Starting phenix.real_space_refine on Thu Mar 6 08:29:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmy_47020/03_2025/9dmy_47020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmy_47020/03_2025/9dmy_47020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dmy_47020/03_2025/9dmy_47020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmy_47020/03_2025/9dmy_47020.map" model { file = "/net/cci-nas-00/data/ceres_data/9dmy_47020/03_2025/9dmy_47020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmy_47020/03_2025/9dmy_47020.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 1.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 3460 2.51 5 N 990 2.21 5 O 1055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5550 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "C" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "E" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1110 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Time building chain proxies: 5.05, per 1000 atoms: 0.91 Number of scatterers: 5550 At special positions: 0 Unit cell: (131.716, 70.414, 46.3904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1055 8.00 N 990 7.00 C 3460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 691.8 milliseconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1250 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 94 through 95 removed outlier: 6.649A pdb=" N GLY A 94 " --> pdb=" O GLN C 95 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY C 94 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 109 through 111 removed outlier: 6.467A pdb=" N LYS A 109 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS C 109 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 114 through 116 removed outlier: 6.412A pdb=" N HIS A 114 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS C 114 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.207A pdb=" N GLY B 130 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY A 130 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 134 through 138 removed outlier: 6.529A pdb=" N GLY A 134 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N MET C 137 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA A 136 " --> pdb=" O MET C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY C 134 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET E 137 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA C 136 " --> pdb=" O MET E 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 141 through 142 removed outlier: 6.484A pdb=" N LEU A 141 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 141 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 147 through 154 removed outlier: 6.551A pdb=" N ASP A 147 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASP C 150 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU A 149 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR C 152 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG A 151 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ARG C 154 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR A 153 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP C 147 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP E 150 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU C 149 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR E 152 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG C 151 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG E 154 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR C 153 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 157 through 159 removed outlier: 6.666A pdb=" N TYR A 158 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR C 158 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 164 through 166 removed outlier: 6.408A pdb=" N VAL A 164 " --> pdb=" O TYR C 165 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL C 164 " --> pdb=" O TYR E 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 171 removed outlier: 6.715A pdb=" N GLN C 171 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 177 through 181 removed outlier: 6.190A pdb=" N THR A 177 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS C 180 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 179 