Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1xgo.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.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_1xgo.prmtop amber.coordinate_file_name=4amber_1xgo.rst7 amber.order_file_name=4amber_1xgo.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_1xgo.rst7 4amber_1xgo.order 4amber_1xgo.prmtop Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_1xgo.pdb" } default_model = "4phenix_1xgo.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.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_1xgo.prmtop coordinate_file_name = 4amber_1xgo.rst7 order_file_name = 4amber_1xgo.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: 4719 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4719 Classifications: {'peptide': 295} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 280} Time building chain proxies: 0.57, per 1000 atoms: 0.12 Number of scatterers: 4719 At special positions: 0 Unit cell: (138.916, 138.916, 63.907, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 423 8.00 N 390 7.00 C 1490 6.00 H 2407 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: 0.96 Conformation dependent library (CDL) restraints added in 97.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 4 sheets defined 32.5% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 removed outlier: 3.528A pdb=" N LYS A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.848A pdb=" N LEU A 44 " --> pdb=" O MET A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.536A pdb=" N PHE A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 No H-bonds generated for 'chain 'A' and resid 237 through 240' Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.702A pdb=" N LEU A 251 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 78 through 84 Processing sheet with id= B, first strand: chain 'A' and resid 183 through 190 Processing sheet with id= C, first strand: chain 'A' and resid 197 through 200 Processing sheet with id= D, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.941A pdb=" N ILE A 205 " --> pdb=" O TYR A 265 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 225 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: 0.81 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2407 1.16 - 1.34: 725 1.34 - 1.52: 904 1.52 - 1.70: 706 1.70 - 1.88: 18 Bond restraints: 4760 Sorted by residual: bond pdb=" NH1 ARG A 123 " pdb="HH11 ARG A 123 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 7 " pdb=" H MET A 7 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG A 215 " pdb="HH11 ARG A 215 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND1 HIS A 281 " pdb=" HD1 HIS A 281 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N GLY A 76 " pdb=" H GLY A 76 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 4755 not shown) Histogram of bond angle deviations from ideal: 95.63 - 103.31: 128 103.31 - 110.98: 4961 110.98 - 118.66: 1711 118.66 - 126.34: 1854 126.34 - 134.02: 35 Bond angle restraints: 8689 Sorted by residual: angle pdb=" N GLY A 68 " pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 114.48 102.68 11.80 1.19e+00 7.06e-01 9.84e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 111.03 100.14 10.89 1.11e+00 8.12e-01 9.62e+01 angle pdb=" N TYR A 237 " pdb=" CA TYR A 237 " pdb=" C TYR A 237 " ideal model delta sigma weight residual 111.36 101.53 9.83 1.09e+00 8.42e-01 8.13e+01 angle pdb=" N THR A 64 " pdb=" CA THR A 64 " pdb=" C THR A 64 " ideal model delta sigma weight residual 110.14 96.77 13.37 1.51e+00 4.39e-01 7.84e+01 angle pdb=" N ASP A 182 " pdb=" CA ASP A 182 " pdb=" C ASP A 182 " ideal model delta sigma weight residual 110.23 97.58 12.65 1.45e+00 4.76e-01 7.61e+01 ... (remaining 8684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1849 17.47 - 34.93: 214 34.93 - 52.40: 81 52.40 - 69.86: 41 69.86 - 87.33: 13 Dihedral angle restraints: 2198 