Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_2ogu.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 amber.topology_file_name=4amber_2ogu.prmtop amber.coordinate_file_name=4amber_2ogu.rst7 amber.order_file_name=4amber_2ogu.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_2ogu.order 4amber_2ogu.prmtop 4amber_2ogu.rst7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_2ogu.pdb" } default_model = "4phenix_2ogu.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } amber { use_amber = True topology_file_name = 4amber_2ogu.prmtop coordinate_file_name = 4amber_2ogu.rst7 order_file_name = 4amber_2ogu.order } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 3448 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3448 Classifications: {'peptide': 221} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Time building chain proxies: 0.48, per 1000 atoms: 0.14 Number of scatterers: 3448 At special positions: 0 Unit cell: (165.889, 165.889, 82.223, 90, 90, 120) Space group: R 3 2 :H (No. 155) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 338 8.00 N 305 7.00 C 1069 6.00 H 1729 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 0.59 Conformation dependent library (CDL) restraints added in 71.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 2 sheets defined 39.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 127 through 130 No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 146 through 155 removed outlier: 4.449A pdb=" N LYS A 150 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 152 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.752A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.456A pdb=" N GLU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 324 through 333 Processing sheet with id= A, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.277A pdb=" N VAL A 181 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN A 158 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA A 143 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 160 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 3.557A pdb=" N GLY A 320 " --> pdb=" O VAL A 265 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 135 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: 0.52 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 1726 1.15 - 1.31: 311 1.31 - 1.48: 654 1.48 - 1.65: 767 1.65 - 1.82: 11 Bond restraints: 3469 Sorted by residual: bond pdb=" CD GLU A 325 " pdb=" OE1 GLU A 325 " ideal model delta sigma weight residual 1.249 1.413 -0.164 1.90e-02 2.77e+03 7.49e+01 bond pdb=" N SER A 273 " pdb=" H SER A 273 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ILE A 201 " pdb=" H ILE A 201 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 207 " pdb=" H ILE A 207 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N ASN A 332 " pdb=" H ASN A 332 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3464 not shown) Histogram of bond angle deviations from ideal: 96.85 - 107.61: 528 107.61 - 118.37: 4323 118.37 - 129.13: 1425 129.13 - 139.89: 9 139.89 - 150.65: 1 Bond angle restraints: 6286 Sorted by residual: angle pdb=" CB ARG A 213 " pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " ideal model delta sigma weight residual 111.30 150.65 -39.35 2.30e+00 1.89e-01 2.93e+02 angle pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " pdb=" NE ARG A 213 " ideal model delta sigma weight residual 112.00 134.35 -22.35 2.20e+00 2.07e-01 1.03e+02 angle pdb=" N ASP A 202 " pdb=" CA ASP A 202 " pdb=" C ASP A 202 " ideal model delta sigma weight residual 107.32 118.69 -11.37 1.65e+00 3.67e-01 4.75e+01 angle pdb=" N THR A 127 " pdb=" CA THR A 127 " pdb=" C THR A 127 " ideal model delta sigma weight residual 112.68 104.82 7.86 1.33e+00 5.65e-01 3.50e+01 angle pdb=" C VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta sigma weight