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/2etc.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2etc/2etc.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2etc.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2etc.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2etc/2etc.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2etc/2etc.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 } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 7817 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 3938 Classifications: {'peptide': 252} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Chain: "B" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3879 Inner-chain residues flagged as termini: ['pdbres="LYS B 201 "', 'pdbres="GLY B 204 "'] Classifications: {'peptide': 248} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 235} Chain breaks: 1 Time building chain proxies: 2.61, per 1000 atoms: 0.33 Number of scatterers: 7817 At special positions: 0 Unit cell: (39.514, 95.862, 164.504, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 742 8.00 N 678 7.00 C 2473 6.00 H 3898 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 206 " distance=2.05 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 206 " distance=2.04 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: 7.26 Conformation dependent library (CDL) restraints added in 928.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 1 sheets defined 50.8% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.684A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 261 through 281 removed outlier: 3.731A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 308 through 318 Processing sheet with id= A, first strand: chain 'B' and resid 156 through 158 134 hydrogen bonds defined for protein. 396 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: 5.63 Time building geometry restraints manager: 3.95 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: 3886 1.15 - 1.31: 685 1.31 - 1.48: 1547 1.48 - 1.65: 1739 1.65 - 1.81: 36 Bond restraints: 7893 Sorted by residual: bond pdb=" N PRO A 72 " pdb=" CD PRO A 72 " ideal model delta sigma weight residual 1.474 1.622 -0.148 1.40e-02 5.10e+03 1.12e+02 bond pdb=" NH1 ARG A 77 " pdb="HH12 ARG A 77 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 131 " pdb=" H GLY A 131 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU B 305 " pdb=" H GLU B 305 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN B 294 " pdb="HE22 GLN B 294 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7888 not shown) Histogram of bond angle deviations from ideal: 86.59 - 96.08: 6 96.08 - 105.56: 171 105.56 - 115.04: 9916 115.04 - 124.52: 3984 124.52 - 134.00: 212 Bond angle restraints: 14289 Sorted by residual: angle pdb=" C GLU A 211 " pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " ideal model delta sigma weight residual 110.42 86.59 23.83 1.99e+00 2.53e-01 1.43e+02 angle pdb=" N PRO A 72 " pdb=" CA PRO A 72 " pdb=" CB PRO A 72 " ideal model delta sigma weight residual 102.60 113.11 -10.51 1.10e+00 8.26e-01 9.13e+01 angle pdb=" N GLN B 200 " pdb=" CA GLN B 200 " pdb=" C GLN B 200 " ideal model delta sigma weight residual 111.56 123.12 -11.56 1.43e+00 4.89e-01 6.53e+01 angle pdb=" N LEU B 212 " pdb=" CA LEU B 212 " pdb=" CB LEU B 212 " ideal model delta sigma weight residual 111.11 132.49 -21.38 2.74e+00 1.33e-01 6.09e+01 angle pdb=" N GLU B 211 " pdb=" CA GLU B 211 " pdb=" C GLU B 211 " ideal model delta sigma weight residual 113.72 125.22 -11.50 1.52e+00 4.33e-01 5.73e+01 ... (remaining 14284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 3278 17.87 - 35.74: 277 35.74 - 53.61: 111 53.61 - 71.48: 31 71.48 - 89.35: 13 Dihedral angle restraints: 3710 sinusoidal: 2042 harmonic: 1668 Sorted by residual: dihedral pdb=" C GLU A 211 " pdb=" N GLU A 211 " pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " ideal model delta harmonic sigma weight residual -122.60 -100.22 -22.38 0 2.50e+00 1.60e-01 8.01e+01 dihedral pdb=" N LEU B 212 " pdb=" C LEU B 212 " pdb=" CA LEU B 212 " pdb=" CB LEU B 212 " ideal model delta harmonic sigma weight residual 122.80 142.47 -19.67 0 2.50e+00 1.60e-01 6.19e+01 dihedral pdb=" CA GLN B 200 " pdb=" C GLN B 200 " pdb=" N LYS B 201 " pdb=" CA LYS B 201 " ideal model delta harmonic sigma weight residual 180.00 146.17 33.83 0 5.00e+00 4.00e-02 4.58e+01 ... (remaining 3707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 554 0.117 - 0.233: 51 0.233 - 0.350: 6 0.350 - 0.467: 2 0.467 - 0.583: 1 Chirality restraints: 614 Sorted by residual: chirality pdb=" CA LEU B 212 " pdb=" N LEU B 212 " pdb=" C LEU B 212 " pdb=" CB LEU B 212 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA LYS B 201 " pdb=" N LYS B 201 " pdb=" C LYS B 201 " pdb=" CB LYS B 201 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA GLU A 71 " pdb=" N GLU A 71 " pdb=" C GLU A 71 " pdb=" CB GLU A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 611 not shown) Planarity restraints: 1182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 71 " -0.067 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO A 72 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 158 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C THR B 158 " -0.032 2.00e-02 2.50e+03 pdb=" O THR B 158 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 159 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 251 " -0.022 2.00e-02 2.50e+03 1.21e-02 3.29e+00 pdb=" CG HIS B 251 " 0.002 2.00e-02 2.50e+03 pdb=" ND1 HIS B 251 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 251 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 251 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 251 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 HIS B 251 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 HIS B 251 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS B 251 " -0.012 2.00e-02 2.50e+03 ... (remaining 1179 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.36: 14 1.36 - 2.17: 651 2.17 - 2.98: 20921 2.98 - 3.79: 35581 3.79 - 4.60: 56744 Warning: very small nonbonded interaction distances. Nonbonded interactions: 113911 Sorted by model distance: nonbonded pdb=" HE1 PHE B 198 " pdb=" HB2 CYS B 206 " model vdw 0.547 2.270 nonbonded pdb=" HZ PHE B 198 " pdb=" SG CYS B 206 " model vdw 0.669 2.850 nonbonded pdb=" CE1 PHE B 198 " pdb=" HB2 CYS B 206 " model vdw 0.810 2.970 nonbonded pdb=" HA CYS B 195 " pdb=" HE2 PHE B 198 " model vdw 0.883 2.270 nonbonded pdb=" CE1 PHE B 198 " pdb=" CB CYS B 206 " model vdw 1.146 3.450 ... (remaining 113906 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 26 15.96 2 O 742 7.97 1 N 678 6.97 1 C 2473 5.97 2 H 3898 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: 3898 of 7817 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7817 n_use_u_iso = 7817 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 = 7817 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7817 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7817 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 77 through 86 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 89 through 92 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 95 through 101 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 109 through 111 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 120 through 126 