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR C 177 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N HIS E 180 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL C 179 " --> pdb=" O HIS E 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 196 removed outlier: 6.534A pdb=" N THR B 186 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLN D 189 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS B 188 " --> pdb=" O GLN D 189 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR D 191 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS B 190 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR D 193 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 192 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR D 195 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR B 194 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR A 186 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN B 189 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 188 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR B 191 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N HIS A 190 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N THR B 193 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 192 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR B 195 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR A 194 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 202 through 206 removed outlier: 6.371A pdb=" N GLU A 203 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE C 206 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASP A 205 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU C 203 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE E 206 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP C 205 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 220 through 223 removed outlier: 6.106A pdb=" N TYR A 221 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR C 221 " --> pdb=" O GLN E 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 226 through 228 removed outlier: 6.514A pdb=" N ALA B 227 " --> pdb=" O TYR D 228 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 227 " --> pdb=" O TYR B 228 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1850 1.34 - 1.46: 1255 1.46 - 1.57: 2505 1.57 - 1.69: 0 1.69 - 1.80: 80 Bond restraints: 5690 Sorted by residual: bond pdb=" C ARG D 139 " pdb=" N PRO D 140 " ideal model delta sigma weight residual 1.335 1.342 -0.007 8.70e-03 1.32e+04 6.54e-01 bond pdb=" C ARG C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 1.335 1.342 -0.007 8.70e-03 1.32e+04 5.91e-01 bond pdb=" C ARG A 139 " pdb=" N PRO A 140 " ideal model delta sigma weight residual 1.335 1.341 -0.006 8.70e-03 1.32e+04 5.46e-01 bond pdb=" C ARG B 139 " pdb=" N PRO B 140 " ideal model delta sigma weight residual 1.335 1.341 -0.006 8.70e-03 1.32e+04 4.73e-01 bond pdb=" C ARG E 139 " pdb=" N PRO E 140 " ideal model delta sigma weight residual 1.335 1.341 -0.006 8.70e-03 1.32e+04 4.35e-01 ... (remaining 5685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 7204 0.85 - 1.69: 416 1.69 - 2.54: 40 2.54 - 3.39: 20 3.39 - 4.23: 20 Bond angle restraints: 7700 Sorted by residual: angle pdb=" N GLY E 126 " pdb=" CA GLY E 126 " pdb=" C GLY E 126 " ideal model delta sigma weight residual 113.18 117.39 -4.21 2.37e+00 1.78e-01 3.16e+00 angle pdb=" N GLY C 126 " pdb=" CA GLY C 126 " pdb=" C GLY C 126 " ideal model delta sigma weight residual 113.18 117.38 -4.20 2.37e+00 1.78e-01 3.15e+00 angle pdb=" N GLY A 126 " pdb=" CA GLY A 126 " pdb=" C GLY A 126 " ideal model delta sigma weight residual 113.18 117.36 -4.18 2.37e+00 1.78e-01 3.11e+00 angle pdb=" C THR E 196 " pdb=" N LYS E 197 " pdb=" CA LYS E 197 " ideal model delta sigma weight residual 122.46 124.93 -2.47 1.41e+00 5.03e-01 3.08e+00 angle pdb=" C THR C 196 " pdb=" N LYS C 197 " pdb=" CA LYS C 197 " ideal model delta sigma weight residual 122.46 124.93 -2.47 1.41e+00 5.03e-01 3.08e+00 ... (remaining 7695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.90: 2915 12.90 - 25.80: 260 25.80 - 38.70: 140 38.70 - 51.60: 25 51.60 - 64.50: 10 Dihedral angle restraints: 3350 sinusoidal: 1355 harmonic: 1995 Sorted by residual: dihedral pdb=" CB CYS E 182 " pdb=" SG CYS E 182 