Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1yab.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.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 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1yab.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1yab.pdb" } 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 } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 2831 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1401 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "B" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1430 Classifications: {'peptide': 87} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Time building chain proxies: 1.10, per 1000 atoms: 0.39 Number of scatterers: 2831 At special positions: 0 Unit cell: (100.173, 100.173, 87.853, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 257 8.00 N 229 7.00 C 865 6.00 H 1476 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: 2.11 Conformation dependent library (CDL) restraints added in 278.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 6 helices and 2 sheets defined 18.6% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 4.330A pdb=" N LEU A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 74' Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 145 through 152 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 6.212A pdb=" N VAL A 118 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A 127 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE A 139 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A 129 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A 137 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 131 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 81 through 84 removed outlier: 3.630A pdb=" N ASP B 115 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 118 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU B 127 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE B 139 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 129 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL B 137 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ILE B 131 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) 26 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.41 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: 1476 1.15 - 1.32: 248 1.32 - 1.49: 442 1.49 - 1.66: 665 1.66 - 1.83: 8 Bond restraints: 2839 Sorted by residual: bond pdb=" NH1 ARG B 87 " pdb="HH12 ARG B 87 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 114 " pdb=" H VAL A 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS A 100 " pdb=" H HIS A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LYS B 108 " pdb=" H LYS B 108 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LEU A 75 " pdb=" H LEU A 75 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 2834 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.19: 59 104.19 - 111.07: 3254 111.07 - 117.94: 912 117.94 - 124.81: 926 124.81 - 131.69: 70 Bond angle restraints: 5221 Sorted by residual: angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 112.92 102.67 10.25 1.23e+00 6.61e-01 6.95e+01 angle pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " ideal model delta sigma weight residual 115.55 123.69 -8.14 1.33e+00 5.65e-01 3.75e+01 angle pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C VAL A 81 " pdb=" CA VAL A 81 " pdb=" CB VAL A 81 " ideal model delta sigma weight residual 110.91 104.61 6.30 1.24e+00 6.50e-01 2.58e+01 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 110.80 120.70 -9.90 2.13e+00 2.20e-01 2.16e+01 ... (remaining 5216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 1127 25.86 - 51.72: 116 51.72 - 77.58: 21 77.58 - 103.44: 5 103.44 - 129.30: 1 Dihedral angle restraints: 1270 sinusoidal: 764 harmonic: 506 Sorted by residual: dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta harmonic sigma weight residual 180.00 50.70 129.30 0 5.00e+00 4.00e-02 6.69e+02 dihedral pdb=" C ASP B 132 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual -122.60 -139.66 17.06 0 2.50e+00 1.60e-01 4.66e+01 dihedral pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual 122.80 139.34 -16.54 0 2.50e+00 1.60e-01 4.38e+01 ... (remaining 1267 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.134: 186 0.134 - 0.267: 45 0.267 - 0.401: 3 0.401 - 0.534: 2 0.534 - 0.667: 2 Chirality restraints: 238 Sorted by residual: chirality pdb=" CA PHE B 135 " pdb=" N PHE B 135 " pdb=" C PHE B 135 " pdb=" CB PHE B 135 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ASP B 132 " pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CB ASP B 132 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASP A 132 " pdb=" N ASP A 132 " pdb=" C ASP A 132 " pdb=" CB ASP A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 235 not shown) Planarity restraints: 394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 134 " -0.004 2.00e-02 2.50e+03 1.16e-02 2.03e+00 pdb=" CG ASN A 134 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 134 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 134 " -0.009 2.00e-02 2.50e+03 pdb="HD22 ASN A 134 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.003 2.00e-02 2.50e+03 6.76e-03 1.37e+00 pdb=" CG PHE B 135 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 135 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE B 135 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 PHE B 135 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE B 135 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE B 135 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 134 " -0.003 2.00e-02 2.50e+03 9.20e-03 1.27e+00 pdb=" CG ASN B 134 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 134 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 134 " -0.007 2.00e-02 2.50e+03 pdb="HD22 ASN B 134 " 0.012 2.00e-02 2.50e+03 ... (remaining 391 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 89 1.84 - 2.53: 2657 2.53 - 3.22: 8856 3.22 - 3.91: 12184 3.91 - 4.60: 18186 Nonbonded interactions: 41972 Sorted by model distance: nonbonded pdb=" HG3 ARG A 89 " pdb="HH11 ARG A 89 " model vdw 1.154 2.270 nonbonded pdb=" HA GLU A 147 " pdb=" HB2 GLU A 150 " model vdw 1.325 2.440 nonbonded pdb="HH22 ARG A 94 " pdb="HD12 ILE A 104 " model vdw 1.340 2.270 nonbonded pdb=" O LEU A 74 " pdb=" H ASP A 76 " model vdw 1.363 1.850 nonbonded pdb=" HA2 GLY B 126 " pdb=" H THR B 140 " model vdw 1.423 2.270 ... (remaining 41967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 4 15.91 1 O 257 7.97 1 N 229 6.97 1 C 865 5.97 1 H 1476 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: 1476 of 2831 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 2831 n_use_u_iso = 2831 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 = 2831 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (2831 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 2831 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 69 through 74 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 92 through 97 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 147 through 151 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'B' and resid 72 through 75 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'B' and resid 94 through 96 helix_type = alpha pi *3_10 unknown } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 145 through 152 } sheet { first_strand = chain 'A' and resid 81 through 84 sheet_id = " A" strand { selection = chain 'A' and