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 135 through 145 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 152 through 154 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 167 through 173 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 177 through 186 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 213 through 219 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 223 through 231 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 249 through 256 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 261 through 281 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 287 through 289 helix_type = alpha pi *3_10 unknown } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 298 through 304 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'A' and resid 308 through 318 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'B' and resid 77 through 85 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'B' and resid 89 through 92 helix_type = alpha pi *3_10 unknown } helix { serial_number = "19" helix_identifier = "19" selection = chain 'B' and resid 95 through 101 } helix { serial_number = "20" helix_identifier = "20" selection = chain 'B' and resid 109 through 111 helix_type = alpha pi *3_10 unknown } helix { serial_number = "21" helix_identifier = "21" selection = chain 'B' and resid 120 through 126 } helix { serial_number = "22" helix_identifier = "22" selection = chain 'B' and resid 135 through 145 } helix { serial_number = "23" helix_identifier = "23" selection = chain 'B' and resid 152 through 154 helix_type = alpha pi *3_10 unknown } helix { serial_number = "24" helix_identifier = "24" selection = chain 'B' and resid 167 through 173 } helix { serial_number = "25" helix_identifier = "25" selection = chain 'B' and resid 177 through 186 } helix { serial_number = "26" helix_identifier = "26" selection = chain 'B' and resid 213 through 218 } helix { serial_number = "27" helix_identifier = "27" selection = chain 'B' and resid 223 through 231 } helix { serial_number = "28" helix_identifier = "28" selection = chain 'B' and resid 249 through 256 } helix { serial_number = "29" helix_identifier = "29" selection = chain 'B' and resid 261 through 281 } helix { serial_number = "30" helix_identifier = "30" selection = chain 'B' and resid 287 through 289 helix_type = alpha pi *3_10 unknown } helix { serial_number = "31" helix_identifier = "31" selection = chain 'B' and resid 298 through 304 } helix { serial_number = "32" helix_identifier = "32" selection = chain 'B' and resid 308 through 318 } sheet { first_strand = chain 'B' and resid 156 through 158 sheet_id = " A" strand { selection = chain 'B' and resid 163 through 166 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 165 and name N bond_start_previous = chain 'B' and resid 157 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2etc_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3898 occupancy sum: 3898.00 (% of total atoms 49.98) Rotatable: count: 1095 occupancy sum: 1095.00 (% of total atoms 14.04) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 47.93 A, n_refl.=11944 (all), 9.83 % free)------------| | | | r_work= 0.4152 r_free= 0.4183 coordinate error (max.