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual -86.00 -114.91 28.91 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CB CYS C 182 " pdb=" SG CYS C 182 " pdb=" SG CYS C 217 " pdb=" CB CYS C 217 " ideal model delta sinusoidal sigma weight residual -86.00 -114.90 28.90 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CB CYS D 182 " pdb=" SG CYS D 182 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual -86.00 -114.89 28.89 1 1.00e+01 1.00e-02 1.19e+01 ... (remaining 3347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 413 0.027 - 0.055: 217 0.055 - 0.082: 55 0.082 - 0.109: 62 0.109 - 0.136: 28 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA ILE C 142 " pdb=" N ILE C 142 " pdb=" C ILE C 142 " pdb=" CB ILE C 142 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE D 142 " pdb=" N ILE D 142 " pdb=" C ILE D 142 " pdb=" CB ILE D 142 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE A 142 " pdb=" N ILE A 142 " pdb=" C ILE A 142 " pdb=" CB ILE A 142 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 772 not shown) Planarity restraints: 1015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 212 " 0.004 2.00e-02 2.50e+03 8.87e-03 7.87e-01 pdb=" C VAL D 212 " -0.015 2.00e-02 2.50e+03 pdb=" O VAL D 212 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL D 213 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 212 " 0.004 2.00e-02 2.50e+03 8.85e-03 7.83e-01 pdb=" C VAL E 212 " -0.015 2.00e-02 2.50e+03 pdb=" O VAL E 212 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL E 213 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 212 " 0.004 2.00e-02 2.50e+03 8.63e-03 7.45e-01 pdb=" C VAL A 212 " -0.015 2.00e-02 2.50e+03 pdb=" O VAL A 212 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL A 213 " 0.005 2.00e-02 2.50e+03 ... (remaining 1012 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1707 2.84 - 3.36: 4893 3.36 - 3.87: 10310 3.87 - 4.39: 11952 4.39 - 4.90: 22467 Nonbonded interactions: 51329 Sorted by model distance: nonbonded pdb=" O GLY B 117 " pdb=" OH TYR C 131 " model vdw 2.331 3.040 nonbonded pdb=" O GLY A 117 " pdb=" OH TYR E 131 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR D 191 " pdb=" NZ LYS D 207 " model vdw 2.353 3.120 nonbonded pdb=" OG1 THR C 191 " pdb=" NZ LYS C 207 " model vdw 2.354 3.120 nonbonded pdb=" OG1 THR A 191 " pdb=" NZ LYS A 207 " model vdw 2.354 3.120 ... (remaining 51324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.600 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.002 0.033 5690 Z= 0.149 Angle : 0.481 4.232 7700 Z= 0.258 Chirality : 0.046 0.136 775 Planarity : 0.002 0.017 1015 Dihedral : 13.079 64.504 2085 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.28), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 102 HIS 0.005 0.001 HIS D 143 PHE 0.010 0.001 PHE D 201 TYR 0.007 0.001 TYR A 131 ARG 0.002 0.000 ARG E 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7328 (t0) cc_final: 0.6841 (t0) REVERT: A 206 ILE cc_start: 0.8560 (mt) cc_final: 0.8298 (mt) REVERT: B 147 ASP cc_start: 0.8643 (t0) cc_final: 0.8434 (t70) REVERT: B 206 ILE cc_start: 0.8537 (mt) cc_final: 0.8330 (mt) REVERT: C 147 ASP cc_start: 0.8747 (t0) cc_final: 0.8543 (t70) REVERT: C 196 THR cc_start: 0.7628 (m) cc_final: 0.7317 (t) REVERT: D 196 THR cc_start: 0.7077 (m) cc_final: 0.6802 (t) REVERT: D 206 ILE cc_start: 0.8294 (mt) cc_final: 0.8048 (mt) REVERT: E 99 HIS cc_start: 0.7994 (m90) cc_final: 0.7754 (m-70) REVERT: E 139 ARG cc_start: 0.6460 (ttp80) cc_final: 0.5896 (ttp-170) REVERT: E 174 ASN cc_start: 0.6997 (m110) cc_final: 0.6337 (m-40) REVERT: E 196 THR cc_start: 0.7670 (m) cc_final: 0.7430 (p) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 1.0386 time to fit residues: 309.5883 Evaluate side-chains 246 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.0060 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 174 ASN A 215 GLN A 220 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 174 ASN B 176 ASN B 215 GLN B 220 GLN B 222 GLN C 156 ASN C 173 ASN C 215 GLN ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 220 GLN E 156 ASN E 173 ASN E 215 GLN E 226 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.165567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151105 restraints weight = 