Starting phenix.real_space_refine on Wed Sep 17 05:48:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmy_47020/09_2025/9dmy_47020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmy_47020/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dmy_47020/09_2025/9dmy_47020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmy_47020/09_2025/9dmy_47020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dmy_47020/09_2025/9dmy_47020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmy_47020/09_2025/9dmy_47020.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.60, per 1000 atoms: 0.29 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: 0.47 Conformation dependent library (CDL) restraints added in 270.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.25 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: 0.99 Time building geometry restraints manager: 0.60 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.790 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- 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 5695 Z= 0.093 Angle : 0.481 4.232 7710 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG E 211 TYR 0.007 0.001 TYR A 131 PHE 0.010 0.001 PHE D 201 TRP 0.003 0.001 TRP E 102 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 5690) covalent geometry : angle 0.48086 ( 7700) SS BOND : bond 0.00321 ( 5) SS BOND : angle 0.36306 ( 10) hydrogen bonds : bond 0.15439 ( 91) hydrogen bonds : angle 9.67355 ( 273) *********************** 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 : 0.290 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: 0.5210 time to fit residues: 155.0868 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 : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 C 220 GLN D 143 HIS ** 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 220 GLN E 226 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142998 restraints weight = 5732.742| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.03 r_work: 0.3754 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 5695 Z= 0.337 Angle : 0.728 6.245 7710 Z= 0.402 Chirality : 0.054 0.166 775 Planarity : 0.005 0.055 1015 Dihedral : 5.714 19.801 780 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.30 % Allowed : 19.83 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 154 TYR 0.014 0.003 TYR E 160 PHE 0.017 0.002 PHE A 201 TRP 0.007 0.002 TRP B 93 HIS 0.011 0.003 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 5690) covalent geometry : angle 0.72533 ( 7700) SS BOND : bond 0.00754 ( 5) SS BOND : angle 1.97285 ( 10) hydrogen bonds : bond 0.03641 ( 91) hydrogen bonds : angle 7.17305 ( 273) *********************** 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 265 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7636 (t0) cc_final: 0.7026 (t70) REVERT: A 196 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7616 (t) REVERT: C 196 THR cc_start: 0.7528 (m) cc_final: 0.7263 (t) REVERT: D 150 ASP cc_start: 0.7540 (t0) cc_final: 0.7231 (t0) REVERT: D 196 THR cc_start: 0.7597 (m) cc_final: 0.7376 (t) REVERT: D 216 MET cc_start: 0.7964 (ttm) cc_final: 0.7675 (ttt) REVERT: D 223 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.7400 (tpp-160) REVERT: E 107 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8057 (mtmm) REVERT: E 196 THR cc_start: 0.7547 (m) cc_final: 0.7346 (t) REVERT: E 216 MET cc_start: 0.8194 (tpp) cc_final: 0.7883 (ttt) outliers start: 31 outliers final: 9 residues processed: 239 average time/residue: 0.5300 time to fit residues: 132.2248 Evaluate side-chains 233 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 209 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 138 SER 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 63 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.149210 restraints weight = 5658.858| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.03 r_work: 0.3845 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5695 Z= 0.146 Angle : 0.576 4.991 7710 Z= 0.308 Chirality : 0.050 0.143 775 Planarity : 0.003 0.023 1015 Dihedral : 5.180 16.987 780 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.91 % Allowed : 22.91 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 154 TYR 0.017 0.001 TYR A 131 PHE 0.014 0.002 PHE A 201 TRP 0.005 0.001 TRP A 93 HIS 0.007 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5690) covalent geometry : angle 0.57488 ( 7700) SS BOND : bond 0.00529 ( 5) SS BOND : angle 1.07978 ( 10) hydrogen bonds : bond 0.02322 ( 91) hydrogen bonds : angle 6.53420 ( 273) *********************** 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 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.218 