-lik. estimate): 0.21 A | | | | normalized target function (ml) (work): 5.788779 | | target function (ml) not normalized (work): 62345.151786 | | target function (ml) not normalized (free): 6853.282930 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.93 - 6.20 0.99 1452 152 0.4913 0.4827 6.5785 6.4828| | 2: 6.20 - 4.92 1.00 1344 159 0.3477 0.4135 5.9528 6.0241| | 3: 4.92 - 4.30 1.00 1358 142 0.3410 0.3231 5.9315 6.0023| | 4: 4.30 - 3.91 1.00 1323 158 0.4012 0.3773 5.8529 5.8753| | 5: 3.91 - 3.63 1.00 1336 129 0.4251 0.4218 5.6811 5.7238| | 6: 3.63 - 3.41 1.00 1340 144 0.4436 0.4587 5.556 5.6799| | 7: 3.41 - 3.24 1.00 1296 151 0.4236 0.4325 5.3674 5.3844| | 8: 3.24 - 3.10 0.99 1321 139 0.4326 0.4646 5.3014 5.4684| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 47.93 - 6.20 1452 152 0.54 46.98 0.74 0.28 68465.19| | 2: 6.20 - 4.92 1344 159 0.57 45.88 0.99 0.36 38528.75| | 3: 4.92 - 4.30 1358 142 0.75 30.74 1.25 0.45 21394.54| | 4: 4.30 - 3.91 1323 158 0.76 29.99 1.45 0.54 18158.20| | 5: 3.91 - 3.63 1336 129 0.77 28.93 1.53 0.59 14688.26| | 6: 3.63 - 3.41 1340 144 0.74 32.09 1.56 0.59 12264.07| | 7: 3.41 - 3.24 1296 151 0.70 35.03 1.56 0.58 10484.99| | 8: 3.24 - 3.10 1321 139 0.63 41.21 1.49 0.56 9962.42| |alpha: min = 0.28 max = 0.59 mean = 0.49| |beta: min = 9962.42 max = 68465.19 mean = 24798.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.91 mean = 36.47| |phase err.(test): min = 0.00 max = 89.94 mean = 35.09| |-----------------------------------------------------------------------------| ----------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 : 0.007 0.148 3995 Z= 0.481 Angle : 1.418 23.826 5414 Z= 0.895 Chirality : 0.079 0.583 614 Planarity : 0.004 0.093 707 Dihedral : 17.234 89.351 1485 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 3.85 % Favored : 95.55 % Rotamer: Outliers : 6.71 % Allowed : 6.71 % Favored : 86.57 % Cbeta Deviations : 1.28 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.31), residues: 494 helix: -2.07 (0.24), residues: 294 sheet: None (None), residues: 0 loop : -1.46 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 197 TYR 0.011 0.002 TYR A 208 PHE 0.010 0.001 PHE A 199 TRP 0.011 0.002 TRP A 223 HIS 0.004 0.001 HIS A 251 Individual atomic B min max mean iso aniso Overall: 30.90 56.89 40.89 0.26 3919 0 Protein: 30.90 56.89 40.89 0.26 3919 0 Chain A: 30.90 56.89 41.00 N/A 1976 0 Chain B: 31.34 56.45 40.78 N/A 1943 0 Histogram: Values Number of atoms 30.90 - 33.50 134 33.50 - 36.10 780 36.10 - 38.70 556 38.70 - 41.30 642 41.30 - 43.90 680 43.90 - 46.49 563 46.49 - 49.09 322 49.09 - 51.69 135 51.69 - 54.29 47 54.29 - 56.89 60 |-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: 3.10 - 47.93 A, n_refl.=11944 (all), 9.83 % free)------------| | | | r_work= 0.4152 r_free= 0.4183 coordinate error (max.-lik. estimate): 0.21 A | | | | normalized target function (ml) (work): 5.788779 | | target function (ml) not normalized (work): 62345.151786 | | target function (ml) not normalized (free): 6853.282930 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4155 0.4152 0.4183 n_refl.: 11944 re-set all scales: r(all,work,free)=0.4155 0.4152 0.4183 n_refl.: 11944 remove outliers: r(all,work,free)=0.4126 0.4124 0.4147 n_refl.: 11936 overall B=0.00 to atoms: r(all,work,free)=0.4126 0.4124 0.4147 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2404 0.2372 0.2694 n_refl.: 11936 remove outliers: r(all,work,free)=0.2404 0.2372 0.2694 n_refl.: 11936 ======================== 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 29.785-15.677 93.20 83 13 0.2885 774.675 701.593 1.443 1.027 0.390 15.606-12.533 99.01 92 8 0.1861 938.923 899.555 1.293 1.026 0.390 12.531-10.071 98.91 168 14 0.1665 1002.975 989.849 1.245 1.024 0.396 10.061-8.090 99.71 322 26 0.1634 985.933 979.849 1.231 1.019 0.403 8.076-6.488 100.00 590 71 0.2035 685.107 665.424 1.107 1.014 0.406 6.485-5.210 100.00 1131 128 0.2405 512.261 488.859 0.945 1.007 0.401 5.208-4.183 99.96 2124 230 0.2130 613.771 592.712 0.969 0.997 0.390 4.182-3.358 99.96 4019 440 0.2555 488.218 465.924 1.056 0.981 0.188 3.358-3.102 99.68 2234 243 0.2976 325.233 300.282 1.021 0.965 0.120 