5631.116| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.03 r_work: 0.3841 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5690 Z= 0.290 Angle : 0.615 5.417 7700 Z= 0.332 Chirality : 0.050 0.147 775 Planarity : 0.004 0.056 1015 Dihedral : 5.044 16.688 780 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.44 % Allowed : 21.20 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.008 0.002 HIS E 143 PHE 0.014 0.002 PHE A 201 TYR 0.010 0.002 TYR A 131 ARG 0.011 0.001 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.544 Fit side-chains REVERT: A 150 ASP cc_start: 0.7440 (t0) cc_final: 0.6860 (t0) REVERT: A 196 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7532 (t) REVERT: A 203 GLU cc_start: 0.7526 (tt0) cc_final: 0.7306 (tt0) REVERT: C 196 THR cc_start: 0.7559 (m) cc_final: 0.7282 (t) REVERT: D 98 THR cc_start: 0.8650 (t) cc_final: 0.8385 (m) REVERT: D 216 MET cc_start: 0.7889 (ttm) cc_final: 0.7585 (ttt) REVERT: D 223 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7321 (tpp-160) REVERT: E 139 ARG cc_start: 0.6896 (ttp80) cc_final: 0.6129 (ttp80) REVERT: E 196 THR cc_start: 0.7540 (m) cc_final: 0.7328 (p) outliers start: 26 outliers final: 6 residues processed: 240 average time/residue: 1.0184 time to fit residues: 255.7635 Evaluate side-chains 233 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 226 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 194 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN C 176 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.162683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148712 restraints weight = 5700.237| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.02 r_work: 0.3822 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5690 Z= 0.274 Angle : 0.598 5.031 7700 Z= 0.324 Chirality : 0.050 0.149 775 Planarity : 0.003 0.037 1015 Dihedral : 5.195 17.923 780 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.76 % Allowed : 23.42 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.009 0.002 HIS E 143 PHE 0.013 0.002 PHE B 201 TYR 0.012 0.002 TYR E 131 ARG 0.005 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.570 Fit side-chains REVERT: A 132 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7687 (mmm) REVERT: A 150 ASP cc_start: 0.7538 (t0) cc_final: 0.7016 (t0) REVERT: B 98 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8381 (m) REVERT: C 132 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7737 (mmm) REVERT: C 196 THR cc_start: 0.7616 (m) cc_final: 0.7321 (t) REVERT: C 209 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7555 (tpt) REVERT: C 216 MET cc_start: 0.8112 (tpp) cc_final: 0.7807 (ttt) REVERT: C 223 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8136 (ttm-80) REVERT: D 98 THR cc_start: 0.8668 (t) cc_final: 0.8451 (m) REVERT: D 216 MET cc_start: 0.7900 (ttm) cc_final: 0.7516 (ttt) REVERT: D 223 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.7322 (tpp-160) REVERT: E 132 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6631 (mtm) REVERT: E 139 ARG cc_start: 0.6986 (ttp80) cc_final: 0.6143 (ttp-170) REVERT: E 154 ARG cc_start: 0.6113 (mmt-90) cc_final: 0.4648 (ttm-80) REVERT: E 167 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.6970 (tpm170) REVERT: E 196 THR cc_start: 0.7549 (m) cc_final: 0.7348 (p) REVERT: E 223 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7089 (ttp-170) outliers start: 22 outliers final: 7 residues processed: 233 average time/residue: 1.0269 time to fit residues: 250.3010 Evaluate side-chains 238 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 53 optimal weight: 0.1980 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 215 GLN E 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140224 restraints weight = 5902.205| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.02 r_work: 0.3758 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 5690 Z= 0.470 Angle : 0.712 5.676 7700 Z= 0.393 Chirality : 0.054 0.169 775 Planarity : 0.005 0.045 1015 Dihedral : 5.815 20.789 780 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.30 % Allowed : 22.91 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 93 HIS 0.012 0.002 HIS E 143 PHE 0.013 0.002 PHE B 201 TYR 0.021 0.003 TYR A 131 ARG 0.003 0.001 