08 % 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: -0.80 (0.28), residues: 856 helix: 0.27 (0.24), residues: 442 sheet: -0.53 (0.64), residues: 60 loop : -1.51 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 168 HIS 0.004 0.001 HIS A 116 PHE 0.027 0.001 PHE A 34 TYR 0.022 0.002 TYR A 114 ARG 0.003 0.000 ARG A 88 *********************** 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 195 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.824 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: A 48 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5115 (t80) REVERT: A 50 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7057 (tt) REVERT: A 51 MET cc_start: 0.5790 (mmm) cc_final: 0.5414 (mmm) REVERT: A 85 LEU cc_start: 0.7994 (mm) cc_final: 0.7737 (mm) REVERT: C 218 LEU cc_start: 0.7187 (mm) cc_final: 0.6859 (tp) REVERT: D 24 MET cc_start: 0.7810 (mtt) cc_final: 0.7347 (mmt) REVERT: D 32 GLU cc_start: 0.1390 (mm-30) cc_final: 0.0894 (mm-30) REVERT: D 246 TRP cc_start: 0.6853 (m-10) cc_final: 0.6424 (m100) outliers start: 19 outliers final: 12 residues processed: 185 average time/residue: 0.3994 time to fit residues: 97.5030 Evaluate side-chains 181 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 53 LEU Chi-restraints excluded: chain C residue 136 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 0.0270 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 7087 Z= 0.276 Angle : 0.699 6.377 9657 Z= 0.367 Chirality : 0.043 0.256 1143 Planarity : 0.005 0.055 1192 Dihedral : 8.907 67.905 1225 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.25 % Allowed : 19.22 % 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: -0.81 (0.28), residues: 856 helix: 0.27 (0.24), residues: 440 sheet: -0.90 (0.59), residues: 64 loop : -1.46 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 39 HIS 0.006 0.001 HIS A 116 PHE 0.027 0.002 PHE A 34 TYR 0.023 0.002 TYR D 91 ARG 0.004 0.000 ARG D 257 *********************** 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 215 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.969 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: 0.6354 (OUTLIER) cc_final: 0.4953 (t80) REVERT: A 51 MET cc_start: 0.6419 (mmm) cc_final: 0.6044 (mmm) REVERT: A 85 LEU cc_start: 0.8060 (mm) cc_final: 0.7767 (mm) REVERT: A 87 ARG cc_start: 0.6789 (ptp-110) cc_final: 0.6566 (ttp-110) REVERT: D 24 MET cc_start: 0.8093 (mtt) cc_final: 0.7578 (mmt) REVERT: D 88 LEU cc_start: 0.6824 (mt) cc_final: 0.6534 (mt) REVERT: D 246 TRP cc_start: 0.6885 (m-10) cc_final: 0.6464 (m100) outliers start: 24 outliers final: 15 residues processed: 202 average time/residue: 0.4116 time to fit residues: 112.2523 Evaluate side-chains 188 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 119 TYR 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 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 41 TYR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 248 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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** D 229 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7087 Z= 0.216 Angle : 0.657 6.469 9657 Z= 0.345 Chirality : 0.042 0.216 1143 Planarity : 0.004 0.055 1192 Dihedral : 8.492 63.941 1225 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.71 % Allowed : 21.92 % Favored : 75.37 % 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: -0.61 (0.28), residues: 856 helix: 0.42 (0.24), residues: 440 sheet: -0.83 (0.57), residues: 66 loop : -1.33 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 168 HIS 0.005 0.001 HIS A 116 PHE 0.027 0.001 PHE A 34 TYR 0.016 0.002 TYR D 91 ARG 0.003 0.000 ARG A 46 *********************** 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 203 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.043 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: A 48 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.4975 (t80) REVERT: A 51 MET cc_start: 0.6185 (mmm) cc_final: 0.5880 (mmm) REVERT: A 71 PHE cc_start: 0.7131 (t80) cc_final: 0.6906 (t80) REVERT: A 85 LEU cc_start: 0.8148 (mm) cc_final: 0.7868 (mm) REVERT: D 24 MET cc_start: 0.8078 (mtt) cc_final: 0.7500 (mmt) REVERT: D 246 TRP cc_start: 0.6762 (m-10) cc_final: 0.6452 (m100) outliers start: 20 outliers final: 16 residues processed: 192 average time/residue: 0.3834 time to fit residues: 99.0777 Evaluate side-chains 186 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 189 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 0.0030 chunk 49 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7087 Z= 0.233 Angle : 0.658 6.328 9657 Z= 0.346 Chirality : 0.042 0.221 1143 Planarity : 0.004 0.050 1192 Dihedral : 8.352 70.648 1225 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.71 % Allowed : 21.92 % Favored : 75.37 % 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: -0.57 (0.28), residues: 856 helix: 0.45 (0.24), residues: 441 sheet: -0.98 (0.55), residues: 72 loop : -1.26 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 168 HIS 0.004 0.001 HIS D 229 PHE 0.028 0.001 PHE A 34 TYR 0.016 0.002 TYR B 116 ARG 0.003 0.000 ARG A 46 *********************** 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 204 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.969 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: 0.6230 (OUTLIER) cc_final: 0.5047 (t80) REVERT: A 85 LEU cc_start: 0.8085 (mm) cc_final: 0.7813 (mm) REVERT: A 120 MET cc_start: 0.5889 (ptm) cc_final: 0.5476 (tpt) REVERT: D 24 MET cc_start: 0.8082 (mtt) cc_final: 0.7466 (mmt) REVERT: D 246 TRP cc_start: 0.6753 (m-90) cc_final: 0.6452 (m100) REVERT: D 257 ARG cc_start: 0.7968 (tpm170) cc_final: 0.7293 (tpm170) outliers start: 20 outliers final: 15 residues processed: 