Starting phenix.real_space_refine on Thu Nov 14 09:51:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmy_47020/11_2024/9dmy_47020.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmy_47020/11_2024/9dmy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmy_47020/11_2024/9dmy_47020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmy_47020/11_2024/9dmy_47020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmy_47020/11_2024/9dmy_47020.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dmy_47020/11_2024/9dmy_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-5513/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: 4.94, per 1000 atoms: 0.89 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: 1.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.78 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: 1.49 Time building geometry restraints manager: 1.55 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: 0.00 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: 2.940 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.130 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- 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 : 0.497 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: 1.0746 time to fit residues: 320.1667 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 : 0.655 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.654 Fit side-chains REVERT: A 150 ASP cc_start: 0.7384 (t0) cc_final: 0.6804 (t0) REVERT: A 203 GLU cc_start: 0.7304 (tt0) cc_final: 0.7097 (tt0) REVERT: B 147 ASP cc_start: 0.8669 (t0) cc_final: 0.8465 (t70) REVERT: C 157 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7566 (tmt) REVERT: C 196 THR cc_start: 0.7630 (m) cc_final: 0.7382 (t) REVERT: D 216 MET cc_start: 0.8048 (ttm) cc_final: 0.7841 (ttt) REVERT: D 223 ARG cc_start: 0.8291 (ttm-80) cc_final: 0.7171 (tpp-160) REVERT: E 139 ARG cc_start: 0.6844 (ttp80) cc_final: 0.6084 (ttp80) outliers start: 26 outliers final: 6 residues processed: 240 average time/residue: 1.1041 time to fit residues: 276.9404 Evaluate side-chains 232 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 157 MET 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 32 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** B 215 GLN C 176 ASN D 143 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2942 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= 0.301 Angle : 0.609 5.219 7700 Z= 0.330 Chirality : 0.050 0.151 775 Planarity : 0.003 0.043 1015 Dihedral : 5.256 18.048 780 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.25 % Allowed : 23.93 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (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 TRP 0.006 0.002 TRP B 93 HIS 0.009 0.002 HIS E 143 PHE 0.013 0.002 PHE B 201 TYR 0.012 0.002 TYR E 131 ARG 0.005 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.627 Fit side-chains REVERT: A 150 ASP cc_start: 0.7496 (t0) cc_final: 0.7001 (t0) REVERT: C 196 THR cc_start: 0.7749 (m) cc_final: 0.7402 (t) REVERT: C 209 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7620 (tpt) REVERT: C 216 MET cc_start: 0.8269 (tpp) cc_final: 0.8044 (ttt) REVERT: C 223 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7948 (ttm-80) REVERT: D 216 MET cc_start: 0.8124 (ttm) cc_final: 0.7820 (ttt) REVERT: D 223 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7224 (tpp-160) REVERT: E 107 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7969 (mtmm) REVERT: E 132 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6683 (mtm) REVERT: E 139 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6149 (ttp-170) REVERT: E 154 ARG cc_start: 0.5824 (mmt-90) cc_final: 0.4472 (ttm-80) REVERT: E 167 ARG cc_start: 0.8076 (ttt-90) cc_final: 0.6864 (tpm170) REVERT: E 223 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7002 (ttp-170) outliers start: 19 outliers final: 7 residues processed: 231 average time/residue: 1.1176 time to fit residues: 269.7325 Evaluate side-chains 231 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 223 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- 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 220 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 215 GLN E 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5690 Z= 0.493 Angle : 0.725 5.813 7700 Z= 0.400 Chirality : 0.055 0.173 775 Planarity : 0.005 0.037 1015 Dihedral : 5.850 21.187 780 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.13 % Allowed : 22.05 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (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 TRP 0.008 0.002 TRP B 93 HIS 0.012 0.002 HIS E 143 PHE 0.013 0.002 PHE B 201 TYR 0.021 0.003 TYR A 131 ARG 0.004 0.001 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7617 (t0) cc_final: 0.7005 (t70) REVERT: A 155 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: A 209 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7948 (tpt) REVERT: A 223 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7842 (tpt90) REVERT: C 132 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7705 (mmm) REVERT: C 154 ARG cc_start: 0.7327 (ttt180) cc_final: 0.7049 (ttt-90) REVERT: D 139 ARG cc_start: 0.6405 (ttm170) cc_final: 0.6034 (mmt-90) REVERT: D 150 ASP cc_start: 0.7532 (t0) cc_final: 0.7221 (t0) REVERT: D 223 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.7369 (tpm170) REVERT: E 132 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6559 (mtm) REVERT: E 223 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6839 (ttp80) outliers