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7547 (mmm) REVERT: A 150 ASP cc_start: 0.7623 (t0) cc_final: 0.7018 (t70) REVERT: A 209 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7865 (tpt) REVERT: A 223 ARG cc_start: 0.8331 (tpt90) cc_final: 0.8081 (tpt90) REVERT: B 98 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8404 (m) REVERT: C 132 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7687 (mtm) REVERT: C 154 ARG cc_start: 0.7449 (ttt180) cc_final: 0.7217 (ttt-90) REVERT: C 196 THR cc_start: 0.7619 (m) cc_final: 0.7294 (t) REVERT: C 216 MET cc_start: 0.8066 (tpp) cc_final: 0.7813 (ttt) REVERT: D 150 ASP cc_start: 0.7540 (t0) cc_final: 0.7248 (t0) REVERT: D 223 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.7536 (tpm170) REVERT: E 132 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6653 (mtm) REVERT: E 141 LEU cc_start: 0.9052 (tp) cc_final: 0.8841 (tp) REVERT: E 196 THR cc_start: 0.7614 (m) cc_final: 0.7359 (t) REVERT: E 223 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6917 (ttp80) outliers start: 31 outliers final: 14 residues processed: 234 average time/residue: 1.0572 time to fit residues: 258.7731 Evaluate side-chains 232 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 220 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN E 220 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.162637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150092 restraints weight = 5666.629| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.00 r_work: 0.3914 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5690 Z= 0.187 Angle : 0.582 9.178 7700 Z= 0.306 Chirality : 0.049 0.139 775 Planarity : 0.002 0.017 1015 Dihedral : 5.214 16.949 780 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.56 % Allowed : 24.27 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.006 0.001 HIS A 143 PHE 0.012 0.001 PHE B 201 TYR 0.018 0.001 TYR A 131 ARG 0.006 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7494 (t0) cc_final: 0.7046 (t0) REVERT: A 196 THR cc_start: 0.7804 (m) cc_final: 0.7533 (t) REVERT: A 223 ARG cc_start: 0.8391 (tpt90) cc_final: 0.8147 (ttt90) REVERT: B 98 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8446 (m) REVERT: B 154 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.7179 (ttt180) REVERT: C 154 ARG cc_start: 0.7439 (ttt180) cc_final: 0.7205 (ttt-90) REVERT: C 196 THR cc_start: 0.7606 (m) cc_final: 0.7272 (t) REVERT: C 214 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6696 (mt-10) REVERT: C 216 MET cc_start: 0.8037 (tpp) cc_final: 0.7785 (ttt) REVERT: D 223 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7254 (tpp-160) REVERT: E 139 ARG cc_start: 0.6382 (ttp-170) cc_final: 0.5935 (ttp-170) REVERT: E 154 ARG cc_start: 0.6178 (mmt-90) cc_final: 0.3836 (ttm-80) REVERT: E 196 THR cc_start: 0.7545 (m) cc_final: 0.7218 (t) REVERT: E 223 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7062 (ttp-170) outliers start: 15 outliers final: 5 residues processed: 243 average time/residue: 1.1873 time to fit residues: 301.8309 Evaluate side-chains 240 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 215 GLN E 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.154875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141894 restraints weight = 5733.345| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 0.99 r_work: 0.3788 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5690 Z= 0.384 Angle : 0.688 10.104 7700 Z= 0.369 Chirality : 0.052 0.166 775 Planarity : 0.004 0.029 1015 Dihedral : 5.650 18.316 780 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.27 % Allowed : 24.96 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 93 HIS 0.012 0.002 HIS E 143 PHE 0.013 0.002 PHE B 201 TYR 0.022 0.002 TYR A 131 ARG 0.005 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7355 (mmm) REVERT: A 150 ASP cc_start: 0.7574 (t0) cc_final: 0.6991 (t70) REVERT: A 170 ASP cc_start: 0.8270 (m-30) cc_final: 0.8070 (m-30) REVERT: A 196 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7543 (t) REVERT: A 223 ARG cc_start: 0.8351 (tpt90) cc_final: 0.8044 (tpt90) REVERT: B 98 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8453 (m) REVERT: B 209 MET cc_start: 0.7851 (mmm) cc_final: 0.7619 (tpt) REVERT: C 154 ARG cc_start: 