residual 110.52 101.59 8.93 1.57e+00 4.06e-01 3.24e+01 ... (remaining 6281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1350 17.94 - 35.89: 146 35.89 - 53.83: 71 53.83 - 71.77: 29 71.77 - 89.72: 2 Dihedral angle restraints: 1598 sinusoidal: 909 harmonic: 689 Sorted by residual: dihedral pdb=" C THR A 261 " pdb=" N THR A 261 " pdb=" CA THR A 261 " pdb=" CB THR A 261 " ideal model delta harmonic sigma weight residual -122.00 -133.67 11.67 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C VAL A 265 " pdb=" N VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta harmonic sigma weight residual -122.00 -111.17 -10.83 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual 122.80 132.91 -10.11 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 1595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 197 0.092 - 0.183: 58 0.183 - 0.275: 13 0.275 - 0.366: 2 0.366 - 0.458: 1 Chirality restraints: 271 Sorted by residual: chirality pdb=" CA ASP A 287 " pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CB ASP A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" CA THR A 261 " pdb=" N THR A 261 " pdb=" C THR A 261 " pdb=" CB THR A 261 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 268 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " 0.012 2.00e-02 2.50e+03 1.08e-02 3.52e+00 pdb=" CG PHE A 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 232 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 232 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 232 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 232 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 232 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 333 " -0.019 2.00e-02 2.50e+03 1.07e-02 3.44e+00 pdb=" CG TYR A 333 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 333 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 333 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 333 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 333 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 333 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 333 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 333 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR A 333 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 333 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 TYR A 333 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 247 " -0.002 2.00e-02 2.50e+03 7.99e-03 1.92e+00 pdb=" CG TYR A 247 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 247 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 247 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 247 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 247 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 247 " -0.001 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.76: 77 1.76 - 2.47: 2367 2.47 - 3.18: 10917 3.18 - 3.89: 15057 3.89 - 4.60: 23031 Nonbonded interactions: 51449 Sorted by model distance: nonbonded pdb="HH21 ARG A 298 " pdb=" HH TYR A 310 " model vdw 1.055 2.100 nonbonded pdb="HH11 ARG A 262 " pdb=" HB ILE A 304 " model vdw sym.op. 1.119 2.270 -x+2,-x+y+1,-z+1 nonbonded pdb=" H ARG A 262 " pdb=" HZ3 LYS A 323 " model vdw 1.121 2.100 nonbonded pdb="HG23 THR A 261 " pdb=" HZ2 LYS A 323 " model vdw 1.123 2.270 nonbonded pdb=" HB3 SER A 126 " pdb=" HD1 PHE A 232 " model vdw sym.op. 1.225 2.270 -x+2,-x+y+1,-z+1 ... (remaining 51444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_2ogu.prmtop atom order : 4amber_2ogu.order coordinates : 4amber_2ogu.