sinusoidal: 1234 harmonic: 964 Sorted by residual: dihedral pdb=" C HIS A 86 " pdb=" N HIS A 86 " pdb=" CA HIS A 86 " pdb=" CB HIS A 86 " ideal model delta harmonic sigma weight residual -122.60 -109.89 -12.71 0 2.50e+00 1.60e-01 2.58e+01 dihedral pdb=" C LEU A 150 " pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " ideal model delta harmonic sigma weight residual -122.60 -133.16 10.56 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C LEU A 131 " pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " ideal model delta harmonic sigma weight residual -122.60 -112.34 -10.26 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 2195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 200 0.107 - 0.215: 103 0.215 - 0.322: 47 0.322 - 0.429: 11 0.429 - 0.536: 4 Chirality restraints: 365 Sorted by residual: chirality pdb=" CA ASN A 53 " pdb=" N ASN A 53 " pdb=" C ASN A 53 " pdb=" CB ASN A 53 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA LEU A 150 " pdb=" N LEU A 150 " pdb=" C LEU A 150 " pdb=" CB LEU A 150 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA VAL A 212 " pdb=" N VAL A 212 " pdb=" C VAL A 212 " pdb=" CB VAL A 212 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 362 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 78 " 0.157 2.00e-02 2.50e+03 6.46e-02 1.25e+02 pdb=" CG TYR A 78 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 78 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 78 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 78 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 78 " 0.125 2.00e-02 2.50e+03 pdb=" HD1 TYR A 78 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 78 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 TYR A 78 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 78 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 265 " -0.144 2.00e-02 2.50e+03 5.64e-02 9.54e+01 pdb=" CG TYR A 265 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 265 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 265 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 265 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 265 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 265 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 265 " -0.095 2.00e-02 2.50e+03 pdb=" HD1 TYR A 265 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR A 265 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TYR A 265 " 0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 265 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 170 " 0.131 2.00e-02 2.50e+03 5.19e-02 8.08e+01 pdb=" CG TYR A 170 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 170 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 170 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 170 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 170 " 0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR A 170 " -0.045 2.00e-02 2.50e+03 pdb=" HD2 TYR A 170 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR A 170 " -0.016 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.57: 68 1.57 - 2.33: 1796 2.33 - 3.08: 15914 3.08 - 3.84: 22466 3.84 - 4.60: 35578 Warning: very small nonbonded interaction distances. Nonbonded interactions: 75822 Sorted by model distance: nonbonded pdb=" HG1 THR A 191 " pdb=" H ILE A 192 " model vdw 0.811 2.100 nonbonded pdb=" HG1 THR A 70 " pdb=" H THR A 71 " model vdw 1.036 2.100 nonbonded pdb=" HE2 PHE A 221 " pdb=" HB3 LYS A 258 " model vdw sym.op. 1.102 2.270 -y+1,x-y,z-1/3 nonbonded pdb=" HA VAL A 285 " pdb="HG12 VAL A 290 " model vdw 1.137 2.440 nonbonded pdb=" HG3 GLU A 138 " pdb=" HZ1 LYS A 141 " model vdw 1.146 2.270 ... (remaining 75817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1xgo.prmtop atom order : 4amber_1xgo.order coordinates : 4amber_1xgo.