Starting phenix.real_space_refine on Mon Sep 23 14:02:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvc_14174/09_2024/7qvc_14174.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvc_14174/09_2024/7qvc_14174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvc_14174/09_2024/7qvc_14174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvc_14174/09_2024/7qvc_14174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvc_14174/09_2024/7qvc_14174.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvc_14174/09_2024/7qvc_14174.cif" } resolution = 2.64 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= 0.000 sd= 0.001 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 21 5.16 5 C 2079 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3255 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 2.78, per 1000 atoms: 0.85 Number of scatterers: 3255 At special positions: 0 Unit cell: (101.78, 91.602, 31.988, 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 21 16.00 O 636 8.00 N 519 7.00 C 2079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 388.1 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 60.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126 removed outlier: 6.736A pdb=" N ASP A 122 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 122 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.823A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 137 through 139 removed outlier: 6.647A pdb=" N GLN A 138 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL B 137 " --> pdb=" O GLN C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 153 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AA8, first strand: chain 'A' and resid 163 through 176 removed outlier: 6.867A pdb=" N ASN A 164 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 165 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 166 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN B 164 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 165 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR B 166 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 187 removed outlier: 6.447A pdb=" N ILE A 184 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 186 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 184 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE C 187 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 192 through 193 removed outlier: 6.590A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET B 192 " --> pdb=" O LYS C 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.419A pdb=" N TYR A 197 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR B 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AB5, first strand: chain 'A' and resid 209 through 213 Processing sheet with id=AB6, first strand: chain 'A' and resid 216 through 219 Processing sheet with id=AB7, first strand: chain 'A' and resid 222 through 228 removed outlier: 5.995A pdb=" N ASN A 223 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 225 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N MET B 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET A 227 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 231 through 253 removed outlier: 5.753A pdb=" N THR A 231 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR B 234 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A 233 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR B 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR A 235 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLY B 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE A 237 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER B 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS A 239 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLN B 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU A 241 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N SER B 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 243 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLU B 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN A 245 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR B 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG A 247 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR B 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLN A 249 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP B 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL A 251 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N THR B 231 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR C 234 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR B 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY C 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE B 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER C 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS B 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLN C 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU B 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER C 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLU C 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN B 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR C 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG B 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N TYR C 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 80 hydrogen bonds defined for protein. 