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 7 15.96 2 O 338 7.97 1 N 305 6.97 1 C 1069 5.97 2 H 1729 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== Setting occupancies to: 1.000: selected atoms: 1729 of 3448 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3448 n_use_u_iso = 3448 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3448 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3448 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3448 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 127 through 130 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 132 through 134 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 146 through 155 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 167 through 172 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 188 through 201 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 214 through 222 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 231 through 243 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 247 through 255 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 280 through 283 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 285 through 289 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 324 through 333 } sheet { first_strand = chain 'A' and resid 207 through 209 sheet_id = " A" strand { selection = chain 'A' and resid 180 through 183 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 181 and name N bond_start_previous = chain 'A' and resid 208 and name O } strand { selection = chain 'A' and resid 118 through 121 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 119 and name N bond_start_previous = chain 'A' and resid 180 and name O } strand { selection = chain 'A' and resid 139 through 143 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 140 and name N bond_start_previous = chain 'A' and resid 118 and name O } strand { selection = chain 'A' and resid 158 through 161 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 158 and name N bond_start_previous = chain 'A' and resid 141 and name O } } sheet { first_strand = chain 'A' and resid 263 through 268 sheet_id = " B" strand { selection = chain 'A' and resid 317 through 322 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 322 and name N bond_start_previous = chain 'A' and resid 263 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_2ogu.prmtop" coordinate_file_name = "4amber_2ogu.rst7" order_file_name = "4amber_2ogu.order" } } output { prefix = "4phenix_2ogu_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.23 - 28.61 A, n_refl.=6717 (all), 4.75 % free)-------------| | | | r_work= 0.4624 r_free= 0.5095 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.058430 | | target function (ml) not normalized (work): 38761.835701 | | target function (ml) not normalized (free): 1913.420206 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 28.61 - 4.07 0.94 3212 159 0.4154 0.4594 6.5978 6.5067| | 2: 4.07 - 3.23 0.96 3186 160 0.6035 0.6524 5.5147 5.4929| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 28.61 - 4.07 3212 159 0.43 57.03 0.98 0.24 84030.82| | 2: 4.07 - 3.23 3186 160 0.53 49.98 1.93 0.59 9849.17| |alpha: min = 0.24 max = 0.59 mean = 0.42| |beta: min = 9849.17 max = 84030.82 mean = 47090.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.48| |phase err.(work): min = 0.00 max = 89.92 mean = 53.52| |phase err.(test): min = 2.36 max = 89.71 mean = 55.65| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.164 1740 Z= 0.880 Angle : 1.793 39.348 2349 Z= 1.075 Chirality : 0.093 0.458 271 Planarity : 0.004 0.014 311 Dihedral : 20.776 89.715 667 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 25.63 Ramachandran Plot: Outliers : 3.20 % Allowed : 14.61 % Favored : 82.19 % Rotamer: Outliers : 20.63 % Allowed : 14.81 % Favored : 64.55 % Cbeta Deviations : 1.48 % 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: -5.26 (0.44), residues: 219 helix: -4.53 (0.27), residues: 89 sheet: -0.37 (0.86), residues: 42 loop : -3.82 (0.47), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 329 TYR 0.014 0.004 TYR A 247 PHE 0.020 0.003 PHE A 232 TRP 0.005 0.002 TRP A 123 HIS 0.003 0.001 