resid 114 through 118 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 117 and name N bond_start_previous = chain 'A' and resid 82 and name O } strand { selection = chain 'A' and resid 121 through 131 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 126 and name N bond_start_previous = chain 'A' and resid 114 and name O } strand { selection = chain 'A' and resid 134 through 142 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 141 and name N bond_start_previous = chain 'A' and resid 125 and name O } } sheet { first_strand = chain 'B' and resid 81 through 84 sheet_id = " B" strand { selection = chain 'B' and resid 114 through 118 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 117 and name N bond_start_previous = chain 'B' and resid 82 and name O } strand { selection = chain 'B' and resid 121 through 131 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 126 and name N bond_start_previous = chain 'B' and resid 114 and name O } strand { selection = chain 'B' and resid 134 through 142 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 141 and name N bond_start_previous = chain 'B' and resid 125 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1yab_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1476 occupancy sum: 1476.00 (% of total atoms 52.17) Rotatable: count: 514 occupancy sum: 514.00 (% of total atoms 18.17) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7246 (all), 4.69 % free)-------------| | | | r_work= 0.4059 r_free= 0.4598 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.289039 | | target function (ml) not normalized (work): 36526.102154 | | target function (ml) not normalized (free): 1841.689129 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.90 - 4.27 1.00 3512 170 0.3818 0.4405 5.9303 6.0787| | 2: 4.27 - 3.40 1.00 3394 170 0.4725 0.5140 4.6255 4.7548| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.90 - 4.27 3512 170 0.47 53.91 0.97 0.49 32804.81| | 2: 4.27 - 3.40 3394 170 0.71 34.58 1.68 1.01 2345.12| |alpha: min = 0.49 max = 1.01 mean = 0.75| |beta: min = 2345.12 max = 32804.81 mean = 17835.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.59| |phase err.(work): min = 0.00 max = 89.99 mean = 44.41| |phase err.(test): min = 0.00 max = 89.81 mean = 43.07| |-----------------------------------------------------------------------------| ----------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 : 0.014 0.080 1363 Z= 0.957 Angle : 1.971 12.009 1839 Z= 1.158 Chirality : 0.128 0.667 238 Planarity : 0.005 0.024 230 Dihedral : 23.170 129.301 543 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 8.33 % Allowed : 10.12 % Favored : 81.55 % Rotamer: Outliers : 24.68 % Allowed : 21.52 % Favored : 53.80 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.83 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.52), residues: 168 helix: -4.84 (0.42), residues: 40 sheet: -3.56 (1.49), residues: 10 loop : -2.51 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 94 PHE 0.008 0.003 PHE B 135 HIS 0.002 0.001 HIS A 100 Individual atomic B min max mean iso aniso Overall: 93.69 154.06 112.45 1.19 1355 0 Protein: 93.69 154.06 112.45 1.19 1355 0 Chain A: 94.35 154.06 112.30 N/A 669 0 Chain B: 93.69 153.95 112.61 N/A 686 0 Histogram: Values Number of atoms 93.69 - 99.73 219 99.73 - 105.76 346 105.76 - 111.80 259 111.80 - 117.84 158 117.84 - 123.88 111 123.88 - 129.91 104 129.91 - 135.95 47 135.95 - 141.99 29 141.99 - 148.02 23 148.02 - 154.06 59 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7246 (all), 4.69 % free)-------------| | | | r_work= 0.4059 r_free= 0.4598 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.289039 | | target function (ml) not normalized (work): 36526.102154 | | target function (ml) not normalized (free): 1841.689129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4088 0.4059 0.4598 n_refl.: 7246 re-set all scales: r(all,work,free)=0.4088 0.4059 0.4598 n_refl.: 7246 remove outliers: r(all,work,free)=0.4086 0.4057 0.4598 n_refl.: 7245 overall B=-8.40 to atoms: r(all,work,free)=0.3843 0.3813 0.4380 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2258 0.2228 0.2845 n_refl.: 7245 remove outliers: r(all,work,free)=0.2258 0.2228 0.2845 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1925 763.916 733.811 1.338 0.999 0.338 12.965-10.793 93.40 95 4 0.1555 722.206 703.625 1.337 0.998 0.330 10.793-8.919 99.47 176 10 0.1458 676.649 670.817 1.301 0.998 0.327 8.905-7.374 99.69 313 12 0.2067 409.798 395.940 1.152 0.996 0.300 7.364-6.089 99.82 547 20 0.2513 296.258 285.152 1.064 0.993 0.273 6.087-5.031 100.00 938 48 0.2290 234.401 224.135 0.961 0.989 0.215 5.030-4.158 99.88 1640 78 0.1969 247.791 238.471 0.978 0.983 0.155 4.156-3.397 99.85 3105 159 0.2879 111.432 103.442 1.032 0.973 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.6281 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.057848 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.185064 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 0.2555 0.2846 0.0292 0.003 0.7 8.1 2.4 21.5 0 0.125 0.2513 0.2854 0.0340 0.003 0.8 7.8 2.4 21.5 0 0.250 0.2473 0.2865 0.0393 0.004 0.8 8.5 3.0 21.5 0 0.500 0.2386 0.2870 0.0484 0.004 0.9 9.9 4.2 20.9 0 1.000 0.2323 0.2856 0.0533 0.006 1.0 12.4 4.2 22.2 0 2.000 0.2294 0.2837 0.0543 0.007 1.1 14.5 4.8 22.8 0 3.000 0.2252 0.2813 0.0560 0.009 1.2 15.6 5.4 24.1 0 4.000 0.2233 0.2804 0.0571 0.010 1.3 18.1 4.8 24.1 0 5.000 0.2216 0.2789 0.0572 0.012 1.3 17.7 5.4 24.7 0 6.000 0.2209 0.2788 0.0580 0.013 1.4 18.8 4.8 25.9 0 7.000 0.2194 0.2778 0.0584 0.015 1.5 20.5 5.4 27.2 0 8.000 0.2184 0.2778 0.0594 0.016 1.5 22.7 6.5 27.2 0 9.000 0.2178 0.2779 0.0601 0.017 1.6 23.0 6.5 28.5 0 10.000 0.2203 0.2784 0.0581 0.014 1.4 20.5 5.4 27.2 0 7.529 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2513 0.2854 0.0340 0.003 0.8 7.8 2.4 21.5 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.13 28.54 3.40 0.822 103.807 0.185 0.062 25.26 28.67 3.41 2.031 103.907 0.006 0.063 24.74 28.35 3.62 2.067 103.914 0.023 0.060 23.87 27.91 4.04 3.337 104.191 0.093 0.056 22.61 27.21 4.61 7.751 105.408 0.185 0.050 22.32 27.07 4.75 9.072 105.834 0.278 0.049 22.13 26.98 4.85 10.010 106.146 0.370 0.048 21.90 26.89 4.99 11.173 106.581 0.463 0.047 21.58 26.73 5.15 12.901 107.272 0.555 0.046 21.49 26.68 5.19 13.462 107.451 0.648 0.045 21.42 26.65 5.23 13.963 107.613 0.740 0.045 21.36 26.63 5.27 14.414 107.760 0.833 0.045 21.29 26.60 5.32 15.004 107.971 0.925 0.044 max suggested for this run: 20.76 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.925 Accepted refinement result: 21.29 26.60 5.32 15.004 107.971 0.925 0.044 Individual atomic B min max mean iso aniso Overall: 80.29 180.44 112.75 12.35 1355 0 Protein: 80.29 180.44 112.75 12.35 1355 0 Chain A: 81.33 180.44 113.41 N/A 669 0 Chain B: 80.29 177.11 112.12 N/A 686 0 Histogram: Values Number of atoms 80.29 - 90.30 245 90.30 - 100.32 212 100.32 - 110.33 237 110.33 - 120.35 210 120.35 - 130.36 152 130.36 - 140.38 131 140.38 - 150.40 90 150.40 - 160.41 38 160.41 - 170.43 26 170.43 - 180.44 14 =========================== Idealize ADP of riding H ========================== r_work=0.2129 r_free=0.2660 r_work=0.2103 r_free=0.2669 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2103 r_free= 0.2669 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ls_wunit_k1) (work): 0.043348 | | target function (ls_wunit_k1) not normalized (work): 299.315845 | | target function (ls_wunit_k1) not normalized (free): 27.290798 