195 average time/residue: 0.3886 time to fit residues: 104.0934 Evaluate side-chains 186 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 78 SER 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 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 48 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7087 Z= 0.213 Angle : 0.642 6.238 9657 Z= 0.337 Chirality : 0.041 0.205 1143 Planarity : 0.004 0.051 1192 Dihedral : 8.138 67.959 1225 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.57 % Allowed : 22.46 % Favored : 74.97 % 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: -0.50 (0.28), residues: 856 helix: 0.48 (0.24), residues: 447 sheet: -0.87 (0.56), residues: 67 loop : -1.24 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 168 HIS 0.004 0.001 HIS D 229 PHE 0.025 0.001 PHE A 34 TYR 0.016 0.002 TYR A 228 ARG 0.004 0.000 ARG A 46 *********************** 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 204 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.083 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: 0.6165 (OUTLIER) cc_final: 0.5182 (t80) REVERT: A 85 LEU cc_start: 0.8085 (mm) cc_final: 0.7828 (mm) REVERT: A 120 MET cc_start: 0.5396 (ptm) cc_final: 0.5194 (tpt) REVERT: C 93 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7159 (tm-30) REVERT: D 24 MET cc_start: 0.8102 (mtt) cc_final: 0.7469 (mmt) REVERT: D 193 MET cc_start: 0.5560 (mmt) cc_final: 0.3205 (pmm) REVERT: D 246 TRP cc_start: 0.6576 (m-90) cc_final: 0.6325 (m100) outliers start: 19 outliers final: 13 residues processed: 194 average time/residue: 0.3593 time to fit residues: 95.4956 Evaluate side-chains 190 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 78 SER Chi-restraints excluded: chain A residue 119 TYR 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 248 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7087 Z= 0.206 Angle : 0.651 6.232 9657 Z= 0.340 Chirality : 0.041 0.203 1143 Planarity : 0.004 0.048 1192 Dihedral : 7.912 65.209 1225 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.44 % Allowed : 23.55 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.28), residues: 856 helix: 0.56 (0.24), residues: 448 sheet: -0.69 (0.63), residues: 54 loop : -1.18 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 168 HIS 0.004 0.001 HIS D 229 PHE 0.016 0.001 PHE D 64 TYR 0.017 0.002 TYR A 114 ARG 0.004 0.000 ARG A 46 *********************** 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 199 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 1.046 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: 0.6243 (OUTLIER) cc_final: 0.5275 (t80) REVERT: A 51 MET cc_start: 0.6097 (mmm) cc_final: 0.5455 (tpp) REVERT: A 85 LEU cc_start: 0.8090 (mm) cc_final: 0.7793 (mm) REVERT: A 153 MET cc_start: 0.6449 (ttm) cc_final: 0.6176 (ttp) REVERT: D 24 MET cc_start: 0.8051 (mtt) cc_final: 0.7393 (mmt) REVERT: D 193 MET cc_start: 0.4767 (mmt) cc_final: 0.3636 (pmm) REVERT: D 246 TRP cc_start: 0.6584 (m-90) cc_final: 0.6338 (m100) outliers start: 18 outliers final: 11 residues processed: 189 average time/residue: 0.3814 time to fit residues: 98.7496 Evaluate side-chains 190 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7087 Z= 0.215 Angle : 0.652 6.164 9657 Z= 0.342 Chirality : 0.040 0.203 1143 Planarity : 0.004 0.050 1192 Dihedral : 7.730 62.710 1225 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.76 % Allowed : 24.09 % Favored : 74.15 % 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: -0.33 (0.29), residues: 856 helix: 0.60 (0.24), residues: 451 sheet: -0.83 (0.56), residues: 70 loop : -1.13 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 168 HIS 0.008 0.001 HIS A 116 PHE 0.037 0.001 PHE A 71 TYR 0.016 0.002 TYR A 228 ARG 0.006 0.000 ARG B 63 ********************** 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 197 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 1.140 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: 0.6217 (OUTLIER) cc_final: 0.5235 (t80) REVERT: A 51 MET cc_start: 0.6207 (mmm) cc_final: 0.5378 (tpp) REVERT: A 85 LEU cc_start: 0.8059 (mm) cc_final: 0.7781 (mm) REVERT: A 153 MET cc_start: 0.6427 (ttm) cc_final: 0.6157 (ttp) REVERT: D 24 MET cc_start: 0.8003 (mtt) cc_final: 0.7401 (mmt) REVERT: D 193 MET cc_start: 0.4664 (mmt) cc_final: 0.3638 (pmm) REVERT: D 246 TRP cc_start: 0.6582 (m-90) cc_final: 0.6348 (m100) outliers start: 13 outliers final: 10 residues processed: 191 average time/residue: 0.3573 time to fit residues: 93.4140 Evaluate side-chains 187 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 119 TYR Chi-restraints excluded: chain A residue 212 LEU 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 248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.191397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.176290 restraints weight = 36617.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.181164 restraints weight = 15889.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.184123 restraints weight = 8508.126| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7087 Z= 0.232 Angle : 0.647 6.229 9657 Z= 0.341 Chirality : 0.041 0.208 1143 Planarity : 0.004 0.047 1192 Dihedral : 7.702 61.737 1225 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.35 % Allowed : 25.58 % Favored : 73.07 % 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 (0.29), residues: 856 helix: 0.58 (0.24), residues: 451 sheet: -0.82 (0.57), residues: 70 loop : -1.16 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 168 HIS 0.007 0.001 HIS A 116 PHE 0.016 0.001 PHE A 71 TYR 0.016 0.002 TYR A 228 ARG 0.004 0.000 ARG B 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.19 seconds wall clock time: 61 minutes 12.94 seconds (3672.94 seconds total)