HIS A 193 Individual atomic B min max mean iso aniso Overall: 91.32 163.00 123.43 0.77 1719 0 Protein: 91.32 163.00 123.43 0.77 1719 0 Chain A: 91.32 163.00 123.43 N/A 1719 0 Histogram: Values Number of atoms 91.32 - 98.49 108 98.49 - 105.66 221 105.66 - 112.82 174 112.82 - 119.99 133 119.99 - 127.16 184 127.16 - 134.33 354 134.33 - 141.50 450 141.50 - 148.66 70 148.66 - 155.83 17 155.83 - 163.00 8 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1 = 5 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6717 (all), 4.75 % free)-------------| | | | r_work= 0.4624 r_free= 0.5095 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.058430 | | target function (ml) not normalized (work): 38761.835701 | | target function (ml) not normalized (free): 1913.420206 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4647 0.4624 0.5095 n_refl.: 6717 re-set all scales: r(all,work,free)=0.4647 0.4624 0.5095 n_refl.: 6717 remove outliers: r(all,work,free)=0.4639 0.4617 0.5095 n_refl.: 6712 overall B=-12.17 to atoms: r(all,work,free)=0.4398 0.4378 0.4749 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2970 0.2963 0.3138 n_refl.: 6712 remove outliers: r(all,work,free)=0.2970 0.2963 0.3138 n_refl.: 6712 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 28.612-12.706 81.97 93 7 0.2696 2116.819 2052.613 1.318 0.964 0.337 12.682-10.260 91.59 95 3 0.1548 2500.298 2448.158 1.255 0.968 0.328 10.240-8.268 91.43 185 7 0.1273 2215.595 2169.867 1.203 0.969 0.291 8.239-6.652 93.16 358 10 0.2208 1353.919 1318.349 1.175 0.975 0.296 6.641-5.360 94.83 677 38 0.3037 820.148 773.707 0.955 0.983 0.240 5.359-4.320 95.50 1280 57 0.2895 759.055 709.855 0.878 0.992 0.160 4.319-3.481 96.04 2452 119 0.3934 427.847 388.170 0.990 1.009 0.052 3.480-3.231 96.10 1253 78 0.4475 240.901 203.262 1.028 1.019 0.026 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9878 b_overall=2.4180 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.014945 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.162423 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3281 0.3352 0.0072 0.014 2.2 0.9 0.9 15.3 3 0.125 0.3125 0.3294 0.0169 0.014 2.2 1.7 0.9 16.9 2 0.250 0.2947 0.3338 0.0391 0.015 2.4 3.8 1.4 14.3 3 0.500 0.2801 0.3341 0.0541 0.018 2.8 6.1 0.9 15.9 4 1.000 0.2655 0.3174 0.0519 0.023 3.3 14.3 0.9 19.0 10 2.000 0.2584 0.3139 0.0555 0.029 3.9 18.9 2.7 19.6 15 3.000 0.2756 0.3083 0.0327 0.027 2.7 20.7 3.2 22.8 2 4.000 0.2607 0.3059 0.0452 0.035 3.7 21.0 3.2 21.7 7 5.000 0.2753 0.3074 0.0321 0.027 2.5 22.1 3.2 22.8 1 6.000 0.2749 0.3069 0.0320 0.028 2.6 22.7 3.2 22.8 1 7.000 0.2797 0.3099 0.0302 0.025 2.3 24.2 2.7 22.2 0 8.000 0.2791 0.3099 0.0308 0.027 2.3 24.5 2.7 22.2 0 9.000 0.2861 0.3132 0.0271 0.022 2.0 25.1 2.7 21.2 0 10.000 0.2733 0.3334 0.0601 0.021 3.0 9.9 1.8 19.6 8 1.507 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2607 0.3059 0.0452 0.035 3.7 21.0 3.2 21.7 7 5.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.07 30.59 4.52 0.548 111.215 0.162 0.061 26.05 30.71 4.66 1.728 111.267 0.005 0.061 25.67 30.44 4.77 1.837 111.283 0.020 0.059 25.00 30.03 5.03 2.890 111.390 0.081 0.057 24.13 29.82 5.69 6.289 112.124 0.162 0.053 23.91 29.77 5.86 7.480 112.422 0.244 0.052 23.77 29.76 5.99 8.341 112.644 0.325 0.052 23.67 29.75 6.08 8.981 112.812 0.406 0.051 23.61 29.72 6.11 9.478 112.947 0.487 0.051 23.46 29.74 6.27 10.434 113.275 0.568 0.050 23.42 29.74 6.33 10.814 113.378 0.650 0.050 23.42 29.75 6.33 10.915 113.383 0.731 0.050 23.17 29.83 6.66 12.967 114.106 0.812 0.049 max suggested for this run: 22.24 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.325 Accepted refinement result: 23.77 29.76 5.99 8.341 112.644 0.325 0.052 Individual atomic B min max mean iso aniso Overall: 75.23 161.57 114.13 7.52 1719 0 Protein: 75.23 161.57 114.13 7.52 1719 0 Chain A: 75.23 161.57 114.13 N/A 1719 0 Histogram: Values Number of atoms 75.23 - 83.87 49 83.87 - 92.50 116 92.50 - 101.13 209 101.13 - 109.77 238 109.77 - 118.40 389 118.40 - 127.03 388 127.03 - 135.67 207 135.67 - 144.30 86 144.30 - 152.93 26 152.93 - 161.57 11 =========================== Idealize ADP of riding H ========================== r_work=0.2377 r_free=0.2976 r_work=0.2369 r_free=0.2964 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6712 (all), 4.75 % free)-------------| | | | r_work= 0.2369 r_free= 0.2964 coordinate error (max.