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 9 15.91 1 O 423 7.97 1 N 390 6.97 1 C 1490 5.97 1 H 2407 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: 2407 of 4719 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4719 n_use_u_iso = 4719 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 = 4719 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4719 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4719 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 3 through 21 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 30 through 44 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 106 through 121 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 128 through 141 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 217 through 230 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 237 through 240 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 246 through 259 helix_type = alpha pi *3_10 unknown } sheet { first_strand = chain 'A' and resid 78 through 84 sheet_id = " A" strand { selection = chain 'A' and resid 93 through 99 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 98 and name N bond_start_previous = chain 'A' and resid 79 and name O } } sheet { first_strand = chain 'A' and resid 183 through 190 sheet_id = " B" strand { selection = chain 'A' and resid 277 through 285 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 283 and name N bond_start_previous = chain 'A' and resid 184 and name O } strand { selection = chain 'A' and resid 290 through 292 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 291 and name N bond_start_previous = chain 'A' and resid 284 and name O } } sheet { first_strand = chain 'A' and resid 197 through 200 sheet_id = " C" strand { selection = chain 'A' and resid 267 through 270 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 269 and name N bond_start_previous = chain 'A' and resid 198 and name O } } sheet { first_strand = chain 'A' and resid 205 through 208 sheet_id = " D" strand { selection = chain 'A' and resid 262 through 265 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 265 and name N bond_start_previous = chain 'A' and resid 205 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_1xgo.prmtop" coordinate_file_name = "4amber_1xgo.rst7" order_file_name = "4amber_1xgo.order" } } output { prefix = "4phenix_1xgo_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: 3.51 - 47.03 A, n_refl.=7571 (all), 9.89 % free)-------------| | | | r_work= 0.3042 r_free= 0.2976 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 2.775301 | | target function (ml) not normalized (work): 18933.104078 | | target function (ml) not normalized (free): 2088.578630 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.03 - 6.00 0.97 1619 177 0.3305 0.3089 3.3925 3.388| | 2: 6.00 - 4.77 0.93 1498 166 0.2493 0.2542 2.7717 2.7747| | 3: 4.77 - 4.16 0.89 1443 156 0.2702 0.2739 2.602 2.6709| | 4: 4.16 - 3.78 0.76 1216 130 0.3199 0.3106 2.4611 2.5704| | 5: 3.78 - 3.51 0.66 1046 120 0.3550 0.3591 2.4295 2.3124| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 47.03 - 6.00 1619 177 0.62 42.02 0.85 0.01 129.79| | 2: 6.00 - 4.77 1498 166 0.55 48.28 1.19 0.01 106.55| | 3: 4.77 - 4.16 1443 156 0.78 30.69 1.26 0.02 57.85| | 4: 4.16 - 3.78 1216 130 0.86 22.39 1.34 0.02 31.88| | 5: 3.78 - 3.51 1046 120 0.93 16.36 1.42 0.02 18.48| |alpha: min = 0.01 max = 0.02 mean = 0.02| |beta: min = 18.48 max = 129.79 mean = 74.95| |figures of merit: min = 0.00 max = 1.00 mean = 0.73| |phase err.(work): min = 0.00 max = 89.67 mean = 33.57| |phase err.