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2131 0.2103 0.2669 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3869 0.3846 0.4283 n_refl.: 7245 remove outliers: r(all,work,free)=0.3869 0.3846 0.4283 n_refl.: 7245 overall B=0.00 to atoms: r(all,work,free)=0.3869 0.3846 0.4283 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2108 0.2079 0.2661 n_refl.: 7245 remove outliers: r(all,work,free)=0.2108 0.2079 0.2661 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1702 481.322 462.792 1.384 0.994 0.339 12.965-10.793 95.19 95 4 0.1131 455.042 454.020 1.356 0.993 0.330 10.793-8.919 99.47 176 10 0.1291 426.338 426.706 1.283 0.993 0.320 8.905-7.374 99.69 313 12 0.1772 258.203 252.693 1.118 0.992 0.290 7.364-6.089 99.82 547 20 0.2124 186.664 183.332 1.049 0.990 0.260 6.087-5.031 100.00 938 48 0.2148 147.690 142.997 0.954 0.986 0.200 5.030-4.158 99.88 1640 78 0.1813 156.126 151.470 0.980 0.982 0.130 4.156-3.397 99.85 3105 159 0.2978 70.210 64.818 1.054 0.976 0.048 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.8271 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.596817 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.041097 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 0.2043 0.2635 0.0592 0.003 0.6 5.3 3.0 17.1 0 0.125 0.1993 0.2652 0.0660 0.003 0.7 7.4 3.0 18.4 0 0.250 0.1952 0.2616 0.0664 0.004 0.8 9.2 3.6 19.6 0 0.500 0.1916 0.2608 0.0692 0.007 1.0 11.7 3.6 21.5 0 1.000 0.1887 0.2585 0.0698 0.012 1.2 17.0 4.8 24.1 0 2.000 0.1873 0.2587 0.0714 0.016 1.5 18.4 4.2 27.2 0 3.000 0.1862 0.2574 0.0711 0.019 1.7 20.2 5.4 27.2 0 4.000 0.1861 0.2602 0.0741 0.023 1.9 20.9 5.4 27.8 0 5.000 0.1856 0.2604 0.0748 0.026 2.1 23.0 6.0 29.1 0 6.000 0.1861 0.2632 0.0770 0.029 2.3 22.7 6.0 29.1 0 7.000 0.1852 0.2607 0.0755 0.031 2.5 25.5 6.5 31.0 0 8.000 0.1846 0.2630 0.0783 0.034 2.6 26.2 6.5 31.0 0 9.000 0.1849 0.2621 0.0772 0.036 2.7 25.1 6.5 31.0 0 10.000 0.1882 0.2591 0.0709 0.013 1.3 17.0 4.8 24.7 0 2.298 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2043 0.2635 0.0592 0.003 0.6 5.3 3.0 17.1 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.43 26.35 5.92 18.611 124.542 0.041 4.937 26.99 30.12 3.13 14.405 134.393 0.001 5.051 24.84 28.48 3.64 13.948 132.740 0.005 5.004 21.81 26.38 4.57 16.799 128.599 0.021 4.934 20.74 26.14 5.40 17.666 126.750 0.041 4.908 20.38 26.05 5.67 18.177 126.400 0.062 4.900 20.26 26.03 5.77 18.695 126.732 0.082 4.895 19.95 25.74 5.79 18.725 126.434 0.103 4.888 19.88 25.72 5.84 18.991 126.603 0.123 4.885 19.83 25.71 5.88 19.237 126.777 0.144 4.883 19.78 25.68 5.90 19.319 126.762 0.164 4.882 19.75 25.66 5.91 19.236 126.576 0.185 4.883 19.73 25.64 5.91 19.391 126.699 0.205 4.881 max suggested for this run: 24.91 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.205 Accepted refinement result: 19.73 25.64 5.91 19.391 126.699 0.205 4.881 Individual atomic B min max mean iso aniso Overall: 75.29 203.07 117.26 17.44 1355 0 Protein: 75.29 203.07 117.26 17.44 1355 0 Chain A: 76.96 195.59 118.58 N/A 669 0 Chain B: 75.29 203.07 115.97 N/A 686 0 Histogram: Values Number of atoms 75.29 - 88.07 179 88.07 - 100.84 226 100.84 - 113.62 264 113.62 - 126.40 234 126.40 - 139.18 169 139.18 - 151.96 133 151.96 - 164.73 89 164.73 - 177.51 40 177.51 - 190.29 17 190.29 - 203.07 4 =========================== Idealize ADP of riding H ========================== r_work=0.1973 r_free=0.2564 r_work=0.1981 r_free=0.2555 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.1981 r_free= 0.2555 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 4.879461 | | target function (ml) not normalized (work): 33692.678635 | | target function (ml) not normalized (free): 1723.535741 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2009 0.1981 0.2555 