-lik. estimate): 0.36 A | | | | normalized target function (ls_wunit_k1) (work): 0.051420 | | target function (ls_wunit_k1) not normalized (work): 328.728858 | | target function (ls_wunit_k1) not normalized (free): 31.260510 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2395 0.2369 0.2964 n_refl.: 6712 re-set all scales: r(all,work,free)=0.4214 0.4186 0.4750 n_refl.: 6712 remove outliers: r(all,work,free)=0.4214 0.4186 0.4750 n_refl.: 6712 overall B=1.06 to atoms: r(all,work,free)=0.4237 0.4209 0.4778 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2398 0.2369 0.2996 n_refl.: 6712 remove outliers: r(all,work,free)=0.2397 0.2369 0.2996 n_refl.: 6711 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 28.612-12.706 81.97 93 7 0.2329 1242.680 1232.820 1.284 0.981 0.332 12.682-10.260 91.59 95 3 0.1201 1467.801 1441.149 1.230 0.983 0.326 10.240-8.268 91.00 185 7 0.0900 1300.666 1290.755 1.160 0.983 0.283 8.239-6.652 93.64 358 10 0.1500 794.819 790.817 1.117 0.984 0.276 6.641-5.360 94.83 677 38 0.2287 481.468 471.643 0.942 0.988 0.228 5.359-4.320 95.50 1280 57 0.2247 445.604 430.179 0.875 0.990 0.138 4.319-3.481 96.08 2452 119 0.3275 251.168 236.354 1.026 0.995 0.033 3.480-3.231 96.03 1252 78 0.4109 141.241 121.473 1.089 0.995 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-0.3114 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.988799 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.028874 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3033 0.3398 0.0365 0.014 2.2 0.6 1.8 15.3 2 0.049 0.2710 0.3406 0.0695 0.016 2.4 5.0 2.3 16.9 2 0.148 0.2525 0.3111 0.0586 0.019 2.8 9.0 1.4 21.2 4 0.297 0.2493 0.3426 0.0933 0.023 3.4 19.8 4.6 21.7 6 0.445 0.2431 0.3151 0.0720 0.026 3.8 20.4 5.9 22.2 11 0.593 0.2401 0.3159 0.0758 0.030 4.2 26.5 6.8 22.2 19 0.742 0.2371 0.2981 0.0611 0.033 3.6 19.5 3.2 22.2 6 0.890 0.2367 0.2993 0.0626 0.034 3.7 21.3 3.2 21.7 7 1.038 0.2471 0.3408 0.0937 0.024 3.5 21.8 4.6 22.8 7 0.494 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2371 0.2981 0.0611 0.033 3.6 19.5 3.2 22.2 6 0.890 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.71 29.81 6.11 17.158 126.795 0.029 6.119 26.50 32.10 5.60 12.697 131.585 0.001 6.164 26.04 31.53 5.49 13.627 131.180 0.004 6.141 25.05 30.29 5.24 16.449 129.858 0.014 6.099 24.04 29.80 5.76 16.702 128.838 0.029 6.077 23.85 29.74 5.89 17.258 129.146 0.043 6.067 23.76 29.76 6.00 17.835 129.485 0.058 6.061 23.75 29.81 6.06 18.530 129.924 0.072 6.057 23.53 29.75 6.23 18.437 129.655 0.087 6.055 23.52 29.81 6.29 18.881 129.880 0.101 6.053 23.38 29.75 6.37 18.494 129.369 0.115 6.055 23.36 29.76 6.40 18.639 129.410 0.130 6.054 23.34 29.77 6.42 18.705 129.390 0.144 6.054 max suggested for this run: 25.36 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.043 Accepted refinement result: 23.85 29.74 5.89 17.258 129.146 0.043 6.067 Individual atomic B min max mean iso aniso Overall: 72.64 180.36 119.91 11.70 1719 0 Protein: 72.64 180.36 119.91 11.70 1719 0 Chain A: 72.64 180.36 119.91 N/A 1719 0 Histogram: Values Number of atoms 72.64 - 83.41 22 83.41 - 94.18 76 94.18 - 104.96 226 104.96 - 115.73 413 115.73 - 126.50 430 126.50 - 137.27 279 137.27 - 148.04 165 148.04 - 158.82 70 158.82 - 169.59 32 169.59 - 180.36 6 =========================== Idealize ADP of riding H ========================== r_work=0.2385 r_free=0.2974 r_work=0.2397 r_free=0.2972 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6711 (all), 4.75 % free)-------------| | | | r_work= 0.2397 r_free= 0.2972 coordinate error (max.