Fit side-chains REVERT: A 150 ASP cc_start: 0.7514 (t0) cc_final: 0.7033 (t0) REVERT: A 206 ILE cc_start: 0.8609 (mt) cc_final: 0.8409 (mt) REVERT: C 196 THR cc_start: 0.7627 (m) cc_final: 0.7286 (t) REVERT: C 216 MET cc_start: 0.8141 (tpp) cc_final: 0.7788 (ttt) REVERT: C 223 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.8181 (ttm-80) REVERT: D 223 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.7384 (tpp-160) REVERT: E 107 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7956 (mtmm) REVERT: E 132 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6583 (mtm) REVERT: E 150 ASP cc_start: 0.7463 (t0) cc_final: 0.7122 (t70) REVERT: E 154 ARG cc_start: 0.6093 (mmt-90) cc_final: 0.4515 (ttm-80) REVERT: E 196 THR cc_start: 0.7535 (m) cc_final: 0.7273 (t) REVERT: E 214 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6655 (mt-10) REVERT: E 223 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7093 (ttp-170) outliers start: 17 outliers final: 7 residues processed: 246 average time/residue: 0.5182 time to fit residues: 133.1261 Evaluate side-chains 240 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 231 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 209 MET Chi-restraints excluded: chain B residue 164 VAL 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 132 MET 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 26 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 162 ASN D 173 ASN E 215 GLN E 220 GLN E 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.144149 restraints weight = 5704.744| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 0.98 r_work: 0.3813 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5695 Z= 0.207 Angle : 0.616 5.279 7710 Z= 0.332 Chirality : 0.050 0.158 775 Planarity : 0.003 0.029 1015 Dihedral : 5.397 17.350 780 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.62 % Allowed : 22.39 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.00 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 154 TYR 0.019 0.002 TYR A 131 PHE 0.013 0.002 PHE B 201 TRP 0.006 0.001 TRP B 93 HIS 0.010 0.002 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 5690) covalent geometry : angle 0.61412 ( 7700) SS BOND : bond 0.00604 ( 5) SS BOND : angle 1.41678 ( 10) hydrogen bonds : bond 0.02464 ( 91) hydrogen bonds : angle 6.44837 ( 273) *********************** 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 257 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.208 Fit side-chains REVERT: A 132 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7339 (mmm) REVERT: A 150 ASP cc_start: 0.7541 (t0) cc_final: 0.6962 (t70) REVERT: A 196 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7605 (t) REVERT: A 223 ARG cc_start: 0.8246 (tpt90) cc_final: 0.8031 (ttt90) REVERT: B 98 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8461 (m) REVERT: C 196 THR cc_start: 0.7593 (m) cc_final: 0.7267 (t) REVERT: D 223 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.7482 (tpm170) REVERT: E 132 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6607 (mtm) REVERT: E 154 ARG cc_start: 0.6113 (mmt-90) cc_final: 0.4412 (ttt-90) REVERT: E 196 THR cc_start: 0.7583 (m) cc_final: 0.7302 (t) REVERT: E 223 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6903 (ttp80) outliers start: 27 outliers final: 14 residues processed: 236 average time/residue: 0.5021 time to fit residues: 123.9160 Evaluate side-chains 245 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 184 ASN 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 109 LYS Chi-restraints excluded: chain B residue 164 VAL 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 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 194 THR 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 48 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 2 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 215 GLN E 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141258 restraints weight = 5821.500| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 0.99 r_work: 0.3774 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5695 Z= 0.280 Angle : 0.674 5.386 7710 Z= 0.368 Chirality : 0.053 0.166 775 Planarity : 0.004 0.033 1015 Dihedral : 5.709 19.031 780 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.62 % Allowed : 23.