Starting phenix.refine on Mon May 20 17:15:26 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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True 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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { 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: 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: 1.46, per 1000 atoms: 0.19 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: 1.95 Conformation dependent library (CDL) restraints added in 260.8 milliseconds 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. 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: 0.56 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: 1.69 Time building geometry restraints manager: 2.23 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2372 r_free=0.2694 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2372 r_free=0.2694 ========================= Local real-space refinement ========================= Before: r_work=0.2372 r_free=0.2694 137 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.323 revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 29 average time/residue: 0.3814 time to fit residues: 13.6483 After: r_work=0.2422 r_free=0.2712 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.762342 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.299684 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 0.2499 0.2732 0.0233 0.003 0.6 2.3 0.0 2.1 0 0.125 0.2452 0.2718 0.0266 0.003 0.6 2.6 0.0 2.1 0 0.250 0.2388 0.2698 0.0309 0.003 0.6 2.4 0.0 2.3 0 0.500 0.2308 0.2685 0.0376 0.004 0.6 2.2 0.0 2.8 0 1.000 0.2229 0.2708 0.0480 0.006 0.7 2.8 0.0 3.7 0 2.000 0.2182 0.2717 0.0535 0.007 0.8 3.6 0.2 3.9 0 3.000 0.2143 0.2715 0.0572 0.009 0.9 4.1 0.2 4.4 0 4.000 0.2115 0.2739 0.0623 0.010 1.0 5.3 0.4 6.0 0 5.000 0.2097 0.2742 0.0645 0.012 1.1 6.3 0.4 6.9 0 6.000 0.2077 0.2743 0.0666 0.013 1.2 6.9 0.4 6.9 0 7.000 0.2056 0.2760 0.0704 0.014 1.3 7.3 0.6 7.9 0 8.000 0.2044 0.2772 0.0728 0.015 1.3 8.5 0.8 8.6 0 9.000 0.2030 0.2774 0.0744 0.017 1.4 9.2 0.8 9.3 0 10.000 0.2068 0.2758 0.0691 0.014 1.2 6.8 0.4 7.6 0 7.381 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2499 0.2732 0.0233 0.003 0.6 2.3 0.0 2.1 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2499 r_free=0.2732 118 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.488 revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2874 time to fit residues: 5.5227 After: r_work=0.2528 r_free=0.2755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.28 27.55 2.27 0.184 40.818 0.300 0.071 25.04 27.47 2.43 1.122 40.850 0.009 0.070 24.56 27.36 2.79 1.323 40.839 0.037 0.067 22.81 26.89 4.09 4.764 41.119 0.150 0.058 22.14 26.81 4.67 6.852 41.696 0.300 0.055 21.84 26.85 5.00 8.049 42.044 0.450 0.053 21.58 26.87 5.29 9.199 42.417 0.599 0.052 21.42 26.89 5.48 10.016 42.671 0.749 0.051 21.36 26.91 5.55 10.392 42.769 0.899 0.051 21.06 26.92 5.86 12.056 43.332 1.049 0.050 20.91 26.97 6.06 13.162 43.676 1.199 0.049 20.84 26.99 6.15 13.719 43.844 1.349 0.049 20.81 27.02 6.22 14.095 43.950 1.498 0.049 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.300 Accepted refinement result: 22.14 26.81 4.67 6.852 41.696 0.300 0.055 Individual atomic B min max mean iso aniso Overall: 25.90 89.99 42.64 6.45 3919 0 Protein: 25.90 89.99 42.64 6.45 3919 0 Chain A: 25.90 78.95 43.02 N/A 1976 0 Chain B: 26.34 89.99 42.25 N/A 1943 0 Histogram: Values Number of atoms 25.90 - 32.31 514 32.31 - 38.72 1029 38.72 - 45.13 1018 45.13 - 51.54 680 51.54 - 57.94 367 57.94 - 64.35 170 64.35 - 70.76 105 70.76 - 77.17 28 77.17 - 83.58 4 83.58 - 89.99 4 =========================== Idealize ADP of riding H ========================== r_work=0.2214 r_free=0.2681 r_work=0.2187 r_free=0.2678 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.2187 r_free= 0.2678 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ls_wunit_k1) (work): 0.053555 | | target function (ls_wunit_k1) not normalized (work): 576.413510 | | target function (ls_wunit_k1) not normalized (free): 96.217064 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2237 0.2187 0.2678 n_refl.: 11936 re-set all scales: r(all,work,free)=0.4035 