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.9374 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.416083 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.301282 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 0.2476 0.2737 0.0261 0.002 0.5 2.2 0.8 5.3 0 0.125 0.2422 0.2721 0.0300 0.002 0.5 2.3 0.8 5.3 0 0.250 0.2360 0.2710 0.0350 0.003 0.6 2.0 1.0 5.6 0 0.500 0.2280 0.2704 0.0424 0.004 0.6 2.7 1.2 6.2 0 1.000 0.2200 0.2725 0.0525 0.005 0.7 3.7 1.0 6.7 0 2.000 0.2159 0.2715 0.0556 0.007 0.8 3.8 1.0 7.4 0 3.000 0.2121 0.2721 0.0600 0.009 0.9 4.4 1.0 7.9 0 4.000 0.2093 0.2718 0.0624 0.010 1.0 5.3 1.0 7.9 0 5.000 0.2069 0.2725 0.0656 0.012 1.1 6.4 1.0 9.0 0 6.000 0.2055 0.2733 0.0677 0.013 1.2 6.5 1.2 9.3 0 7.000 0.2037 0.2741 0.0704 0.014 1.2 7.9 1.4 10.4 0 8.000 0.2026 0.2738 0.0712 0.015 1.3 8.6 1.4 11.1 0 9.000 0.2012 0.2751 0.0739 0.017 1.4 8.8 1.6 11.3 0 10.000 0.2050 0.2741 0.0692 0.013 1.2 6.7 1.2 9.3 0 7.208 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2476 0.2737 0.0261 0.002 0.5 2.2 0.8 5.3 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.76 27.37 2.61 0.184 40.818 0.301 0.068 24.52 27.25 2.72 1.115 40.854 0.009 0.067 24.05 27.11 3.06 1.319 40.848 0.038 0.064 22.31 26.35 4.04 4.682 41.146 0.151 0.056 21.77 26.22 4.45 6.378 41.543 0.301 0.053 21.34 26.08 4.73 7.884 42.028 0.452 0.051 21.16 26.07 4.91 8.700 42.265 0.603 0.050 20.98 26.05 5.07 9.598 42.550 0.753 0.049 20.89 26.06 5.17 10.120 42.702 0.904 0.049 20.82 26.06 5.24 10.533 42.821 1.054 0.049 20.50 26.04 5.54 12.588 43.503 1.205 0.047 20.43 26.07 5.63 13.099 43.656 1.356 0.047 20.37 26.09 5.72 13.705 43.840 1.506 0.047 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.205 Accepted refinement result: 20.50 26.04 5.54 12.588 43.503 1.205 0.047 Individual atomic B min max mean iso aniso Overall: 25.90 109.39 46.25 11.91 3919 0 Protein: 25.90 109.39 46.25 11.91 3919 0 Chain A: 25.90 104.12 46.62 N/A 1976 0 Chain B: 26.34 109.39 45.86 N/A 1943 0 Histogram: Values Number of atoms 25.90 - 34.25 775 34.25 - 42.60 1196 42.60 - 50.95 773 50.95 - 59.30 503 59.30 - 67.65 292 67.65 - 76.00 198 76.00 - 84.35 102 84.35 - 92.70 60 92.70 - 101.05 17 101.05 - 109.39 3 =========================== Idealize ADP of riding H ========================== r_work=0.2050 r_free=0.2604 r_work=0.2028 r_free=0.2604 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.2028 r_free= 0.2604 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ls_wunit_k1) (work): 0.046228 | | target function (ls_wunit_k1) not normalized (work): 497.550805 | | target function (ls_wunit_k1) not normalized (free): 91.860618 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2086 0.2028 0.2604 n_refl.: 11936 re-set all scales: r(all,work,free)=0.4031 0.4022 0.4111 n_refl.: 11936 remove outliers: r(all,work,free)=0.4031 0.4022 0.4111 n_refl.: 11936 overall B=0.03 to atoms: r(all,work,free)=0.4032 0.4023 0.4112 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2083 0.2023 0.2612 n_refl.: 11936 remove outliers: r(all,work,free)=0.2083 0.2023 0.2612 n_refl.: 11936 ======================== 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 29.785-15.677 93.20 83 13 0.3232 497.322 470.475 1.394 1.018 0.387 15.606-12.533 99.01 92 8 0.1933 602.765 537.453 1.129 1.017 0.385 12.531-10.071 98.91 168 14 0.1750 643.885 647.350 1.205 1.016 0.388 10.061-8.090 99.71 322 26 0.1550 632.945 643.143 1.182 1.012 0.395 8.076-6.488 100.00 590 71 0.1794 439.822 436.218 1.087 1.008 0.400 6.485-5.210 100.00 1131 128 0.2104 328.859 319.451 0.940 1.003 0.400 5.208-4.183 99.96 2124 230 0.1754 394.026 386.416 0.957 0.996 0.360 4.182-3.358 99.96 4019 440 0.2089 313.424 303.020 1.066 0.986 0.133 3.358-3.102 