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.12 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 154 TYR 0.023 0.002 TYR A 131 PHE 0.013 0.002 PHE B 201 TRP 0.007 0.002 TRP A 93 HIS 0.011 0.002 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 5690) covalent geometry : angle 0.67117 ( 7700) SS BOND : bond 0.00723 ( 5) SS BOND : angle 1.79969 ( 10) hydrogen bonds : bond 0.02743 ( 91) hydrogen bonds : angle 6.57604 ( 273) *********************** 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 250 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7287 (mmm) REVERT: A 150 ASP cc_start: 0.7626 (t0) cc_final: 0.7045 (t70) REVERT: A 196 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7586 (t) REVERT: A 223 ARG cc_start: 0.8305 (tpt90) cc_final: 0.8076 (ttt90) REVERT: B 98 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8475 (m) REVERT: B 132 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7571 (mmm) REVERT: C 196 THR cc_start: 0.7536 (m) cc_final: 0.7236 (t) REVERT: D 150 ASP cc_start: 0.7557 (t0) cc_final: 0.7210 (t70) REVERT: E 132 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6681 (mtm) REVERT: E 196 THR cc_start: 0.7591 (m) cc_final: 0.7278 (t) REVERT: E 223 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7150 (ttp-170) outliers start: 27 outliers final: 14 residues processed: 235 average time/residue: 0.5053 time to fit residues: 123.9405 Evaluate side-chains 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 109 LYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 163 GLN 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 194 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 8 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 17 optimal weight: 0.0020 chunk 7 optimal weight: 0.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.160041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147671 restraints weight = 5649.287| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 0.94 r_work: 0.3875 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5695 Z= 0.144 Angle : 0.591 5.138 7710 Z= 0.314 Chirality : 0.050 0.146 775 Planarity : 0.003 0.035 1015 Dihedral : 5.338 16.989 780 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.59 % Allowed : 24.27 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.06 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 139 TYR 0.022 0.001 TYR A 131 PHE 0.012 0.001 PHE B 201 TRP 0.005 0.001 TRP B 93 HIS 0.007 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5690) covalent geometry : angle 0.58995 ( 7700) SS BOND : bond 0.00280 ( 5) SS BOND : angle 1.00625 ( 10) hydrogen bonds : bond 0.02113 ( 91) hydrogen bonds : angle 6.15677 ( 273) *********************** 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 256 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.212 Fit side-chains REVERT: A 132 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7203 (mmm) REVERT: A 147 ASP cc_start: 0.8643 (t0) cc_final: 0.8419 (t0) REVERT: A 150 ASP cc_start: 0.7516 (t0) cc_final: 0.6945 (t70) REVERT: A 196 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7564 (t) REVERT: A 223 ARG cc_start: 0.8299 (tpt90) cc_final: 0.8022 (tpt90) REVERT: B 98 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8432 (m) REVERT: B 132 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7790 (mmp) REVERT: C 196 THR cc_start: 0.7551 (m) cc_final: 0.7229 (t) REVERT: D 223 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7138 (tpp-160) REVERT: E 132 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6539 (mtm) REVERT: E 154 ARG cc_start: 0.6128 (mmt-90) cc_final: 0.3799 (ttm-80) REVERT: E 196 THR cc_start: 0.7518 (m) cc_final: 0.7186 (t) REVERT: E 223 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7125 (ttp-170) outliers start: 21 outliers final: 8 residues processed: 240 average time/residue: 0.4943 time to fit residues: 124.2113 Evaluate side-chains 240 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 209 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 164 VAL 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 210 GLU Chi-restraints excluded: chain E residue 132 MET 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 13 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 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 = 0.4005 r_free = 0.4005 target = 0.153657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140828 restraints weight = 5820.351| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 0.99 r_work: 0.3780 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5695 Z= 0.286 Angle : 0.694 6.498 7710 Z= 0.377 Chirality : 0.053 0.171 775 Planarity : 0.004 0.030 1015 Dihedral : 5.752 18.661 780 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.30 % Allowed : 23.59 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.16 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 167 TYR 0.023 0.003 TYR A 131 PHE 0.014 0.002 PHE B 201 TRP 0.007 0.002 TRP B 93 HIS 0.011 0.002 