start: 30 outliers final: 14 residues processed: 233 average time/residue: 1.1302 time to fit residues: 274.7457 Evaluate side-chains 236 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 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 52 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN A 222 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3368 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= 0.259 Angle : 0.615 9.437 7700 Z= 0.329 Chirality : 0.050 0.151 775 Planarity : 0.003 0.025 1015 Dihedral : 5.470 18.300 780 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.59 % Allowed : 24.96 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (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 0.013 0.002 PHE B 201 TYR 0.021 0.002 TYR A 131 ARG 0.005 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7709 (mmm) REVERT: A 150 ASP cc_start: 0.7523 (t0) cc_final: 0.6956 (t70) REVERT: A 223 ARG cc_start: 0.8204 (tpt90) cc_final: 0.7850 (tpt90) REVERT: B 132 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.8021 (mmm) REVERT: C 154 ARG cc_start: 0.7256 (ttt180) cc_final: 0.7005 (ttt-90) REVERT: C 223 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7966 (ttm-80) REVERT: D 139 ARG cc_start: 0.6417 (ttm170) cc_final: 0.6092 (mmt-90) REVERT: D 196 THR cc_start: 0.7447 (m) cc_final: 0.7172 (t) REVERT: E 132 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6525 (mtm) REVERT: E 214 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6567 (mt-10) REVERT: E 223 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6962 (ttp-170) outliers start: 21 outliers final: 7 residues processed: 241 average time/residue: 1.1237 time to fit residues: 282.6900 Evaluate side-chains 240 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 202 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 D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 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 56 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 5690 Z= 0.503 Angle : 0.742 10.587 7700 Z= 0.405 Chirality : 0.055 0.175 775 Planarity : 0.004 0.036 1015 Dihedral : 5.968 20.247 780 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.96 % Allowed : 24.27 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (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 TRP 0.008 0.002 TRP A 93 HIS 0.013 0.002 HIS E 143 PHE 0.012 0.002 PHE B 201 TYR 0.025 0.003 TYR A 131 ARG 0.005 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7758 (mmm) REVERT: A 150 ASP cc_start: 0.7638 (t0) cc_final: 0.7024 (t70) REVERT: A 172 TYR cc_start: 0.6947 (m-80) cc_final: 0.6630 (m-80) REVERT: A 223 ARG cc_start: 0.8193 (tpt90) cc_final: 0.7826 (tpt90) REVERT: B 132 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8089 (mmm) REVERT: B 214 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6654 (mt-10) REVERT: C 163 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: D 139 ARG cc_start: 0.6421 (ttm170) cc_final: 0.6013 (mmt-90) REVERT: D 150 ASP cc_start: 0.7518 (t0) cc_final: 0.7220 (t0) REVERT: D 196 THR cc_start: 0.7596 (m) cc_final: 0.7343 (t) REVERT: D 223 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.7173 (tpp-160) REVERT: E 132 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6654 (mtm) REVERT: E 223 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6943 (ttp-170) outliers start: 29 outliers final: 12 residues processed: 235 average time/residue: 1.2014 time to fit residues: 294.2051 Evaluate side-chains 235 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 187 VAL 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 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3567 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 : 0.628 9.675 7700 Z= 0.331 Chirality : 0.051 0.166 775 Planarity : 0.003 0.017 1015 Dihedral : 5.546 17.487 780 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.59 % Allowed : 26.84 % Favored : 69.57 % 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 0.005 0.001 TRP B 93 HIS 0.008 0.001 HIS A 143 PHE 0.013 0.002 PHE B 201 TYR 0.023 0.001 TYR A 131 ARG 0.006 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7535 (t0) cc_final: 0.7040 (t0) REVERT: A 206 ILE cc_start: 0.8628 (mt) cc_final: 0.8423 (mt) REVERT: A 223 ARG cc_start: 0.8200 (tpt90) cc_final: 0.7830 (tpt90) REVERT: C 154 ARG cc_start: 0.7244 (ttt180) cc_final: 0.6969 (ttt-90) REVERT: D 139 ARG cc_start: 0.6533 (ttm170) cc_final: 0.6161 (mmt-90) REVERT: D 223 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7915 (ttm-80) REVERT: E 132 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6587 (mtm) REVERT: E 196 THR cc_start: 0.7910 (p) cc_final: 0.7552 (t) REVERT: E 223 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6917 (ttp-170) outliers start: 21 outliers final: 9 residues processed: 237 average time/residue: 1.1442 time to fit residues: 283.1453 Evaluate side-chains 236 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 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 12 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 215 GLN C 226 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 5690 Z= 0.520 Angle : 0.775 10.508 7700 Z= 0.419 Chirality : 0.056 0.187 775 Planarity : 0.004 0.043 1015 Dihedral : 6.062 19.621 780 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.30 % Allowed : 24.27 % 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: -4.30 (0.23), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 93 HIS 0.012 0.002 HIS E 143 PHE 0.013 0.002 PHE A 201 TYR 0.025 0.003 