Starting phenix.real_space_refine on Tue Jan 14 04:20:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmy_47020/01_2025/9dmy_47020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmy_47020/01_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_47020/01_2025/9dmy_47020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmy_47020/01_2025/9dmy_47020.map" model { file = "/net/cci-nas-00/data/ceres_data/9dmy_47020/01_2025/9dmy_47020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmy_47020/01_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-5571/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: 4.50, per 1000 atoms: 0.81 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 673.5 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: 0.83 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: 1.56 Time building geometry restraints manager: 1.53 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: 0.05 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 31.830 ------------------------------------------------------------------------------- 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 : 0.551 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: 1.0409 time to fit residues: 310.4897 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 : 0.598 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.151076 restraints weight = 5631.116| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.04 r_work: 0.3840 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- 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 : 0.621 Fit side-chains REVERT: A 150 ASP cc_start: 0.7440 (t0) cc_final: 0.6861 (t0) REVERT: A 196 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7542 (t) REVERT: A 203 GLU cc_start: 0.7529 (tt0) cc_final: 0.7310 (tt0) REVERT: C 196 THR cc_start: 0.7566 (m) cc_final: 0.7292 (t) REVERT: D 98 THR cc_start: 0.8652 (t) cc_final: 0.8387 (m) REVERT: D 216 MET cc_start: 0.7889 (ttm) cc_final: 0.7585 (ttt) REVERT: D 223 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7321 (tpp-160) REVERT: E 139 ARG cc_start: 0.6894 (ttp80) cc_final: 0.6126 (ttp80) REVERT: E 196 THR cc_start: 0.7547 (m) cc_final: 0.7338 (p) outliers start: 26 outliers final: 6 residues processed: 240 average time/residue: 1.0723 time to fit residues: 269.2097 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 : 0.604 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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** B 215 GLN C 176 ASN C 220 GLN D 143 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN E 220 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.158125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144242 restraints weight = 5690.766| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.02 r_work: 0.3771 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5690 Z= 0.367 Angle : 0.657 5.384 7700 Z= 0.360 Chirality : 0.052 0.161 775 Planarity : 0.004 0.032 1015 Dihedral : 5.534 20.132 780 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.10 % Allowed : 23.42 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (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 0.014 0.002 PHE B 201 TYR 0.014 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 254 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.576 Fit side-chains REVERT: A 132 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7678 (mmm) REVERT: A 150 ASP cc_start: 0.7608 (t0) cc_final: 0.6989 (t70) REVERT: A 203 GLU cc_start: 0.7576 (tt0) cc_final: 0.7356 (tt0) REVERT: A 209 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7802 (tpt) REVERT: B 98 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8381 (m) REVERT: C 132 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7739 (mmm) REVERT: C 196 THR cc_start: 0.7650 (m) cc_final: 0.7322 (t) REVERT: C 209 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7790 (tpt) REVERT: C 216 MET cc_start: 0.8124 (tpp) cc_final: 0.7868 (ttt) REVERT: C 223 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8113 (ttm-80) REVERT: D 223 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.7515 (tpm170) REVERT: E 132 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6621 (mtm) REVERT: E 139 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6204 (ttp-170) REVERT: E 154 ARG cc_start: 0.6187 (mmt-90) cc_final: 0.4563 (ttt180) REVERT: E 167 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.6968 (tpm170) REVERT: E 196 THR cc_start: 0.7552 (m) cc_final: 0.7350 (p) REVERT: E 223 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7141 (ttp-170) outliers start: 24 outliers final: 8 residues processed: 232 average time/residue: 1.0799 time to fit residues: 261.6663 Evaluate side-chains 235 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 A residue 209 MET 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 D residue 210 GLU 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: 0.0170 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.158856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145662 restraints weight = 5817.313| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.02 r_work: 0.3836 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5690 Z= 0.248 Angle : 0.597 5.399 7700 Z= 0.320 Chirality : 0.050 0.150 775 Planarity : 0.003 0.018 1015 Dihedral : 5.310 17.523 780 