99.68 2234 243 0.2541 208.791 195.012 1.030 0.975 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0383 ============================ 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 = 3.941489 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.064517 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 0.1948 0.2606 0.0658 0.002 0.5 2.6 1.2 4.9 0 0.125 0.1899 0.2580 0.0682 0.003 0.5 2.2 1.0 5.3 0 0.250 0.1860 0.2588 0.0728 0.005 0.6 2.4 0.8 6.2 0 0.500 0.1823 0.2600 0.0777 0.008 0.8 3.5 0.8 6.9 0 1.000 0.1793 0.2591 0.0798 0.014 1.2 4.9 0.8 6.2 0 2.000 0.1775 0.2594 0.0819 0.019 1.4 4.9 0.8 6.0 0 3.000 0.1746 0.2660 0.0914 0.022 1.6 9.9 1.4 11.1 0 4.000 0.1733 0.2664 0.0931 0.025 1.8 11.7 1.8 12.0 0 5.000 0.1724 0.2670 0.0946 0.028 2.0 12.3 2.0 13.7 0 6.000 0.1712 0.2665 0.0954 0.031 2.2 13.2 2.0 14.6 0 7.000 0.1703 0.2673 0.0970 0.033 2.4 14.2 2.2 16.2 0 8.000 0.1696 0.2666 0.0970 0.036 2.5 14.6 2.4 15.0 0 9.000 0.1690 0.2675 0.0985 0.039 2.7 15.0 2.4 16.0 0 10.000 0.1788 0.2617 0.0829 0.013 1.1 7.3 0.8 8.6 0 1.971 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1899 0.2580 0.0682 0.003 0.5 2.2 1.0 5.3 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.99 25.80 6.82 10.851 50.845 0.065 5.817 21.95 26.10 4.15 8.601 54.607 0.002 5.860 21.17 25.64 4.48 8.665 53.648 0.008 5.840 19.55 25.08 5.53 9.807 51.417 0.032 5.802 18.98 25.17 6.18 10.527 50.731 0.065 5.791 18.78 25.22 6.45 11.048 50.663 0.097 5.788 18.67 25.27 6.60 11.468 50.718 0.129 5.787 18.60 25.34 6.74 11.784 50.779 0.161 5.786 18.55 25.38 6.82 12.053 50.846 0.194 5.786 18.52 25.39 6.88 12.337 50.945 0.226 5.786 18.49 25.43 6.94 12.540 51.005 0.258 5.786 18.47 25.47 7.00 12.720 51.059 0.290 5.787 18.45 25.49 7.04 12.866 51.103 0.323 5.787 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.032 Accepted refinement result: 19.55 25.08 5.53 9.807 51.417 0.032 5.802 Individual atomic B min max mean iso aniso Overall: 22.37 104.42 47.41 7.49 3919 0 Protein: 22.37 104.42 47.41 7.49 3919 0 Chain A: 23.22 99.14 47.86 N/A 1976 0 Chain B: 22.37 104.42 46.96 N/A 1943 0 Histogram: Values Number of atoms 22.37 - 30.57 268 30.57 - 38.78 918 38.78 - 46.98 966 46.98 - 55.19 796 55.19 - 63.39 463 63.39 - 71.60 260 71.60 - 79.80 145 79.80 - 88.01 76 88.01 - 96.21 24 96.21 - 104.42 3 =========================== Idealize ADP of riding H ========================== r_work=0.1955 r_free=0.2508 r_work=0.1974 r_free=0.2507 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.1974 r_free= 0.2507 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 5.804846 | | target function (ml) not normalized (work): 62477.557455 | | target function (ml) not normalized (free): 7018.958852 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2028 0.1974 0.2507 n_refl.: 11936 re-set all scales: r(all,work,free)=0.4062 0.4053 0.4148 n_refl.: 11936 remove outliers: r(all,work,free)=0.4062 0.4053 0.4148 n_refl.: 11936 overall B=-3.07 to atoms: r(all,work,free)=0.3929 0.3919 0.4024 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2011 0.1957 0.2486 n_refl.: 11936 remove outliers: r(all,work,free)=0.2011 0.1957 0.2486 n_refl.: 11936 ======================== 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 29.785-15.677 93.20 83 13 0.3050 497.322 467.817 1.278 1.076 0.385 15.606-12.533 99.01 92 8 0.1787 602.765 590.685 1.138 1.072 0.381 12.531-10.071 98.91 168 14 0.1674 643.885 633.847 1.099 1.067 0.382 10.061-8.090 99.71 322 26 0.1542 632.945 634.514 1.100 1.056 0.384 8.076-6.488 100.00 590 71 0.1763 439.822 431.854 1.017 1.042 0.386 6.485-5.210 100.00 1131 128 0.2101 328.859 317.153 0.896 1.021 0.379 5.208-4.183 99.96 2124 230 0.1653 394.026 383.951 0.942 0.990 0.332 4.182-3.358 