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3890 0.3868 0.4311 n_refl.: 7245 remove outliers: r(all,work,free)=0.3890 0.3868 0.4311 n_refl.: 7245 overall B=-4.00 to atoms: r(all,work,free)=0.3764 0.3741 0.4193 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.1994 0.1966 0.2540 n_refl.: 7245 remove outliers: r(all,work,free)=0.1994 0.1966 0.2540 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1622 481.322 462.090 1.416 0.991 0.340 12.965-10.793 95.19 95 4 0.1121 455.042 451.893 1.372 0.991 0.332 10.793-8.919 99.47 176 10 0.1260 426.338 425.818 1.279 0.992 0.313 8.905-7.374 99.69 313 12 0.1859 258.203 251.016 1.106 0.991 0.284 7.364-6.089 99.82 547 20 0.2109 186.664 181.822 1.033 0.991 0.246 6.087-5.031 100.00 938 48 0.2210 147.690 141.800 0.953 0.990 0.196 5.030-4.158 99.88 1640 78 0.1736 156.126 150.927 0.966 0.989 0.116 4.156-3.397 99.85 3105 159 0.2536 70.210 64.867 1.028 0.988 0.043 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.4630 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1966 r_free=0.2540 After: r_work=0.1966 r_free=0.2540 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.903484 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.038991 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 0.1966 0.2542 0.0576 0.003 0.6 5.7 3.0 17.1 0 0.125 0.1964 0.2545 0.0581 0.003 0.6 5.3 3.0 17.1 0 0.250 0.1943 0.2554 0.0610 0.005 0.7 7.4 3.0 17.1 0 0.500 0.1873 0.2553 0.0680 0.010 1.2 12.0 3.0 17.7 0 1.000 0.1842 0.2549 0.0707 0.012 1.7 20.9 4.2 20.3 0 2.000 0.1829 0.2555 0.0726 0.015 2.0 23.4 4.2 21.5 0 3.000 0.1813 0.2547 0.0734 0.019 2.1 27.6 4.2 22.2 0 4.000 0.1801 0.2544 0.0743 0.021 2.3 26.9 4.2 22.2 0 5.000 0.1793 0.2543 0.0749 0.024 2.6 29.7 4.8 24.1 0 6.000 0.1782 0.2538 0.0755 0.026 2.7 30.1 4.8 23.4 0 7.000 0.1778 0.2529 0.0752 0.029 2.9 31.2 5.4 24.1 0 8.000 0.1774 0.2523 0.0749 0.031 3.0 30.8 4.8 24.7 0 9.000 0.1772 0.2515 0.0743 0.033 3.2 31.5 5.4 24.1 0 10.000 0.1833 0.2554 0.0720 0.014 1.8 22.7 4.2 20.9 0 2.452 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1964 0.2545 0.0581 0.003 0.6 5.3 3.0 17.1 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.64 25.45 5.81 21.050 125.440 0.039 4.881 26.05 29.77 3.73 16.059 134.859 0.001 5.015 25.36 28.87 3.51 16.449 135.160 0.005 5.005 21.90 26.47 4.57 17.673 129.801 0.019 4.941 20.64 25.87 5.23 18.071 127.818 0.039 4.904 20.15 25.52 5.37 18.335 127.319 0.058 4.889 19.91 25.32 5.41 18.590 127.274 0.078 4.881 19.77 25.25 5.48 18.791 127.503 0.097 4.876 19.60 25.25 5.65 19.100 127.455 0.117 4.870 19.51 25.23 5.72 19.451 127.400 0.136 4.867 19.45 25.21 5.76 19.714 127.455 0.156 4.865 19.41 25.21 5.79 19.961 127.322 0.175 4.863 19.39 25.20 5.81 20.139 127.419 0.195 4.862 max suggested for this run: 25.09 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.195 Accepted refinement result: 19.39 25.20 5.81 20.139 127.419 0.195 4.862 Individual atomic B min max mean iso aniso Overall: 66.29 209.57 117.40 19.76 1355 0 Protein: 66.29 209.57 117.40 19.76 1355 0 Chain A: 69.33 204.36 119.02 N/A 669 0 Chain B: 66.29 209.57 115.81 N/A 686 0 Histogram: Values Number of atoms 66.29 - 80.62 93 80.62 - 94.95 200 94.95 - 109.27 288 109.27 - 123.60 277 123.60 - 137.93 191 137.93 - 152.26 138 152.26 - 166.59 100 166.59 - 180.91 45 180.91 - 195.24 18 195.24 - 209.57 5 =========================== Idealize ADP of riding H ========================== r_work=0.1939 r_free=0.2520 r_work=0.1942 r_free=0.2517 ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.1942 r_free= 0.2517 coordinate error (max.