240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 904 1.33 - 1.45: 541 1.45 - 1.57: 1828 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 3309 Sorted by residual: bond pdb=" CZ ARG C 247 " pdb=" NH2 ARG C 247 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.65e+00 bond pdb=" CZ ARG B 247 " pdb=" NH2 ARG B 247 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.31e+00 bond pdb=" CZ ARG B 180 " pdb=" NH2 ARG B 180 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.87e+00 bond pdb=" CZ ARG B 140 " pdb=" NH2 ARG B 140 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.23e+00 bond pdb=" CZ ARG C 247 " pdb=" NH1 ARG C 247 " ideal model delta sigma weight residual 1.323 1.285 0.038 1.40e-02 5.10e+03 7.21e+00 ... (remaining 3304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 3458 2.31 - 4.62: 858 4.62 - 6.93: 162 6.93 - 9.24: 17 9.24 - 11.55: 2 Bond angle restraints: 4497 Sorted by residual: angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" C GLU C 246 " ideal model delta sigma weight residual 108.55 120.10 -11.55 1.62e+00 3.81e-01 5.08e+01 angle pdb=" CB ASN A 183 " pdb=" CG ASN A 183 " pdb=" ND2 ASN A 183 " ideal model delta sigma weight residual 116.40 106.12 10.28 1.50e+00 4.44e-01 4.70e+01 angle pdb=" CA ASP B 136 " pdb=" CB ASP B 136 " pdb=" CG ASP B 136 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.48e+01 angle pdb=" CA ASP A 136 " pdb=" CB ASP A 136 " pdb=" CG ASP A 136 " ideal model delta sigma weight residual 112.60 118.07 -5.47 1.00e+00 1.00e+00 2.99e+01 angle pdb=" CA ASN A 183 " pdb=" CB ASN A 183 " pdb=" CG ASN A 183 " ideal model delta sigma weight residual 112.60 117.92 -5.32 1.00e+00 1.00e+00 2.83e+01 ... (remaining 4492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1816 17.73 - 35.46: 131 35.46 - 53.19: 27 53.19 - 70.92: 7 70.92 - 88.65: 14 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" CA ILE C 152 " pdb=" C ILE C 152 " pdb=" N THR C 153 " pdb=" CA THR C 153 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N THR B 153 " pdb=" CA THR B 153 " ideal model delta harmonic sigma weight residual 180.00 151.42 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" C GLN C 138 " pdb=" N GLN C 138 " pdb=" CA GLN C 138 " pdb=" CB GLN C 138 " ideal model delta harmonic sigma weight residual -122.60 -136.80 14.20 0 2.50e+00 1.60e-01 3.23e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 353 0.108 - 0.216: 152 0.216 - 0.324: 24 0.324 - 0.432: 6 0.432 - 0.540: 5 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA GLN C 138 " pdb=" N GLN C 138 " pdb=" C GLN C 138 " pdb=" CB GLN C 138 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" CA GLN B 194 " pdb=" N GLN B 194 " pdb=" C GLN B 194 " pdb=" CB GLN B 194 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CA THR B 166 " pdb=" N THR B 166 " pdb=" C THR B 166 " pdb=" CB THR B 166 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 537 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.137 2.00e-02 2.50e+03 7.13e-02 1.02e+02 pdb=" CG TYR A 143 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 250 " -0.096 2.00e-02 2.50e+03 5.62e-02 6.32e+01 pdb=" CG TYR A 250 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 250 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR A 250 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR A 250 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 250 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 250 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 250 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 250 " -0.084 2.00e-02 2.50e+03 5.28e-02 5.57e+01 pdb=" CG TYR B 250 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR B 250 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR B 250 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR B 250 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR B 250 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR B 250 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 250 " -0.092 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1633 3.00 - 3.47: 2841 3.47 - 3.95: 5424 3.95 - 4.42: 5665 4.42 - 4.90: 10525 Nonbonded interactions: 26088 Sorted by model distance: nonbonded pdb=" OG SER B 134 " pdb=" OD1 ASP B 136 " model vdw 2.525 3.040 nonbonded pdb=" OE2 GLU B 241 " pdb=" OG SER C 120 " model vdw 2.529 3.040 nonbonded pdb=" OE2 GLU A 241 " pdb=" OG SER B 120 " model vdw 2.542 3.040 nonbonded pdb=" OG SER C 134 " pdb=" OD1 ASP C 136 " model vdw 2.565 3.040 nonbonded pdb=" OE2 GLU A 205 " pdb=" OG SER A 208 " model vdw 2.566 3.040 ... (remaining 26083 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' } 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.010 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.012 0.047 3309 Z= 0.788 Angle : 2.095 11.548 4497 Z= 1.353 Chirality : 0.122 0.540 540 Planarity : 0.013 0.095 558 Dihedral : 15.485 88.647 1206 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.53 % Allowed : 4.50 % Favored : 94.97 % Cbeta Deviations : 2.