99.96 4019 440 0.2009 313.424 301.431 1.088 0.942 0.129 3.358-3.102 99.68 2234 243 0.2520 208.791 193.460 1.083 0.898 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.6429 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1957 r_free=0.2486 After: r_work=0.1957 r_free=0.2486 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.748106 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.063744 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 0.1959 0.2490 0.0531 0.003 0.5 2.6 1.2 5.3 0 0.125 0.1955 0.2487 0.0532 0.003 0.5 2.6 1.2 5.3 0 0.250 0.1930 0.2490 0.0561 0.005 0.6 2.9 1.2 5.3 0 0.500 0.1841 0.2501 0.0660 0.012 1.1 5.3 1.0 6.0 0 1.000 0.1773 0.2538 0.0766 0.015 1.6 10.2 1.0 6.9 0 2.000 0.1752 0.2545 0.0792 0.018 1.8 12.9 0.8 8.6 0 3.000 0.1729 0.2561 0.0832 0.021 2.2 12.4 1.2 7.6 0 4.000 0.1703 0.2572 0.0869 0.026 2.5 14.0 1.2 8.3 0 5.000 0.1689 0.2589 0.0899 0.029 2.8 15.8 1.2 8.8 0 6.000 0.1699 0.2588 0.0889 0.028 2.7 20.1 2.0 13.2 0 7.000 0.1670 0.2585 0.0915 0.036 3.2 15.6 1.2 8.3 0 8.000 0.1670 0.2616 0.0945 0.035 3.2 22.9 2.6 15.5 1 9.000 0.1666 0.2573 0.0907 0.040 3.3 15.4 1.0 7.6 0 10.000 0.1778 0.2535 0.0756 0.014 1.6 10.4 0.8 6.9 0 1.874 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1955 0.2487 0.0532 0.003 0.5 2.6 1.2 5.3 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.55 24.87 5.32 8.717 48.952 0.064 5.801 22.43 26.17 3.74 7.783 52.388 0.002 5.878 21.55 25.64 4.09 7.805 51.097 0.008 5.857 19.57 24.77 5.20 8.522 48.850 0.032 5.798 19.26 24.81 5.55 8.947 48.796 0.064 5.791 19.04 24.81 5.77 9.365 48.729 0.096 5.786 18.58 24.81 6.23 10.558 48.872 0.127 5.775 18.50 24.85 6.35 10.842 48.989 0.159 5.774 18.45 24.90 6.45 11.082 49.092 0.191 5.774 18.42 24.94 6.52 11.288 49.177 0.223 5.774 18.39 24.97 6.58 11.470 49.253 0.255 5.774 18.36 25.00 6.64 11.630 49.319 0.287 5.774 18.34 25.02 6.68 11.773 49.376 0.319 5.774 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.032 Accepted refinement result: 19.57 24.77 5.20 8.522 48.850 0.032 5.798 Individual atomic B min max mean iso aniso Overall: 18.73 98.23 44.14 6.28 3919 0 Protein: 18.73 98.23 44.14 6.28 3919 0 Chain A: 21.20 95.47 44.61 N/A 1976 0 Chain B: 18.73 98.23 43.66 N/A 1943 0 Histogram: Values Number of atoms 18.73 - 26.68 144 26.68 - 34.63 905 34.63 - 42.58 995 42.58 - 50.53 845 50.53 - 58.48 488 58.48 - 66.43 263 66.43 - 74.38 144 74.38 - 82.33 98 82.33 - 90.28 29 90.28 - 98.23 8 =========================== Idealize ADP of riding H ========================== r_work=0.1957 r_free=0.2477 r_work=0.1958 r_free=0.2475 ----------X-ray data---------- |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.1958 r_free= 0.2475 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.798089 | | target function (ml) not normalized (work): 62404.832343 | | target function (ml) not normalized (free): 7009.212336 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.79 - 6.19 0.99 1454 152 0.1827 0.2236 6.1563 6.2828| | 2: 6.19 - 4.92 1.00 1344 158 0.1980 0.2396 5.8431 5.956| | 3: 4.92 - 4.30 1.00 1355 145 0.1606 0.2025 5.816 6.0106| | 4: 4.30 - 3.91 1.00 1321 156 0.1779 0.2276 5.8416 6.0354| | 5: 3.91 - 3.63 1.00 1335 128 0.1980 0.2502 5.8068 6.0079| | 6: 3.63 - 3.41 1.00 1341 144 0.2176 0.3060 5.7218 6.0198| | 7: 3.41 - 3.24 1.00 1293 151 0.2345 0.2911 5.6211 5.6983| | 8: 3.24 - 3.10 0.99 1320 139 0.2571 0.3193 5.5378 5.7829| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.79 - 6.19 1454 152 0.84 20.67 0.99 0.93 32632.20| | 2: 6.19 - 4.92 1344 158 0.80 25.02 1.00 0.95 24752.92| | 3: 4.92 - 4.30 1355 145 0.86 19.45 0.99 0.97 21227.39| | 4: 4.30 - 3.91 1321 156 0.84 21.75 1.03 0.98 22164.01| | 5: 3.91 - 3.63 1335 128 0.84 22.65 1.02 0.97 21928.62| | 6: 3.63 - 3.41 1341 144 0.80 26.45 0.97 0.93 20389.25| | 7: 3.41 - 3.24 1293 151 0.75 30.81 1.01 0.91 18067.47| | 8: 3.24 - 3.10 1320 139 0.70 35.64 0.97 0.90 16948.70| |alpha: min = 0.90 max = 0.98 mean = 0.94| |beta: min = 16948.70 max = 32632.20 mean = 22401.