(test): min = 0.00 max = 85.68 mean = 33.49| |-----------------------------------------------------------------------------| ----------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 : 0.016 0.079 2353 Z= 1.034 Angle : 2.306 13.371 3178 Z= 1.460 Chirality : 0.158 0.536 365 Planarity : 0.016 0.129 405 Dihedral : 20.740 87.330 901 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 83.28 Ramachandran Plot: Outliers : 8.19 % Allowed : 22.18 % Favored : 69.62 % Rotamer: Outliers : 27.16 % Allowed : 18.52 % Favored : 54.32 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 7.14 % 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: -6.45 (0.33), residues: 293 helix: -4.64 (0.26), residues: 96 sheet: -3.34 (0.65), residues: 50 loop : -4.43 (0.36), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG A 25 TYR 0.131 0.025 TYR A 78 PHE 0.083 0.011 PHE A 221 TRP 0.019 0.007 TRP A 239 HIS 0.006 0.001 HIS A 281 Individual atomic B min max mean iso aniso Overall: 2.00 107.66 31.50 4.99 2312 0 Protein: 2.00 107.66 31.50 4.99 2312 0 Chain A: 2.00 107.66 31.50 N/A 2312 0 Histogram: Values Number of atoms 2.00 - 12.57 417 12.57 - 23.13 473 23.13 - 33.70 490 33.70 - 44.26 393 44.26 - 54.83 220 54.83 - 65.40 164 65.40 - 75.96 98 75.96 - 86.53 29 86.53 - 97.09 20 97.09 - 107.66 8 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7571 (all), 9.89 % free)-------------| | | | r_work= 0.3042 r_free= 0.2976 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 2.775301 | | target function (ml) not normalized (work): 18933.104078 | | target function (ml) not normalized (free): 2088.578630 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3035 0.3042 0.2976 n_refl.: 7571 re-set all scales: r(all,work,free)=0.3035 0.3042 0.2976 n_refl.: 7571 remove outliers: r(all,work,free)=0.3035 0.3041 0.2976 n_refl.: 7570 overall B=3.43 to atoms: r(all,work,free)=0.3157 0.3164 0.3097 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1931 0.1923 0.1997 n_refl.: 7570 remove outliers: r(all,work,free)=0.1931 0.1923 0.1997 n_refl.: 7570 ======================== 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 47.029-15.950 98.06 89 12 0.2996 1414.272 1333.028 1.446 0.997 0.359 15.935-12.710 100.00 89 10 0.1558 1568.936 1549.834 1.367 0.997 0.261 12.669-10.064 98.05 182 19 0.1367 1430.146 1406.210 1.262 0.998 0.232 10.054-8.008 99.48 344 37 0.1288 1203.373 1189.449 1.190 0.998 0.221 7.993-6.350 95.81 662 70 0.1846 763.248 742.162 1.119 0.998 0.216 6.344-5.045 94.08 1288 142 0.2017 645.546 615.863 0.983 0.997 0.146 5.041-4.007 88.08 2360 262 0.1881 666.904 633.570 0.962 0.995 0.057 4.004-3.512 68.80 1807 197 0.2240 609.281 569.116 1.061 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.0008 ============================ 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 = 3.957559 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.538891 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1833 0.2581 0.0748 0.020 3.1 17.4 6.5 27.2 4 1.979 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.33 25.81 7.48 3.509 34.906 0.539 0.043 19.11 26.45 7.34 4.385 35.497 0.016 0.046 18.93 26.44 7.51 4.347 35.525 0.067 0.045 18.37 26.45 8.08 4.591 35.650 0.269 0.042 17.89 26.44 8.55 5.486 35.875 0.539 0.040 17.58 26.45 8.86 6.411 36.073 0.808 0.039 17.36 26.48 9.12 7.349 36.297 1.078 0.038 17.21 26.49 9.28 8.014 36.438 1.347 0.037 17.11 26.48 9.38 8.541 36.552 1.617 0.037 17.00 26.48 9.48 9.240 36.747 1.886 0.037 16.75 26.56 9.81 11.463 37.574 2.156 0.036 16.67 26.57 9.90 12.234 37.798 2.425 0.035 16.62 26.59 9.97 12.651 37.888 2.694 0.035 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.067 Accepted refinement result: 18.93 26.44 7.51 4.347 35.525 0.067 0.045 Individual atomic B min max mean iso aniso Overall: 12.78 106.09 36.19 3.63 2312 0 Protein: 12.78 106.09 36.19 3.63 2312 0 Chain A: 12.78 106.09 36.19 N/A 2312 0 Histogram: Values Number of atoms 12.78 - 22.11 524 22.11 - 31.44 575 31.44 - 40.77 479 40.77 - 50.10 309 50.10 - 59.43 158 59.43 - 68.76 138 68.76 - 78.09 78 78.09 - 87.43 23 87.43 - 96.76 18 96.76 - 106.09 10 =========================== Idealize ADP of riding H ========================== r_work=0.1893 r_free=0.2644 r_work=0.1894 r_free=0.2642 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1894 r_free= 0.2642 coordinate error (max.