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS B 239 PHE 0.032 0.010 PHE A 171 TYR 0.137 0.025 TYR A 143 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8619 (mttp) cc_final: 0.7767 (mmpt) REVERT: A 190 LEU cc_start: 0.9097 (mp) cc_final: 0.8874 (mm) REVERT: B 234 THR cc_start: 0.8258 (t) cc_final: 0.8021 (m) outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 1.0146 time to fit residues: 136.9243 Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 151 ASN A 182 ASN A 242 GLN B 145 ASN B 182 ASN B 194 GLN C 138 GLN C 145 ASN C 182 ASN C 249 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3309 Z= 0.274 Angle : 0.780 8.743 4497 Z= 0.420 Chirality : 0.059 0.160 540 Planarity : 0.003 0.028 558 Dihedral : 7.513 31.432 449 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.29 % Allowed : 13.76 % Favored : 80.95 % 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: -2.12 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.013 0.003 PHE B 213 TYR 0.024 0.002 TYR C 143 ARG 0.002 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.409 Fit side-chains REVERT: A 124 LYS cc_start: 0.8646 (mttp) cc_final: 0.7905 (mmtt) REVERT: B 140 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7381 (mtt90) REVERT: B 180 ARG cc_start: 0.7659 (mtm-85) cc_final: 0.7344 (mtp85) REVERT: C 140 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7368 (mtt90) outliers start: 20 outliers final: 10 residues processed: 106 average time/residue: 1.2019 time to fit residues: 130.5845 Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 170 GLN B 239 HIS C 170 GLN C 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 3309 Z= 0.426 Angle : 0.780 9.547 4497 Z= 0.423 Chirality : 0.060 0.166 540 Planarity : 0.003 0.017 558 Dihedral : 7.475 26.653 447 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.03 % Allowed : 15.87 % Favored : 79.10 % 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: -2.22 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 239 PHE 0.014 0.003 PHE B 237 TYR 0.025 0.002 TYR C 143 ARG 0.007 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.361 Fit side-chains REVERT: A 124 LYS cc_start: 0.8684 (mttp) cc_final: 0.7873 (mmtt) REVERT: A 140 ARG cc_start: 0.7349 (ttm170) cc_final: 0.6626 (ppt170) REVERT: A 194 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: B 140 ARG cc_start: 0.8140 (mtm180) cc_final: 0.7312 (mtt90) REVERT: B 180 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7388 (mtp85) REVERT: C 140 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7454 (mtt90) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 1.2064 time to fit residues: 131.2389 Evaluate side-chains 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.0470 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 164 ASN B 194 GLN C 145 ASN C 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3309 Z= 0.266 Angle : 0.668 6.858 4497 Z= 0.363 Chirality : 0.057 0.153 540 Planarity : 0.002 0.017 558 Dihedral : 7.048 26.364 447 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.61 % Allowed : 16.40 % Favored : 76.98 % 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: -2.23 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 239 PHE 0.011 0.002 PHE B 237 TYR 0.021 0.002 TYR B 143 ARG 0.003 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.405 Fit side-chains REVERT: A 124 LYS cc_start: 0.8674 (mttp) cc_final: 0.7871 (mmtt) REVERT: B 140 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7418 (mtt90) REVERT: B 180 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7336 (mtp85) REVERT: B 253 CYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6813 (m) REVERT: C 140 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7474 (mtt90) outliers start: 25 outliers final: 11 residues processed: 107 average time/residue: 1.1978 time to fit residues: 131.5980 Evaluate side-chains 102 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 194 GLN C 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3309 Z= 0.267 Angle : 0.657 7.062 4497 Z= 0.358 Chirality : 0.057 0.154 540 Planarity : 0.002 0.017 558 Dihedral : 6.853 25.312 447 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.35 % Allowed : 18.52 % Favored : 75.13 % 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: -2.26 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 239 PHE 0.011 0.002 PHE B 237 TYR 0.020 0.002 TYR B 143 ARG 0.003 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.384 Fit side-chains REVERT: A 124 LYS cc_start: 0.8660 (mttp) cc_final: 0.7875 (mmtt) REVERT: B 140 ARG cc_start: 0.8145 (mtm180) cc_final: 0.7345 (mtt90) REVERT: B 180 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7307 (mtp85) REVERT: B 253 CYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6801 (m) REVERT: C 140 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7472 (mtt90) outliers start: 24 outliers final: 12 residues processed: 106 average time/residue: 1.0468 time to fit residues: 114.2006 Evaluate side-chains 105 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 208 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 249 GLN B 194 GLN C 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3309 Z= 0.307 Angle : 0.686 10.553 4497 Z= 0.368 Chirality : 0.057 0.143 540 Planarity : 0.003 0.018 558 Dihedral : 6.880 25.981 447 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.35 % Allowed : 20.11 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 239 PHE 0.011 0.003 PHE B 171 TYR 0.020 0.002 TYR A 143 ARG 0.002 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 0.392 Fit side-chains REVERT: A 124 LYS cc_start: 0.8670 (mttp) cc_final: 0.7843 (mmtt) REVERT: B 140 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7363 (mtt90) REVERT: B 144 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8619 (tt) REVERT: B 180 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7350 (mtp85) REVERT: B 253 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6741 (m) outliers start: 24 outliers final: 15 residues processed: 105 average time/residue: 1.1005 time to fit residues: 118.7266 Evaluate side-chains 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 0.0040 chunk 37 optimal weight: 0.4980 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 overall best weight: 2.