-lik. estimate): 0.16 A | | | | normalized target function (ml) (work): 4.862029 | | target function (ml) not normalized (work): 33572.308016 | | target function (ml) not normalized (free): 1719.970591 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.90 - 4.27 0.99 3511 170 0.1816 0.2368 5.2859 5.5325| | 2: 4.27 - 3.40 1.00 3394 170 0.2290 0.2934 4.4235 4.585| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.90 - 4.27 3511 170 0.80 25.94 1.00 0.98 8273.95| | 2: 4.27 - 3.40 3394 170 0.78 28.24 1.03 1.01 1563.47| |alpha: min = 0.98 max = 1.01 mean = 0.99| |beta: min = 1563.47 max = 8273.95 mean = 4975.56| |figures of merit: min = 0.00 max = 1.00 mean = 0.79| |phase err.(work): min = 0.00 max = 89.94 mean = 27.07| |phase err.(test): min = 0.00 max = 88.35 mean = 27.78| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1970 0.1942 0.2517 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3846 0.3823 0.4280 n_refl.: 7245 remove outliers: r(all,work,free)=0.3846 0.3823 0.4280 n_refl.: 7245 overall B=-6.55 to atoms: r(all,work,free)=0.3636 0.3612 0.4085 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.1958 0.1930 0.2497 n_refl.: 7245 remove outliers: r(all,work,free)=0.1958 0.1930 0.2497 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1639 481.322 461.523 1.483 0.991 0.341 12.965-10.793 95.19 95 4 0.1111 455.042 452.459 1.436 0.991 0.334 10.793-8.919 99.47 176 10 0.1286 426.338 425.930 1.330 0.992 0.315 8.905-7.374 99.69 313 12 0.1870 258.203 251.175 1.143 0.991 0.287 7.364-6.089 99.82 547 20 0.2145 186.664 181.762 1.057 0.991 0.239 6.087-5.031 100.00 938 48 0.2176 147.690 141.976 0.964 0.990 0.190 5.030-4.158 99.88 1640 78 0.1718 156.126 150.900 0.976 0.990 0.119 4.156-3.397 99.85 3105 159 0.2390 70.210 65.460 1.035 0.989 0.034 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.9588 ================= 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 : 0.4059 0.4598 0.014 1.971 93.7 154.1 112.5 0 0.000 1_bss: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_settarget: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_weight: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_xyzrec: 0.2513 0.2854 0.003 0.754 85.3 145.7 104.1 0 0.267 1_adp: 0.2129 0.2660 0.003 0.754 80.3 180.4 112.8 0 0.267 1_regHadp: 0.2103 0.2669 0.003 0.754 80.3 180.4 112.8 0 0.267 2_bss: 0.2079 0.2661 0.003 0.754 80.3 180.4 112.8 0 0.267 2_settarget: 0.2079 0.2661 0.003 0.754 80.3 180.4 112.8 0 0.267 2_updatecdl: 0.2079 0.2661 0.004 0.807 80.3 180.4 112.8 0 0.267 2_weight: 0.2079 0.2661 0.004 0.807 80.3 180.4 112.8 0 0.267 2_xyzrec: 0.2043 0.2635 0.003 0.613 80.3 180.4 112.8 0 0.316 2_adp: 0.1973 0.2564 0.003 0.613 75.3 203.1 117.3 0 0.316 2_regHadp: 0.1981 0.2555 0.003 0.613 75.3 203.1 117.3 0 0.316 3_bss: 0.1966 0.2540 0.003 0.613 71.3 199.1 113.3 0 0.316 3_settarget: 0.1966 0.2540 0.003 0.613 71.3 199.1 113.3 0 0.316 3_updatecdl: 0.1966 0.2540 0.003 0.651 71.3 199.1 113.3 0 0.316 3_setrh: 0.1966 0.2540 0.003 0.651 71.3 199.1 113.3 0 0.316 3_weight: 0.1966 0.2540 0.003 0.651 71.3 199.1 113.3 0 0.316 3_xyzrec: 0.1964 0.2545 0.003 0.628 71.3 199.1 113.3 0 0.316 3_adp: 0.1939 0.2520 0.003 0.628 66.3 209.6 117.4 0 0.316 3_regHadp: 0.1942 0.2517 0.003 0.628 66.3 209.6 117.4 0 0.316 end: 0.1930 0.2497 0.003 0.628 59.7 203.0 110.8 0 0.316 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1yab_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1yab_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1000 Refinement macro-cycles (run) : 138.2700 Write final files (write_after_run_outputs) : 17.6200 Total : 159.9900 Total CPU time: 3.09 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:28:57 PDT -0700 (1716251337.59 s) Start R-work = 0.2228, R-free = 0.2845 Final R-work = 0.1930, R-free = 0.2497 =============================================================================== Job complete usr+sys time: 201.91 seconds wall clock time: 12 minutes 4.66 seconds (724.66 seconds total)