0.7429 (ttt180) cc_final: 0.7203 (ttt-90) REVERT: C 196 THR cc_start: 0.7535 (m) cc_final: 0.7226 (t) REVERT: D 150 ASP cc_start: 0.7499 (t0) cc_final: 0.7169 (t70) REVERT: D 223 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.7463 (tpm170) REVERT: E 141 LEU cc_start: 0.9014 (tp) cc_final: 0.8805 (tp) REVERT: E 167 ARG cc_start: 0.8099 (ttt-90) cc_final: 0.7005 (tpm170) REVERT: E 196 THR cc_start: 0.7555 (m) cc_final: 0.7246 (t) REVERT: E 223 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7166 (ttp-170) outliers start: 25 outliers final: 10 residues processed: 243 average time/residue: 1.0689 time to fit residues: 271.5819 Evaluate side-chains 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.0040 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150432 restraints weight = 5602.945| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 0.91 r_work: 0.3917 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5690 Z= 0.182 Angle : 0.601 9.145 7700 Z= 0.311 Chirality : 0.050 0.174 775 Planarity : 0.002 0.016 1015 Dihedral : 5.225 17.148 780 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.22 % Allowed : 26.32 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.006 0.001 HIS C 143 PHE 0.011 0.001 PHE C 201 TYR 0.020 0.001 TYR A 131 ARG 0.008 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 245 time to evaluate : 0.647 Fit side-chains REVERT: A 150 ASP cc_start: 0.7517 (t0) cc_final: 0.7051 (t0) REVERT: A 196 THR cc_start: 0.7846 (m) cc_final: 0.7579 (t) REVERT: A 223 ARG cc_start: 0.8325 (tpt90) cc_final: 0.8033 (tpt90) REVERT: B 98 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8418 (m) REVERT: B 141 LEU cc_start: 0.9073 (tp) cc_final: 0.8758 (tp) REVERT: B 181 ASP cc_start: 0.7930 (t70) cc_final: 0.7727 (t70) REVERT: C 196 THR cc_start: 0.7603 (m) cc_final: 0.7276 (t) REVERT: D 223 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.7346 (tpp-160) REVERT: E 139 ARG cc_start: 0.6270 (ttp-170) cc_final: 0.6010 (ttp-170) REVERT: E 154 ARG cc_start: 0.6147 (mmt-90) cc_final: 0.3719 (ttm-80) REVERT: E 196 THR cc_start: 0.7547 (m) cc_final: 0.7216 (t) REVERT: E 223 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7079 (ttp-170) outliers start: 13 outliers final: 5 residues processed: 247 average time/residue: 1.0890 time to fit residues: 281.2007 Evaluate side-chains 246 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 239 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 48 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 overall best weight: 2.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142382 restraints weight = 5625.534| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 0.95 r_work: 0.3803 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5690 Z= 0.357 Angle : 0.689 9.574 7700 Z= 0.364 Chirality : 0.052 0.168 775 Planarity : 0.004 0.033 1015 Dihedral : 5.616 17.627 780 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.76 % Allowed : 24.62 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 93 HIS 0.011 0.002 HIS E 143 PHE 0.013 0.002 PHE B 201 TYR 0.020 0.002 TYR A 131 ARG 0.008 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.580 Fit side-chains REVERT: A 147 ASP cc_start: 0.8782 (t0) cc_final: 0.8393 (t70) REVERT: A 150 ASP cc_start: 0.7552 (t0) cc_final: 0.6998 (t70) REVERT: A 196 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7587 (t) REVERT: A 223 ARG cc_start: 0.8350 (tpt90) cc_final: 0.8044 (tpt90) REVERT: B 98 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8401 (m) REVERT: C 154 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7191 (ttt-90) REVERT: C 163 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: C 196 THR cc_start: 0.7566 (m) cc_final: 0.7263 (t) REVERT: D 150 ASP cc_start: 0.7480 (t0) cc_final: 0.7156 (t70) REVERT: D 223 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.7528 (tpm170) REVERT: E 154 ARG cc_start: 0.6243 (mmt-90) cc_final: 0.3926 (ttm-80) REVERT: E 196 THR cc_start: 0.7544 (m) cc_final: 0.7238 (t) REVERT: E 223 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7119 (ttp-170) outliers start: 22 outliers final: 10 residues processed: 246 average time/residue: 1.1042 time to fit residues: 283.7156 Evaluate side-chains 249 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 