-lik. estimate): 0.24 A | | | | normalized target function (ml) (work): 6.065954 | | target function (ml) not normalized (work): 38773.578264 | | target function (ml) not normalized (free): 1979.165233 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2422 0.2397 0.2972 n_refl.: 6711 re-set all scales: r(all,work,free)=0.4305 0.4275 0.4888 n_refl.: 6711 remove outliers: r(all,work,free)=0.4305 0.4275 0.4888 n_refl.: 6711 overall B=-17.75 to atoms: r(all,work,free)=0.3913 0.3888 0.4397 n_refl.: 6711 bulk-solvent and scaling: r(all,work,free)=0.2372 0.2348 0.2900 n_refl.: 6711 remove outliers: r(all,work,free)=0.2372 0.2348 0.2900 n_refl.: 6711 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 28.612-12.706 81.97 93 7 0.2385 1242.680 1222.463 1.418 0.975 0.329 12.682-10.260 91.59 95 3 0.1199 1467.801 1435.233 1.338 0.977 0.321 10.240-8.268 91.00 185 7 0.0983 1300.666 1281.267 1.231 0.976 0.280 8.239-6.652 93.64 358 10 0.1601 794.819 785.308 1.172 0.979 0.283 6.641-5.360 94.83 677 38 0.2389 481.468 464.249 0.981 0.984 0.239 5.359-4.320 95.50 1280 57 0.2457 445.604 425.428 0.863 0.987 0.134 4.319-3.481 96.08 2452 119 0.2954 251.168 237.851 0.964 0.995 0.034 3.480-3.231 96.03 1252 78 0.3764 141.241 123.172 1.003 0.998 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=6.4931 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.040025 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.033348 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2868 0.3328 0.0460 0.014 2.2 1.5 0.9 15.3 2 0.052 0.2602 0.3308 0.0706 0.016 2.5 4.7 2.7 16.4 1 0.156 0.2452 0.3233 0.0781 0.019 2.9 10.2 4.6 19.0 3 0.312 0.2396 0.3255 0.0859 0.023 3.4 16.0 5.5 20.6 7 0.468 0.2365 0.3282 0.0917 0.026 3.7 22.7 7.8 23.8 11 0.624 0.2346 0.2981 0.0635 0.029 3.8 18.9 3.2 21.2 11 0.780 0.2332 0.2880 0.0548 0.032 3.6 21.8 3.7 21.7 6 0.936 0.2345 0.2895 0.0550 0.033 3.6 20.1 3.2 22.2 6 1.092 0.2364 0.3110 0.0746 0.024 3.5 18.9 3.7 20.6 9 0.520 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2332 0.2880 0.0548 0.032 3.6 21.8 3.7 21.7 6 0.936 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.32 28.80 5.48 19.073 114.456 0.033 6.057 27.43 32.38 4.95 12.353 123.272 0.001 6.144 25.76 30.64 4.88 13.665 120.072 0.004 6.116 24.51 30.12 5.61 15.735 118.497 0.017 6.089 23.48 29.58 6.10 16.391 117.306 0.033 6.061 22.99 29.48 6.49 16.847 117.896 0.050 6.045 22.63 29.18 6.55 17.575 117.261 0.067 6.031 22.52 29.12 6.60 18.312 117.063 0.083 6.026 22.45 29.16 6.71 18.931 117.309 0.100 6.022 22.40 29.21 6.81 19.579 117.676 0.117 6.020 22.38 29.05 6.68 19.518 117.060 0.133 6.019 22.36 29.07 6.72 19.851 117.198 0.150 6.018 22.34 29.07 6.73 20.154 117.326 0.167 6.017 max suggested for this run: 22.89 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.017 Accepted refinement result: 24.51 30.12 5.61 15.735 118.497 0.017 6.089 Individual atomic B min max mean iso aniso Overall: 70.40 183.32 110.26 6.35 1719 0 Protein: 70.40 183.32 110.26 6.35 1719 0 Chain A: 70.40 183.32 110.26 N/A 1719 0 Histogram: Values Number of atoms 70.40 - 81.69 40 81.69 - 92.98 243 92.98 - 104.28 411 104.28 - 115.57 399 115.57 - 126.86 360 126.86 - 138.15 172 138.15 - 149.44 48 149.44 - 160.73 27 160.73 - 172.03 16 172.03 - 183.32 3 =========================== Idealize ADP of riding H ========================== r_work=0.2451 r_free=0.3012 r_work=0.2464 r_free=0.3007 ----------X-ray data---------- |--(resolution: 3.23 - 28.61 A, n_refl.=6711 (all), 4.75 % free)-------------| | | | r_work= 0.2464 r_free= 0.3007 coordinate error (max.