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 5690) covalent geometry : angle 0.69120 ( 7700) SS BOND : bond 0.00477 ( 5) SS BOND : angle 1.89489 ( 10) hydrogen bonds : bond 0.02671 ( 91) hydrogen bonds : angle 6.48537 ( 273) *********************** 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 252 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7359 (mmm) REVERT: A 150 ASP cc_start: 0.7631 (t0) cc_final: 0.7038 (t70) REVERT: A 196 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7601 (t) REVERT: A 223 ARG cc_start: 0.8309 (tpt90) cc_final: 0.8006 (tpt90) REVERT: B 98 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8428 (m) REVERT: B 209 MET cc_start: 0.7880 (mmm) cc_final: 0.7657 (tpt) REVERT: C 163 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: C 196 THR cc_start: 0.7521 (m) cc_final: 0.7244 (t) REVERT: D 150 ASP cc_start: 0.7512 (t0) cc_final: 0.7215 (t0) REVERT: D 223 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7131 (tpp-160) REVERT: E 132 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6685 (mtm) REVERT: E 196 THR cc_start: 0.7536 (m) cc_final: 0.7253 (t) REVERT: E 223 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7120 (ttp-170) outliers start: 31 outliers final: 11 residues processed: 233 average time/residue: 0.5400 time to fit residues: 131.1082 Evaluate side-chains 234 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 109 LYS Chi-restraints excluded: chain B residue 164 VAL 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 210 GLU Chi-restraints excluded: chain E residue 106 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4122 r_free = 0.4122 target = 0.161481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.149186 restraints weight = 5633.513| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 0.93 r_work: 0.3908 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5695 Z= 0.131 Angle : 0.603 7.300 7710 Z= 0.318 Chirality : 0.051 0.160 775 Planarity : 0.003 0.027 1015 Dihedral : 5.344 17.088 780 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.59 % Allowed : 25.47 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG C 167 TYR 0.021 0.001 TYR A 131 PHE 0.012 0.001 PHE C 201 TRP 0.005 0.001 TRP A 93 HIS 0.007 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5690) covalent geometry : angle 0.60280 ( 7700) SS BOND : bond 0.00547 ( 5) SS BOND : angle 0.87116 ( 10) hydrogen bonds : bond 0.01909 ( 91) hydrogen bonds : angle 6.03104 ( 273) *********************** 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 259 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.218 Fit side-chains REVERT: A 132 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7208 (mmm) REVERT: A 147 ASP cc_start: 0.8597 (t0) cc_final: 0.8345 (t70) REVERT: A 150 ASP cc_start: 0.7533 (t0) cc_final: 0.7089 (t0) REVERT: A 196 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7585 (t) REVERT: A 223 ARG cc_start: 0.8307 (tpt90) cc_final: 0.8000 (tpt90) REVERT: B 98 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8432 (m) REVERT: C 196 THR cc_start: 0.7591 (m) cc_final: 0.7291 (t) REVERT: D 223 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7233 (ttm170) REVERT: E 132 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6521 (mtm) REVERT: E 154 ARG cc_start: 0.6238 (mmt-90) cc_final: 0.3856 (ttm-80) REVERT: E 196 THR cc_start: 0.7524 (m) cc_final: 0.7214 (t) REVERT: E 223 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7073 (ttp-170) outliers start: 21 outliers final: 8 residues processed: 243 average time/residue: 0.4576 time to fit residues: 116.4699 Evaluate side-chains 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 109 LYS 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 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 51 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.0010 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.158949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.146248 restraints weight = 5615.999| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 0.97 r_work: 0.3863 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5695 Z= 0.176 Angle : 0.646 7.590 7710 Z= 0.339 Chirality : 0.051 0.156 775 Planarity : 0.003 0.038 1015 Dihedral : 5.506 16.708 780 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.08 % Allowed : 27.