36 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.155506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143005 restraints weight = 5675.081| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 0.92 r_work: 0.3813 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5690 Z= 0.345 Angle : 0.696 9.783 7700 Z= 0.366 Chirality : 0.052 0.178 775 Planarity : 0.004 0.077 1015 Dihedral : 5.706 18.005 780 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.08 % Allowed : 26.50 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 93 HIS 0.011 0.002 HIS E 143 PHE 0.013 0.002 PHE B 201 TYR 0.023 0.002 TYR A 131 ARG 0.019 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8781 (t0) cc_final: 0.8382 (t70) REVERT: A 150 ASP cc_start: 0.7548 (t0) cc_final: 0.6984 (t70) REVERT: A 196 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7589 (t) REVERT: A 223 ARG cc_start: 0.8349 (tpt90) cc_final: 0.8041 (tpt90) REVERT: B 98 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8466 (m) REVERT: B 209 MET cc_start: 0.7861 (mmm) cc_final: 0.7648 (tpt) REVERT: C 163 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: C 196 THR cc_start: 0.7528 (m) cc_final: 0.7242 (t) REVERT: D 223 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.7555 (tpm170) REVERT: E 196 THR cc_start: 0.7531 (m) cc_final: 0.7241 (t) REVERT: E 223 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7122 (ttp-170) outliers start: 18 outliers final: 11 residues processed: 238 average time/residue: 1.0355 time to fit residues: 257.8274 Evaluate side-chains 247 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN E 215 GLN E 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.162215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.150541 restraints weight = 5745.696| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 0.84 r_work: 0.3939 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5690 Z= 0.195 Angle : 0.633 9.456 7700 Z= 0.326 Chirality : 0.050 0.180 775 Planarity : 0.003 0.065 1015 Dihedral : 5.401 17.094 780 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.74 % Allowed : 27.35 % Favored : 69.91 % 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: -4.13 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.008 0.001 HIS A 143 PHE 0.012 0.001 PHE C 201 TYR 0.020 0.001 TYR A 131 ARG 0.013 0.001 ARG B 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.567 Fit side-chains REVERT: A 139 ARG cc_start: 0.7246 (ttp-110) cc_final: 0.6927 (ttm170) REVERT: A 147 ASP cc_start: 0.8695 (t0) cc_final: 0.8307 (t70) REVERT: A 150 ASP cc_start: 0.7505 (t0) cc_final: 0.7045 (t0) REVERT: A 196 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7588 (t) REVERT: B 98 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8382 (m) REVERT: B 132 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7600 (mmp) REVERT: C 196 THR cc_start: 0.7591 (m) cc_final: 0.7275 (t) REVERT: D 139 ARG cc_start: 0.6207 (mmt-90) cc_final: 0.5996 (mmt-90) REVERT: D 223 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7308 (tpp-160) REVERT: E 154 ARG cc_start: 0.6169 (mmt-90) cc_final: 0.3804 (ttm-80) REVERT: E 196 THR cc_start: 0.7521 (m) cc_final: 0.7213 (t) REVERT: E 223 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7069 (ttp-170) outliers start: 16 outliers final: 10 residues processed: 247 average time/residue: 0.9680 time to fit residues: 250.6397 Evaluate side-chains 252 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN D 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.167151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.154511 restraints weight = 5709.738| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.00 r_work: 0.3987 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5690 Z= 0.202 Angle : 0.651 8.737 7700 Z= 0.335 Chirality : 0.051 0.210 775 Planarity : 0.005 0.103 1015 Dihedral : 5.399 17.166 780 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.74 % Allowed : 27.01 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 93 HIS 0.005 0.001 HIS C 143 PHE 0.012 0.001 PHE A 201 TYR 0.019 0.001 TYR A 131 ARG 0.015 0.001 ARG C 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5854.93 seconds wall clock time: 100 minutes 50.76 seconds (6050.76 seconds total)