-lik. estimate): 0.54 A | | | | normalized target function (ls_wunit_k1) (work): 0.044913 | | target function (ls_wunit_k1) not normalized (work): 306.352729 | | target function (ls_wunit_k1) not normalized (free): 64.036539 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1970 0.1894 0.2642 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3288 0.3252 0.3598 n_refl.: 7570 remove outliers: r(all,work,free)=0.3288 0.3252 0.3598 n_refl.: 7570 overall B=3.16 to atoms: r(all,work,free)=0.3403 0.3370 0.3688 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1939 0.1864 0.2605 n_refl.: 7570 remove outliers: r(all,work,free)=0.1939 0.1864 0.2605 n_refl.: 7570 ======================== 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 47.029-15.950 99.02 89 12 0.2082 962.720 942.484 1.701 0.996 0.369 15.935-12.710 100.00 89 10 0.1132 1068.003 1063.478 1.380 0.997 0.279 12.669-10.064 99.01 182 19 0.1066 973.526 962.941 1.315 0.998 0.258 10.054-8.008 99.48 344 37 0.1190 819.158 813.702 1.230 0.998 0.247 7.993-6.350 96.06 662 70 0.1681 519.556 508.215 1.142 0.999 0.246 6.344-5.045 94.20 1288 142 0.1972 439.435 418.094 0.960 0.998 0.166 5.041-4.007 88.19 2360 262 0.1915 453.974 428.790 0.944 0.995 0.077 4.004-3.512 68.84 1807 197 0.2299 414.748 384.225 1.104 0.986 0.009 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.5324 ============================ 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 = 1.160862 wxc_scale = 0.246 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.192279 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2649 0.2850 0.0201 0.014 2.2 2.5 2.4 22.2 2 0.029 0.2326 0.2750 0.0424 0.014 2.3 3.0 3.4 23.9 3 0.086 0.2133 0.2709 0.0576 0.016 2.5 5.1 4.8 23.9 5 0.171 0.2032 0.2674 0.0642 0.017 2.7 8.7 5.1 25.5 5 0.257 0.1970 0.2681 0.0711 0.019 2.9 11.2 6.5 26.7 5 0.343 0.1926 0.2684 0.0758 0.020 3.1 14.8 7.2 28.4 7 0.429 0.1856 0.2586 0.0730 0.021 3.2 16.1 7.5 26.7 5 0.514 0.1854 0.2595 0.0741 0.021 3.1 17.2 6.5 27.2 5 0.600 0.2014 0.2680 0.0666 0.018 2.8 9.3 6.1 25.9 5 0.286 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1856 0.2586 0.0730 0.021 3.2 16.1 7.5 26.7 5 0.514 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.56 25.86 7.30 6.229 43.003 0.192 6.203 19.41 26.42 7.01 7.403 44.144 0.006 6.225 18.90 26.23 7.33 7.172 43.641 0.024 6.213 17.83 25.99 8.15 7.581 43.203 0.096 6.189 17.52 25.91 8.39 8.311 43.429 0.192 6.182 17.35 25.90 8.55 9.190 43.771 0.288 6.179 17.29 25.89 8.60 9.559 43.899 0.385 6.177 17.21 25.88 8.67 10.160 44.109 0.481 6.176 17.17 25.87 8.71 10.676 44.281 0.577 6.175 17.13 25.87 8.74 11.120 44.427 0.673 6.174 17.10 25.86 8.76 11.491 44.549 0.769 6.174 17.07 25.86 8.78 11.803 44.651 0.865 6.173 17.05 25.86 8.81 12.083 44.741 0.961 6.173 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.024 Accepted refinement result: 18.90 26.23 7.33 7.172 43.641 0.024 6.213 Individual atomic B min max mean iso aniso Overall: 15.17 104.25 40.66 3.31 2312 0 Protein: 15.17 104.25 40.66 3.31 2312 0 Chain A: 15.17 104.25 40.66 N/A 2312 0 Histogram: Values Number of atoms 15.17 - 24.08 98 24.08 - 32.99 733 32.99 - 41.90 629 41.90 - 50.80 408 50.80 - 59.71 184 59.71 - 68.62 132 68.62 - 77.53 76 77.53 - 86.44 27 86.44 - 95.34 14 95.34 - 104.25 11 =========================== Idealize ADP of riding H ========================== r_work=0.1890 r_free=0.2623 r_work=0.1890 r_free=0.2622 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1890 r_free= 0.2622 coordinate error (max.