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.93 % Allowed : 22.91 % 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: -4.00 (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 TRP 0.005 0.001 TRP B 93 HIS 0.008 0.001 HIS E 143 PHE 0.012 0.002 PHE B 201 TYR 0.018 0.001 TYR A 131 ARG 0.009 0.001 ARG A 154 *********************** 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: 23 poor density : 233 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7537 (mmm) REVERT: A 150 ASP cc_start: 0.7527 (t0) cc_final: 0.7044 (t0) REVERT: A 196 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7561 (t) REVERT: B 98 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8434 (m) REVERT: B 154 ARG cc_start: 0.7427 (ttt-90) cc_final: 0.7223 (ttt180) REVERT: C 196 THR cc_start: 0.7608 (m) cc_final: 0.7273 (t) REVERT: C 209 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7652 (tpt) REVERT: C 216 MET cc_start: 0.8060 (tpp) cc_final: 0.7836 (ttt) REVERT: D 139 ARG cc_start: 0.6409 (ttm170) cc_final: 0.6199 (mmt-90) REVERT: D 216 MET cc_start: 0.7903 (ttm) cc_final: 0.7679 (ttt) REVERT: D 223 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.7292 (tpp-160) REVERT: E 132 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6379 (mtm) REVERT: E 139 ARG cc_start: 0.7051 (ttp80) cc_final: 0.6190 (ttp-170) REVERT: E 141 LEU cc_start: 0.8997 (tp) cc_final: 0.8793 (tp) REVERT: E 154 ARG cc_start: 0.6113 (mmt-90) cc_final: 0.4372 (ttt-90) REVERT: E 196 THR cc_start: 0.7557 (m) cc_final: 0.7282 (t) REVERT: E 214 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6684 (mt-10) REVERT: E 223 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6965 (ttp80) outliers start: 23 outliers final: 9 residues processed: 239 average time/residue: 1.0573 time to fit residues: 264.5118 Evaluate side-chains 244 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 155 GLU 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 C residue 209 MET Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR 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: 4.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 220 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN E 215 GLN E 220 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.149938 restraints weight = 5708.647| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.01 r_work: 0.3902 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3231 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= 0.201 Angle : 0.585 9.049 7700 Z= 0.309 Chirality : 0.049 0.144 775 Planarity : 0.003 0.033 1015 Dihedral : 5.154 15.761 780 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.76 % Allowed : 23.25 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.006 0.001 HIS E 143 PHE 0.011 0.001 PHE B 201 TYR 0.020 0.001 TYR A 131 ARG 0.007 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7518 (t0) cc_final: 0.7040 (t0) REVERT: A 196 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7568 (t) REVERT: B 98 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8420 (m) REVERT: B 132 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7603 (mmm) REVERT: B 141 LEU cc_start: 0.9083 (tp) cc_final: 0.8725 (tp) REVERT: C 196 THR cc_start: 0.7592 (m) cc_final: 0.7251 (t) REVERT: C 214 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6780 (mt-10) REVERT: D 139 ARG cc_start: 0.6404 (ttm170) cc_final: 0.6200 (mmt-90) REVERT: D 223 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.7253 (tpp-160) REVERT: E 107 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7913 (mtmm) REVERT: E 132 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6473 (mtm) REVERT: E 139 ARG cc_start: 0.6933 (ttp80) cc_final: 0.5983 (ttp-170) REVERT: E 154 ARG cc_start: 0.6037 (mmt-90) cc_final: 0.4328 (ttt-90) REVERT: E 196 THR cc_start: 0.7568 (m) cc_final: 0.7216 (t) REVERT: E 223 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.7025 (ttp-170) outliers start: 22 outliers final: 10 residues processed: 241 average time/residue: 1.0765 time to fit residues: 271.4770 Evaluate side-chains 245 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 0.0870 chunk 11 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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 ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 220 GLN 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 = 0.3994 r_free = 0.3994 target = 0.154114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140902 restraints weight = 5731.137| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 0.98 r_work: 0.3780 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5690 Z= 0.404 Angle : 0.696 9.935 7700 Z= 0.377 Chirality : 0.053 0.169 775 Planarity : 0.004 0.032 1015 Dihedral : 5.685 18.477 780 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 5.81 % Allowed : 22.22 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (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 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 0.003 TYR A 131 ARG 0.005 0.001 ARG A 154 *********************** 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 262 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7516 (mmm) REVERT: A 147 ASP cc_start: 0.8808 (t0) cc_final: 0.8404 (t70) REVERT: A 150 ASP cc_start: 0.7637 (t0) cc_final: 0.7054 (t70) REVERT: A 196 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7561 (t) REVERT: B 98 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8441 (m) REVERT: C 196 THR cc_start: 0.7550 (m) cc_final: 0.7240 (t) REVERT: D 139 ARG cc_start: 0.6550 (ttm170) cc_final: 0.6196 (mmt-90) REVERT: D 150 ASP cc_start: 0.7500 (t0) cc_final: 0.7179 (t70) REVERT: D 223 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.7482 (tpm170) REVERT: E 132 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6570 (mtm) REVERT: E 139 ARG cc_start: 0.7125 (ttp80) cc_final: 0.6213 (ttp-170) REVERT: E 196 THR cc_start: 0.7549 (m) cc_final: 0.7229 (t) REVERT: E 223 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7122 (ttp-170) outliers start: 34 outliers final: 15 residues processed: 236 average time/residue: 1.1257 time to fit residues: 277.2273 Evaluate side-chains 246 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 139 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 155 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 40 optimal weight: 0.0020 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.161556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148472 restraints weight = 5667.394| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.00 r_work: 0.3897 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5690 Z= 0.219 Angle : 0.618 9.428 7700 Z= 0.325 Chirality : 0.050 0.164 775 Planarity : 0.003 0.019 1015 Dihedral : 5.380 17.029 780 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.44 % Allowed : 23.42 % 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 (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 0.005 0.001 TRP A 93 HIS 0.007 0.001 HIS C 143 PHE 0.012 0.001 PHE B 201 TYR 0.021 0.001 TYR A 131 ARG 0.006 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8738 (t0) cc_final: 0.8391 (t70) REVERT: A 150 ASP cc_start: 0.7525 (t0) cc_final: 0.7081 (t0) REVERT: A 196 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7506 (t) REVERT: B 98 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8424 (m) REVERT: B 181 ASP cc_start: 0.7951 (t70) cc_final: 0.7741 (t70) REVERT: C 196 THR cc_start: 0.7560 (m) cc_final: 0.7232 (t) REVERT: D 132 MET cc_start: 0.7807 (mmm) cc_final: 0.7528 (mmp) REVERT: D 139 ARG cc_start: 0.6524 (ttm170) cc_final: 0.6248 (mmt-90) REVERT: D 223 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.7317 (tpp-160) REVERT: E 132 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6531 (mtm) REVERT: E 139 ARG cc_start: 0.6951 (ttp80) cc_final: 0.6163 (ttp-170) REVERT: E 154 ARG cc_start: 0.6126 (mmt-90) cc_final: 0.3760 (ttm-80) REVERT: E 196 THR cc_start: 0.7520 (m) cc_final: 0.7186 (t) REVERT: E 223 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7053 (ttp-170) outliers start: 26 outliers final: 11 residues processed: 245 average time/residue: 1.0937 time to fit residues: 280.2815 Evaluate side-chains 251 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 128 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** C 215 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.154974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141879 restraints weight = 5668.749| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 0.98 r_work: 0.3793 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3655 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= 0.373 Angle : 0.703 9.797 7700 Z= 0.373 Chirality : 0.053 0.167 775 Planarity : 0.003 0.020 1015 Dihedral : 5.709 17.893 780 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.64 % Allowed : 23.93 % 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: -4.23 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 93 HIS 0.011 0.002 HIS E 143 PHE 0.013 0.002 PHE B 201 TYR 0.022 0.002 TYR A 131 ARG 0.006 0.001 ARG C 223 *********************** 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 264 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7576 (mmm) REVERT: A 147 ASP cc_start: 0.8779 (t0) cc_final: 0.8442 (t70) REVERT: A 150 ASP cc_start: 0.7585 (t0) cc_final: 0.7005 (t70) REVERT: A 196 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7574 (t) REVERT: B 98 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8375 (m) REVERT: C 163 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: C 196 THR cc_start: 0.7539 (m) cc_final: 0.7239 (t) REVERT: D 139 ARG cc_start: 0.6562 (ttm170) cc_final: 0.6196 (mmt-90) REVERT: D 150 ASP cc_start: 0.7500 (t0) cc_final: 0.7170 (t70) REVERT: D 223 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.7489 (tpm170) REVERT: E 132 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6554 (mtm) REVERT: E 139 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6241 (ttp-170) REVERT: E 196 THR cc_start: 0.7534 (m) cc_final: 0.7238 (t) REVERT: E 223 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7088 (ttp-170) outliers start: 33 outliers final: 16 residues processed: 240 average time/residue: 1.1105 time to fit residues: 278.3296 Evaluate side-chains 248 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 128 LEU Chi-restraints excluded: chain B residue 139 ARG 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 C residue 209 MET Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 128 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 40 optimal weight: 0.0040 chunk 36 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 162 