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 249 GLN B 194 GLN C 194 GLN C 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3309 Z= 0.214 Angle : 0.632 5.752 4497 Z= 0.344 Chirality : 0.055 0.145 540 Planarity : 0.002 0.016 558 Dihedral : 6.701 25.822 447 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.03 % Allowed : 21.69 % Favored : 73.28 % 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: -2.22 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 239 PHE 0.010 0.002 PHE B 171 TYR 0.018 0.002 TYR B 143 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.349 Fit side-chains REVERT: A 124 LYS cc_start: 0.8631 (mttp) cc_final: 0.7858 (mmtt) REVERT: B 140 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7376 (mtt90) REVERT: B 144 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8593 (tt) REVERT: B 180 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7295 (mtp85) REVERT: B 253 CYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6682 (m) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 1.0751 time to fit residues: 121.5550 Evaluate side-chains 107 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 0.0060 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN C 194 GLN C 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3309 Z= 0.345 Angle : 0.709 10.804 4497 Z= 0.377 Chirality : 0.057 0.158 540 Planarity : 0.003 0.017 558 Dihedral : 6.886 26.174 447 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.56 % Allowed : 22.49 % Favored : 71.96 % 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: -2.27 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 239 PHE 0.013 0.003 PHE B 213 TYR 0.021 0.002 TYR A 143 ARG 0.002 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.401 Fit side-chains REVERT: A 124 LYS cc_start: 0.8671 (mttp) cc_final: 0.7878 (mmtt) REVERT: B 140 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7412 (mtt90) REVERT: B 144 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 180 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7354 (mtp85) REVERT: B 253 CYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6754 (m) outliers start: 21 outliers final: 13 residues processed: 104 average time/residue: 1.1869 time to fit residues: 126.6040 Evaluate side-chains 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.0020 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 194 GLN C 194 GLN C 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3309 Z= 0.257 Angle : 0.668 9.368 4497 Z= 0.358 Chirality : 0.056 0.152 540 Planarity : 0.002 0.017 558 Dihedral : 6.774 26.045 447 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.56 % Allowed : 22.22 % Favored : 72.22 % 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: -2.26 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 239 PHE 0.013 0.003 PHE B 213 TYR 0.018 0.002 TYR B 143 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.353 Fit side-chains REVERT: A 124 LYS cc_start: 0.8654 (mttp) cc_final: 0.7877 (mmtt) REVERT: B 140 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7390 (mtt90) REVERT: B 144 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8599 (tt) REVERT: B 180 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7297 (mtp85) REVERT: B 253 CYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6677 (m) REVERT: C 208 SER cc_start: 0.8964 (p) cc_final: 0.8593 (m) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 1.1584 time to fit residues: 125.9867 Evaluate side-chains 107 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 0.0000 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 194 GLN C 194 GLN C 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3309 Z= 0.286 Angle : 0.703 11.112 4497 Z= 0.369 Chirality : 0.056 0.144 540 Planarity : 0.002 0.016 558 Dihedral : 6.819 26.440 447 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.29 % Allowed : 24.34 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 239 PHE 0.014 0.003 PHE B 213 TYR 0.019 0.002 TYR C 143 ARG 0.002 0.000 ARG C 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.416 Fit side-chains REVERT: A 124 LYS cc_start: 0.8674 (mttp) cc_final: 0.7851 (mmtt) REVERT: B 140 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7403 (mtt90) REVERT: B 144 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8593 (tt) REVERT: B 180 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7291 (mtp85) REVERT: B 253 CYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6704 (m) REVERT: C 208 SER cc_start: 0.8975 (p) cc_final: 0.8605 (m) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 1.1688 time to fit residues: 124.7381 Evaluate side-chains 107 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 0.0370 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 overall best weight: 6.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN B 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.131598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.115401 restraints weight = 3724.203| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.68 r_work: 0.3759 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 3309 Z= 0.507 Angle : 0.784 10.565 4497 Z= 0.424 Chirality : 0.060 0.194 540 Planarity : 0.003 0.017 558 Dihedral : 7.168 26.787 447 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.29 % Allowed : 23.81 % Favored : 70.90 % 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: -2.39 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 239 PHE 0.022 0.004 PHE B 213 TYR 0.025 0.003 TYR A 143 ARG 0.003 0.001 ARG B 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.69 seconds wall clock time: 41 minutes 24.96 seconds (2484.96 seconds total)