-lik. estimate): 0.55 A | | | | normalized target function (ml) (work): 6.213915 | | target function (ml) not normalized (work): 42385.113088 | | target function (ml) not normalized (free): 4780.559099 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1964 0.1890 0.2622 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3484 0.3452 0.3757 n_refl.: 7570 remove outliers: r(all,work,free)=0.3484 0.3452 0.3757 n_refl.: 7570 overall B=0.00 to atoms: r(all,work,free)=0.3484 0.3452 0.3757 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1959 0.1885 0.2620 n_refl.: 7570 remove outliers: r(all,work,free)=0.1959 0.1885 0.2620 n_refl.: 7570 ======================== 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 47.029-15.950 99.02 89 12 0.1927 962.720 944.933 1.672 0.996 0.370 15.935-12.710 100.00 89 10 0.1071 1068.003 1062.315 1.403 0.997 0.295 12.669-10.064 99.01 182 19 0.1027 973.526 962.431 1.363 0.997 0.290 10.054-8.008 99.48 344 37 0.1156 819.158 813.169 1.239 0.998 0.270 7.993-6.350 96.06 662 70 0.1677 519.556 506.219 1.148 0.998 0.270 6.344-5.045 94.20 1288 142 0.1982 439.435 416.523 0.947 0.997 0.180 5.041-4.007 88.19 2360 262 0.1954 453.974 426.636 0.922 0.995 0.090 4.004-3.512 68.84 1807 197 0.2381 414.748 381.208 1.093 0.987 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.5725 ============================ 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 = 1.158408 wxc_scale = 0.541 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.188389 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2396 0.2794 0.0398 0.014 2.3 3.4 3.8 21.0 3 0.063 0.2115 0.2699 0.0583 0.016 2.6 5.9 4.8 22.6 5 0.188 0.1966 0.2687 0.0721 0.020 3.0 12.9 6.8 26.3 6 0.376 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 0.564 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 0.752 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 0.940 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 1.129 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 1.317 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 0.627 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 0.564 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 0.752 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 0.940 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 1.129 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 1.317 0.1885 0.2620 0.0734 0.021 3.2 16.1 7.5 26.7 5 0.627 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.85 26.20 7.34 6.577 44.896 0.188 6.208 20.15 26.60 6.45 7.012 46.571 0.006 6.234 19.03 26.25 7.22 7.016 45.697 0.024 6.213 18.40 26.12 7.72 6.903 44.785 0.094 6.199 17.63 25.94 8.31 8.684 45.355 0.188 6.181 17.49 25.92 8.43 9.385 45.685 0.283 6.179 17.39 25.92 8.52 10.118 45.994 0.377 6.177 17.33 25.92 8.59 10.734 46.232 0.471 6.176 17.29 25.93 8.64 11.293 46.437 0.565 6.175 17.26 25.93 8.67 11.714 46.589 0.659 6.175 17.23 25.94 8.70 12.101 46.724 0.754 6.174 17.21 25.93 8.72 12.623 46.890 0.848 6.173 17.21 25.94 8.73 12.605 46.903 0.942 6.174 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.094 Accepted refinement result: 18.40 26.12 7.72 6.903 44.785 0.094 6.199 Individual atomic B min max mean iso aniso Overall: 10.19 102.70 40.43 4.02 2312 0 Protein: 10.19 102.70 40.43 4.02 2312 0 Chain A: 10.19 102.70 40.43 N/A 2312 0 Histogram: Values Number of atoms 10.19 - 19.44 23 19.44 - 28.69 473 28.69 - 37.94 692 37.94 - 47.20 542 47.20 - 56.45 266 56.45 - 65.70 148 65.70 - 74.95 107 74.95 - 84.20 29 84.20 - 93.45 16 93.45 - 102.70 16 =========================== Idealize ADP of riding H ========================== r_work=0.1840 r_free=0.2612 r_work=0.1836 r_free=0.2611 ----------X-ray data---------- |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1836 r_free= 0.2611 coordinate error (max.