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.163385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.150384 restraints weight = 5657.167| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 0.98 r_work: 0.3915 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5690 Z= 0.201 Angle : 0.621 9.256 7700 Z= 0.323 Chirality : 0.050 0.153 775 Planarity : 0.002 0.021 1015 Dihedral : 5.374 17.355 780 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.59 % Allowed : 25.81 % Favored : 70.60 % 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: -4.15 (0.24), 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 TRP 0.004 0.001 TRP A 93 HIS 0.007 0.001 HIS A 143 PHE 0.012 0.001 PHE A 201 TYR 0.020 0.001 TYR A 131 ARG 0.008 0.001 ARG C 167 *********************** 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 257 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7445 (mmm) REVERT: A 150 ASP cc_start: 0.7536 (t0) cc_final: 0.7047 (t0) REVERT: A 196 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7553 (t) REVERT: B 98 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8378 (m) REVERT: B 141 LEU cc_start: 0.9071 (tp) cc_final: 0.8820 (tp) REVERT: C 196 THR cc_start: 0.7587 (m) cc_final: 0.7258 (t) REVERT: C 223 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7777 (tpt90) REVERT: D 132 MET cc_start: 0.7813 (mmm) cc_final: 0.7578 (mmp) REVERT: D 139 ARG cc_start: 0.6578 (ttm170) cc_final: 0.6197 (mmt-90) REVERT: D 223 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7309 (tpp-160) REVERT: E 132 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6515 (mtm) REVERT: E 139 ARG cc_start: 0.6913 (ttp80) cc_final: 0.6004 (ttp-170) REVERT: E 154 ARG cc_start: 0.6132 (mmt-90) cc_final: 0.3731 (ttm-80) REVERT: E 196 THR cc_start: 0.7514 (m) cc_final: 0.7195 (t) REVERT: E 223 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7080 (ttp-170) outliers start: 21 outliers final: 12 residues processed: 240 average time/residue: 1.0383 time to fit residues: 260.9288 Evaluate side-chains 250 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 155 GLU 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 139 ARG 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 132 MET 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 33 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 39 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.148804 restraints weight = 5650.520| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.01 r_work: 0.3898 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5690 Z= 0.232 Angle : 0.653 9.111 7700 Z= 0.340 Chirality : 0.051 0.149 775 Planarity : 0.003 0.051 1015 Dihedral : 5.424 16.872 780 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.42 % Allowed : 26.15 % 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: -4.16 (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 0.005 0.001 TRP B 93 HIS 0.008 0.001 HIS E 143 PHE 0.012 0.001 PHE A 201 TYR 0.019 0.002 TYR A 131 ARG 0.006 0.001 ARG C 167 ********************** 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 253 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.606 Fit side-chains REVERT: A 147 ASP cc_start: 0.8729 (t0) cc_final: 0.8326 (t70) REVERT: A 150 ASP cc_start: 0.7533 (t0) cc_final: 0.7068 (t0) REVERT: A 196 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7513 (t) REVERT: B 98 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8312 (m) REVERT: B 209 MET cc_start: 0.7876 (mmm) cc_final: 0.7674 (tpt) REVERT: C 196 THR cc_start: 0.7578 (m) cc_final: 0.7242 (t) REVERT: C 223 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7798 (tpt90) REVERT: D 139 ARG cc_start: 0.6523 (ttm170) cc_final: 0.6239 (mmt-90) REVERT: D 154 ARG cc_start: 0.7356 (tpp80) cc_final: 0.7125 (tpt170) REVERT: D 223 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.7277 (tpp-160) REVERT: E 132 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6539 (mtm) REVERT: E 139 ARG cc_start: 0.6968 (ttp80) cc_final: 0.6026 (ttp-170) REVERT: E 154 ARG cc_start: 0.6146 (mmt-90) cc_final: 0.3766 (ttm-80) REVERT: E 196 THR cc_start: 0.7503 (m) cc_final: 0.7183 (t) REVERT: E 223 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7072 (ttp-170) outliers start: 20 outliers final: 11 residues processed: 238 average time/residue: 1.0449 time to fit residues: 260.3701 Evaluate side-chains 243 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 139 ARG 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 132 MET 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: 0.8980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.162600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.149381 restraints weight = 5664.207| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 0.98 r_work: 0.3904 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3648 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= 0.241 Angle : 0.668 9.118 7700 Z= 0.347 Chirality : 0.051 0.146 775 Planarity : 0.003 0.048 1015 Dihedral : 5.484 18.304 780 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % 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: -4.18 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.008 0.001 HIS E 143 PHE 0.011 0.002 PHE A 201 TYR 0.019 0.002 TYR A 131 ARG 0.007 0.001 ARG C 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5411.51 seconds wall clock time: 96 minutes 3.98 seconds (5763.98 seconds total)