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 250 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: A 150 ASP cc_start: 0.7643 (t0) cc_final: 0.7020 (t70) REVERT: A 172 TYR cc_start: 0.6975 (m-80) cc_final: 0.6696 (m-80) REVERT: A 223 ARG cc_start: 0.8217 (tpt90) cc_final: 0.7825 (tpt90) REVERT: B 214 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6739 (mt-10) REVERT: C 139 ARG cc_start: 0.7670 (ttm170) cc_final: 0.7177 (ttp80) REVERT: C 163 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: D 139 ARG cc_start: 0.6509 (tpm170) cc_final: 0.6064 (mmt-90) REVERT: D 150 ASP cc_start: 0.7498 (t0) cc_final: 0.7174 (t70) REVERT: D 223 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7053 (tpp-160) REVERT: E 214 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6702 (mt-10) REVERT: E 223 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6897 (ttp-170) outliers start: 31 outliers final: 14 residues processed: 234 average time/residue: 1.3020 time to fit residues: 316.6101 Evaluate side-chains 232 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 MET 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 C residue 106 SER Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 106 SER 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 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 25 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5690 Z= 0.228 Angle : 0.638 9.486 7700 Z= 0.334 Chirality : 0.051 0.149 775 Planarity : 0.003 0.020 1015 Dihedral : 5.584 18.116 780 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.05 % Allowed : 27.01 % 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 (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: -4.22 (0.24), 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 0.005 0.001 TRP A 93 HIS 0.009 0.002 HIS A 143 PHE 0.013 0.002 PHE A 201 TYR 0.022 0.001 TYR A 131 ARG 0.007 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 236 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7538 (t0) cc_final: 0.7045 (t0) REVERT: A 209 MET cc_start: 0.8021 (mmt) cc_final: 0.7799 (tpt) REVERT: A 223 ARG cc_start: 0.8214 (tpt90) cc_final: 0.7837 (tpt90) REVERT: B 181 ASP cc_start: 0.7838 (t70) cc_final: 0.7578 (t70) REVERT: C 154 ARG cc_start: 0.7207 (ttt180) cc_final: 0.6955 (ttt-90) REVERT: C 157 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7568 (tmt) REVERT: D 139 ARG cc_start: 0.6458 (tpm170) cc_final: 0.6178 (mmt-90) REVERT: D 223 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7205 (tpm170) REVERT: E 132 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6905 (mtm) REVERT: E 196 THR cc_start: 0.7843 (p) cc_final: 0.7492 (t) REVERT: E 223 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6915 (ttp-170) outliers start: 12 outliers final: 7 residues processed: 230 average time/residue: 1.1308 time to fit residues: 271.5871 Evaluate side-chains 227 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 157 MET 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 64 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5690 Z= 0.261 Angle : 0.659 9.695 7700 Z= 0.345 Chirality : 0.051 0.156 775 Planarity : 0.003 0.021 1015 Dihedral : 5.613 17.240 780 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.39 % Allowed : 27.52 % Favored : 70.09 % 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: -4.24 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.008 0.001 HIS E 143 PHE 0.013 0.002 PHE A 201 TYR 0.021 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 242 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7543 (t0) cc_final: 0.7050 (t0) REVERT: A 223 ARG cc_start: 0.8223 (tpt90) cc_final: 0.7838 (tpt90) REVERT: B 141 LEU cc_start: 0.9099 (tp) cc_final: 0.8789 (tp) REVERT: B 181 ASP cc_start: 0.7814 (t70) cc_final: 0.7562 (t70) REVERT: B 209 MET cc_start: 0.8060 (mmm) cc_final: 0.7850 (tpt) REVERT: C 157 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7569 (tmt) REVERT: D 139 ARG cc_start: 0.6466 (tpm170) cc_final: 0.6148 (mmt-90) REVERT: D 223 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7247 (tpm170) REVERT: E 132 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6901 (mtm) REVERT: E 196 THR cc_start: 0.7809 (p) cc_final: 0.7450 (t) REVERT: E 223 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6911 (ttp-170) outliers start: 14 outliers final: 7 residues processed: 234 average time/residue: 1.1549 time to fit residues: 281.7800 Evaluate side-chains 229 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 157 MET 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 14 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 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 = 0.4010 r_free = 0.4010 target = 0.154406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141594 restraints weight = 5670.519| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 0.97 r_work: 0.3791 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3787 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= 0.383 Angle : 0.729 9.412 7700 Z= 0.389 Chirality : 0.053 0.167 775 Planarity : 0.004 0.030 1015 Dihedral : 5.908 18.472 780 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.08 % Allowed : 27.18 % Favored : 69.74 % 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: -4.26 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (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 0.024 0.002 TYR A 131 ARG 0.006 0.001 ARG C 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.64 seconds wall clock time: 75 minutes 19.28 seconds (4519.28 seconds total)