-lik. estimate): 0.56 A | | | | normalized target function (ml) (work): 6.197963 | | target function (ml) not normalized (work): 42276.303537 | | target function (ml) not normalized (free): 4775.708180 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.03 - 6.00 0.97 1618 177 0.1422 0.1901 6.2527 6.4506| | 2: 6.00 - 4.77 0.93 1498 166 0.1899 0.2571 6.1423 6.2835| | 3: 4.77 - 4.16 0.89 1443 156 0.1874 0.2951 6.1767 6.4611| | 4: 4.16 - 3.78 0.76 1216 130 0.2184 0.3320 6.1896 6.3704| | 5: 3.78 - 3.51 0.66 1046 120 0.2331 0.3087 6.232 6.2901| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 47.03 - 6.00 1618 177 0.91 15.45 1.01 1.04 48382.08| | 2: 6.00 - 4.77 1498 166 0.87 22.05 1.00 1.02 51912.34| | 3: 4.77 - 4.16 1443 156 0.86 22.64 0.99 0.96 59308.37| | 4: 4.16 - 3.78 1216 130 0.82 27.40 0.98 0.90 66563.08| | 5: 3.78 - 3.51 1046 120 0.80 29.14 1.00 0.87 70308.04| |alpha: min = 0.87 max = 1.04 mean = 0.97| |beta: min = 48382.08 max = 70308.04 mean = 58072.39| |figures of merit: min = 0.01 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 88.90 mean = 22.65| |phase err.(test): min = 0.00 max = 86.55 mean = 24.02| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1915 0.1836 0.2611 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3449 0.3414 0.3739 n_refl.: 7570 remove outliers: r(all,work,free)=0.3449 0.3414 0.3739 n_refl.: 7570 overall B=0.00 to atoms: r(all,work,free)=0.3449 0.3414 0.3739 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1916 0.1838 0.2610 n_refl.: 7570 remove outliers: r(all,work,free)=0.1916 0.1838 0.2610 n_refl.: 7570 ======================== 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 47.029-15.950 99.02 89 12 0.1923 962.720 945.171 1.681 0.995 0.370 15.935-12.710 100.00 89 10 0.1067 1068.003 1062.310 1.410 0.996 0.295 12.669-10.064 99.01 182 19 0.1023 973.526 962.621 1.369 0.997 0.290 10.054-8.008 99.48 344 37 0.1142 819.158 812.953 1.249 0.997 0.273 7.993-6.350 96.06 662 70 0.1651 519.556 507.803 1.123 0.998 0.237 6.344-5.045 94.20 1288 142 0.1928 439.435 417.063 0.954 0.997 0.180 5.041-4.007 88.19 2360 262 0.1896 453.974 427.468 0.922 0.994 0.080 4.004-3.512 68.84 1807 197 0.2312 414.748 382.660 1.090 0.986 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.6883 ================= 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 : 0.3042 0.2976 0.016 2.306 2.0 107.7 31.5 0 0.000 1_bss: 0.1923 0.1997 0.016 2.306 5.4 111.1 34.9 0 0.000 1_settarget: 0.1923 0.1997 0.016 2.306 5.4 111.1 34.9 0 0.000 1_weight: 0.1923 0.1997 0.016 2.306 5.4 111.1 34.9 0 0.000 1_xyzrec: 0.1833 0.2581 0.020 3.102 5.4 111.1 34.9 0 0.406 1_adp: 0.1893 0.2644 0.020 3.102 12.8 106.1 36.2 0 0.406 1_regHadp: 0.1894 0.2642 0.020 3.102 12.8 106.1 36.2 0 0.406 2_bss: 0.1864 0.2605 0.020 3.102 15.9 109.3 39.4 0 0.406 2_settarget: 0.1864 0.2605 0.020 3.102 15.9 109.3 39.4 0 0.406 2_updatecdl: 0.1864 0.2605 0.020 3.101 15.9 109.3 39.4 0 0.406 2_weight: 0.1864 0.2605 0.020 3.101 15.9 109.3 39.4 0 0.406 2_xyzrec: 0.1856 0.2586 0.021 3.182 15.9 109.3 39.4 0 0.409 2_adp: 0.1890 0.2623 0.021 3.182 15.2 104.3 40.7 0 0.409 2_regHadp: 0.1890 0.2622 0.021 3.182 15.2 104.3 40.7 0 0.409 3_bss: 0.1885 0.2620 0.021 3.182 15.2 104.3 40.7 0 0.409 3_settarget: 0.1885 0.2620 0.021 3.182 15.2 104.3 40.7 0 0.409 3_updatecdl: 0.1885 0.2620 0.021 3.183 15.2 104.3 40.7 0 0.409 3_setrh: 0.1885 0.2620 0.021 3.183 15.2 104.3 40.7 0 0.409 3_weight: 0.1885 0.2620 0.021 3.183 15.2 104.3 40.7 0 0.409 3_xyzrec: 0.1885 0.2620 0.021 3.183 15.2 104.3 40.7 0 0.409 3_adp: 0.1840 0.2612 0.021 3.183 10.2 102.7 40.4 0 0.409 3_regHadp: 0.1836 0.2611 0.021 3.183 10.2 102.7 40.4 0 0.409 end: 0.1838 0.2610 0.021 3.183 10.2 102.7 40.4 0 0.409 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1xgo_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1xgo_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1200 Refinement macro-cycles (run) : 226.7600 Write final files (write_after_run_outputs) : 9.1400 Total : 239.0200 Total CPU time: 4.43 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:38:52 PDT -0700 (1723221532.41 s) Start R-work = 0.1923, R-free = 0.1997 Final R-work = 0.1838, R-free = 0.2610 =============================================================================== Job complete usr+sys time: 273.99 seconds wall clock time: 7 minutes 24.86 seconds (444.86 seconds total)