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.14 (0.24), 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 ARG 0.007 0.001 ARG C 167 TYR 0.018 0.002 TYR A 131 PHE 0.011 0.002 PHE B 201 TRP 0.006 0.001 TRP B 93 HIS 0.009 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 5690) covalent geometry : angle 0.64393 ( 7700) SS BOND : bond 0.00420 ( 5) SS BOND : angle 1.47022 ( 10) hydrogen bonds : bond 0.02112 ( 91) hydrogen bonds : angle 6.04066 ( 273) *********************** 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 251 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 0.218 Fit side-chains REVERT: A 147 ASP cc_start: 0.8662 (t0) cc_final: 0.8445 (t0) REVERT: A 150 ASP cc_start: 0.7543 (t0) cc_final: 0.7066 (t0) REVERT: A 196 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7527 (t) REVERT: B 98 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8337 (m) REVERT: B 209 MET cc_start: 0.7860 (mmm) cc_final: 0.7636 (tpt) REVERT: C 196 THR cc_start: 0.7484 (m) cc_final: 0.7170 (t) REVERT: C 216 MET cc_start: 0.7967 (tpp) cc_final: 0.7760 (ttt) REVERT: D 223 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7108 (tpp-160) REVERT: E 132 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6569 (mtm) REVERT: E 154 ARG cc_start: 0.6172 (mmt-90) cc_final: 0.3798 (ttm-80) REVERT: E 196 THR cc_start: 0.7496 (m) cc_final: 0.7188 (t) REVERT: E 223 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7089 (ttp-170) outliers start: 18 outliers final: 9 residues processed: 237 average time/residue: 0.4816 time to fit residues: 119.3739 Evaluate side-chains 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 109 LYS 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 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 5 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** 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 = 0.4033 r_free = 0.4033 target = 0.154841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.142131 restraints weight = 5751.106| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 0.97 r_work: 0.3804 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5695 Z= 0.260 Angle : 0.718 7.268 7710 Z= 0.382 Chirality : 0.053 0.170 775 Planarity : 0.004 0.030 1015 Dihedral : 5.808 18.504 780 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.08 % Allowed : 27.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.22 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 154 TYR 0.023 0.002 TYR B 131 PHE 0.014 0.002 PHE B 201 TRP 0.007 0.002 TRP B 93 HIS 0.011 0.002 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 5690) covalent geometry : angle 0.71464 ( 7700) SS BOND : bond 0.00403 ( 5) SS BOND : angle 1.92549 ( 10) hydrogen bonds : bond 0.02559 ( 91) hydrogen bonds : angle 6.25689 ( 273) ********************** 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 246 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7608 (t0) cc_final: 0.7028 (t70) REVERT: A 196 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7561 (t) REVERT: A 223 ARG cc_start: 0.8289 (tpt90) cc_final: 0.8037 (tpt90) REVERT: B 98 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8384 (m) REVERT: B 209 MET cc_start: 0.7933 (mmm) cc_final: 0.7724 (tpt) REVERT: C 196 THR cc_start: 0.7481 (m) cc_final: 0.7191 (t) REVERT: C 216 MET cc_start: 0.7960 (tpp) cc_final: 0.7330 (ttt) REVERT: D 150 ASP cc_start: 0.7482 (t0) cc_final: 0.7144 (t70) REVERT: D 223 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7122 (tpp-160) REVERT: E 196 THR cc_start: 0.7513 (m) cc_final: 0.7218 (t) REVERT: E 223 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7063 (ttp-170) outliers start: 18 outliers final: 9 residues processed: 233 average time/residue: 0.5200 time to fit residues: 126.6702 Evaluate side-chains 237 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 109 LYS 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 210 GLU Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** E 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.159028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.146552 restraints weight = 5595.399| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 0.90 r_work: 0.3865 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5695 Z= 0.177 Angle : 0.672 7.429 7710 Z= 0.351 Chirality : 0.052 0.149 775 Planarity : 0.003 0.040 1015 Dihedral : 5.642 17.194 780 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.74 % Allowed : 28.03 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.19 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 167 TYR 0.020 0.002 TYR A 131 PHE 0.012 0.002 PHE B 201 TRP 0.005 0.001 TRP A 93 HIS 0.009 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5690) covalent geometry : angle 0.67079 ( 7700) SS BOND : bond 0.00281 ( 5) SS BOND : angle 1.41347 ( 10) hydrogen bonds : bond 0.02053 ( 91) hydrogen bonds : angle 6.04523 ( 273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2808.15 seconds wall clock time: 48 minutes 54.45 seconds (2934.45 seconds total)