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.95 mean = 25.21| |phase err.(test): min = 0.00 max = 89.70 mean = 23.67| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2010 0.1958 0.2475 n_refl.: 11936 re-set all scales: r(all,work,free)=0.3935 0.3925 0.4024 n_refl.: 11936 remove outliers: r(all,work,free)=0.3935 0.3925 0.4024 n_refl.: 11936 overall B=0.22 to atoms: r(all,work,free)=0.3945 0.3935 0.4033 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2010 0.1958 0.2473 n_refl.: 11936 remove outliers: r(all,work,free)=0.2010 0.1958 0.2473 n_refl.: 11936 ======================== 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 29.785-15.677 93.20 83 13 0.3055 497.322 466.774 1.271 1.088 0.384 15.606-12.533 99.01 92 8 0.1789 602.765 590.634 1.133 1.084 0.380 12.531-10.071 98.91 168 14 0.1679 643.885 633.629 1.093 1.077 0.379 10.061-8.090 99.71 322 26 0.1549 632.945 634.316 1.096 1.066 0.380 8.076-6.488 100.00 590 71 0.1767 439.822 431.829 1.015 1.049 0.380 6.485-5.210 100.00 1131 128 0.2100 328.859 317.086 0.904 1.026 0.379 5.208-4.183 99.96 2124 230 0.1657 394.026 383.965 0.955 0.990 0.329 4.182-3.358 99.96 4019 440 0.2011 313.424 301.526 1.116 0.935 0.122 3.358-3.102 99.68 2234 243 0.2506 208.791 193.620 1.121 0.885 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0857 ================= 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 : 0.4152 0.4183 0.007 1.418 30.9 56.9 40.9 0 0.000 1_bss: 0.2372 0.2694 0.007 1.418 30.9 56.9 40.9 0 0.000 1_settarget: 0.2372 0.2694 0.007 1.418 30.9 56.9 40.9 0 0.000 1_weight: 0.2372 0.2694 0.007 1.418 30.9 56.9 40.9 0 0.000 1_xyzrec: 0.2476 0.2737 0.002 0.545 30.9 56.9 40.9 0 0.165 1_adp: 0.2050 0.2604 0.002 0.545 25.9 109.4 46.2 0 0.165 1_regHadp: 0.2028 0.2604 0.002 0.545 25.9 109.4 46.2 0 0.165 2_bss: 0.2023 0.2612 0.002 0.545 25.9 109.4 46.3 0 0.165 2_settarget: 0.2023 0.2612 0.002 0.545 25.9 109.4 46.3 0 0.165 2_updatecdl: 0.2023 0.2612 0.003 0.587 25.9 109.4 46.3 0 0.165 2_weight: 0.2023 0.2612 0.003 0.587 25.9 109.4 46.3 0 0.165 2_xyzrec: 0.1899 0.2580 0.003 0.542 25.9 109.4 46.3 0 0.197 2_adp: 0.1955 0.2508 0.003 0.542 22.4 104.4 47.4 0 0.197 2_regHadp: 0.1974 0.2507 0.003 0.542 22.4 104.4 47.4 0 0.197 3_bss: 0.1957 0.2486 0.003 0.542 19.3 101.3 44.3 0 0.197 3_settarget: 0.1957 0.2486 0.003 0.542 19.3 101.3 44.3 0 0.197 3_updatecdl: 0.1957 0.2486 0.003 0.560 19.3 101.3 44.3 0 0.197 3_setrh: 0.1957 0.2486 0.003 0.560 19.3 101.3 44.3 0 0.197 3_weight: 0.1957 0.2486 0.003 0.560 19.3 101.3 44.3 0 0.197 3_xyzrec: 0.1955 0.2487 0.003 0.540 19.3 101.3 44.3 0 0.197 3_adp: 0.1957 0.2477 0.003 0.540 18.7 98.2 44.1 0 0.197 3_regHadp: 0.1958 0.2475 0.003 0.540 18.7 98.2 44.1 0 0.197 end: 0.1958 0.2473 0.003 0.540 19.0 98.5 44.4 0 0.197 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2etc_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2etc_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 12.4500 Refinement macro-cycles (run) : 309.1700 Write final files (write_after_run_outputs) : 16.9600 Total : 338.5800 Total CPU time: 6.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:32 PDT -0700 (1716251732.09 s) Start R-work = 0.2372, R-free = 0.2694 Final R-work = 0.1958, R-free = 0.2473 =============================================================================== Job complete usr+sys time: 404.21 seconds wall clock time: 18 minutes 19.03 seconds (1099.03 seconds total)