-lik. estimate): 0.22 A | | | | normalized target function (ml) (work): 6.093034 | | target function (ml) not normalized (work): 38946.676096 | | target function (ml) not normalized (free): 1977.944639 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 28.61 - 4.07 0.94 3209 159 0.2150 0.2679 6.4741 6.6009| | 2: 4.07 - 3.23 0.96 3183 160 0.3407 0.3942 5.7089 5.8025| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 28.61 - 4.07 3209 159 0.73 31.90 1.00 0.83 83649.41| | 2: 4.07 - 3.23 3183 160 0.63 41.11 1.05 0.91 18252.77| |alpha: min = 0.83 max = 0.91 mean = 0.87| |beta: min = 18252.77 max = 83649.41 mean = 51084.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.79 mean = 36.48| |phase err.(test): min = 0.00 max = 88.88 mean = 39.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2488 0.2464 0.3007 n_refl.: 6711 re-set all scales: r(all,work,free)=0.4073 0.4045 0.4635 n_refl.: 6711 remove outliers: r(all,work,free)=0.4073 0.4045 0.4635 n_refl.: 6711 overall B=0.95 to atoms: r(all,work,free)=0.4094 0.4065 0.4661 n_refl.: 6711 bulk-solvent and scaling: r(all,work,free)=0.2450 0.2428 0.2919 n_refl.: 6711 remove outliers: r(all,work,free)=0.2449 0.2427 0.2919 n_refl.: 6710 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 28.612-12.706 81.97 93 7 0.2327 1242.680 1221.056 1.330 0.980 0.327 12.682-10.260 91.59 95 3 0.1220 1467.801 1443.907 1.227 0.980 0.309 10.240-8.268 91.00 185 7 0.0933 1300.666 1285.371 1.161 0.979 0.279 8.239-6.652 93.64 358 10 0.1673 794.819 782.823 1.107 0.980 0.259 6.641-5.360 94.83 677 38 0.2483 481.468 466.358 0.957 0.981 0.218 5.359-4.320 95.50 1280 57 0.2503 445.604 423.813 0.886 0.979 0.129 4.319-3.481 96.04 2451 119 0.3145 251.013 234.709 1.021 0.979 0.029 3.480-3.231 96.03 1252 78 0.3854 141.241 122.117 1.108 0.975 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.2922 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4624 0.5095 0.013 1.793 91.3 163.0 123.4 0 0.000 1_bss: 0.2963 0.3138 0.013 1.793 79.2 150.8 111.3 0 0.000 1_settarget: 0.2963 0.3138 0.013 1.793 79.2 150.8 111.3 0 0.000 1_weight: 0.2963 0.3138 0.013 1.793 79.2 150.8 111.3 0 0.000 1_xyzrec: 0.2607 0.3059 0.035 3.668 79.2 150.8 111.3 0 0.128 1_adp: 0.2377 0.2976 0.035 3.668 75.2 161.6 114.1 0 0.128 1_regHadp: 0.2369 0.2964 0.035 3.668 75.2 161.6 114.1 0 0.128 2_bss: 0.2369 0.2996 0.035 3.668 76.3 162.6 115.2 0 0.128 2_settarget: 0.2369 0.2996 0.035 3.668 76.3 162.6 115.2 0 0.128 2_updatecdl: 0.2369 0.2996 0.035 3.672 76.3 162.6 115.2 0 0.128 2_weight: 0.2369 0.2996 0.035 3.672 76.3 162.6 115.2 0 0.128 2_xyzrec: 0.2371 0.2981 0.033 3.586 76.3 162.6 115.2 0 0.131 2_adp: 0.2385 0.2974 0.033 3.586 72.6 180.4 119.9 0 0.131 2_regHadp: 0.2397 0.2972 0.033 3.586 72.6 180.4 119.9 0 0.131 3_bss: 0.2348 0.2900 0.033 3.586 54.9 162.6 102.2 0 0.131 3_settarget: 0.2348 0.2900 0.033 3.586 54.9 162.6 102.2 0 0.131 3_updatecdl: 0.2348 0.2900 0.033 3.586 54.9 162.6 102.2 0 0.131 3_setrh: 0.2348 0.2900 0.033 3.586 54.9 162.6 102.2 0 0.131 3_weight: 0.2348 0.2900 0.033 3.586 54.9 162.6 102.2 0 0.131 3_xyzrec: 0.2332 0.2880 0.032 3.609 54.9 162.6 102.2 0 0.137 3_adp: 0.2451 0.3012 0.032 3.609 70.4 183.3 110.3 0 0.137 3_regHadp: 0.2464 0.3007 0.032 3.609 70.4 183.3 110.3 0 0.137 end: 0.2427 0.2919 0.032 3.609 71.4 184.3 111.2 0 0.137 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2ogu_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2ogu_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.5700 Refinement macro-cycles (run) : 241.8400 Write final files (write_after_run_outputs) : 8.2500 Total : 252.6600 Total CPU time: 4.84 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:42:53 PDT -0700 (1723221773.56 s) Start R-work = 0.2963, R-free = 0.3138 Final R-work = 0.2427, R-free = 0.2919 =============================================================================== Job complete usr+sys time: 297.85 seconds wall clock time: 11 minutes 23.87 seconds (683.87 seconds total)