0.4024 0.4129 n_refl.: 11936 remove outliers: r(all,work,free)=0.4035 0.4024 0.4129 n_refl.: 11936 overall B=0.80 to atoms: r(all,work,free)=0.4067 0.4056 0.4160 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2226 0.2177 0.2664 n_refl.: 11936 remove outliers: r(all,work,free)=0.2226 0.2177 0.2664 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 0.3317 513.271 476.776 1.266 1.078 0.387 15.606-12.533 99.01 92 8 0.2007 622.096 616.900 1.168 1.075 0.385 12.531-10.071 98.91 168 14 0.1904 664.535 654.146 1.118 1.070 0.388 10.061-8.090 99.71 322 26 0.1659 653.243 656.966 1.107 1.059 0.390 8.076-6.488 100.00 590 71 0.2018 453.927 444.825 1.018 1.045 0.390 6.485-5.210 100.00 1131 128 0.2282 339.406 328.231 0.905 1.023 0.389 5.208-4.183 99.96 2124 230 0.1945 406.662 394.669 0.952 0.991 0.366 4.182-3.358 99.96 4019 440 0.2217 323.475 311.379 1.100 0.941 0.156 3.358-3.102 99.68 2234 243 0.2691 215.487 201.071 1.110 0.895 0.108 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.3105 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2177 r_free=0.2664 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 259 ASN B 127 ASN B 222 GLN Total number of N/Q/H flips: 4 r_work=0.2180 r_free=0.2670 ========================= Local real-space refinement ========================= Before: r_work=0.2180 r_free=0.2670 114 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.840 outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.5284 time to fit residues: 4.5353 After: r_work=0.2180 r_free=0.2665 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.675665 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.069068 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 0.2084 0.2606 0.0522 0.002 0.5 1.9 0.0 0.9 0 0.125 0.2026 0.2593 0.0567 0.003 0.6 2.3 0.0 1.4 0 0.250 0.1965 0.2580 0.0615 0.006 0.7 2.6 0.0 1.9 0 0.500 0.1908 0.2608 0.0700 0.009 0.8 4.4 0.0 4.2 0 1.000 0.1860 0.2636 0.0776 0.014 1.2 6.0 0.0 5.6 0 2.000 0.1829 0.2661 0.0832 0.019 1.4 9.7 0.6 7.6 0 3.000 0.1804 0.2676 0.0872 0.023 1.7 11.1 0.8 10.2 0 4.000 0.1787 0.2676 0.0889 0.027 1.9 12.2 0.8 11.1 0 5.000 0.1772 0.2678 0.0906 0.030 2.1 13.3 0.8 12.7 0 6.000 0.1760 0.2692 0.0932 0.034 2.3 14.0 0.8 14.1 0 7.000 0.1752 0.2692 0.0940 0.036 2.5 15.1 1.0 15.0 0 8.000 0.1742 0.2690 0.0947 0.039 2.6 15.2 1.0 14.8 0 9.000 0.1736 0.2701 0.0965 0.042 2.8 15.6 1.0 15.0 0 10.000 0.1864 0.2639 0.0775 0.014 1.1 6.1 0.0 5.6 0 1.838 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2084 0.2606 0.0522 0.002 0.5 1.9 0.0 0.9 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2084 r_free=0.2606 117 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.532 revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3342 time to fit residues: 3.5337 After: r_work=0.2095 r_free=0.2624 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.95 26.24 5.28 7.644 47.595 0.069 5.900 23.46 26.80 3.35 5.765 51.392 0.002 5.947 22.34 25.65 3.31 6.978 49.302 0.009 5.913 20.82 25.81 4.99 7.590 47.439 0.035 5.884 20.18 25.34 5.16 8.775 47.599 0.069 5.856 19.91 25.38 5.47 9.404 47.830 0.104 5.850 19.76 25.43 5.68 9.915 48.032 0.138 5.847 19.66 25.47 5.81 10.371 48.215 0.173 5.845 19.58 25.49 5.91 10.782 48.371 0.207 5.844 19.55 25.53 5.98 11.020 48.448 0.242 5.844 19.51 25.56 6.05 11.318 48.555 0.276 5.843 19.49 25.59 6.10 11.516 48.620 0.311 5.843 19.46 25.61 6.14 11.724 48.691 0.345 5.843 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.069 Accepted refinement result: 20.18 25.34 5.16 8.775 47.599 0.069 5.856 Individual atomic B min max mean iso aniso Overall: 21.70 95.73 43.45 7.69 3919 0 Protein: 21.70 95.73 43.45 7.69 3919 0 Chain A: 21.70 89.84 43.91 N/A 1976 0 Chain B: 22.14 95.73 42.99 N/A 1943 0 Histogram: Values Number of atoms 21.70 - 29.11 372 29.11 - 36.51 946 36.51 - 43.91 975 43.91 - 51.31 730 51.31 - 58.72 424 58.72 - 66.12 235 66.12 - 73.52 128 73.52 - 80.92 64 80.92 - 88.32 38 88.32 - 95.73 7 =========================== Idealize ADP of riding H ========================== r_work=0.2018 r_free=0.2534 r_work=0.2017 r_free=0.2527 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.2017 r_free= 0.2527 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.853933 | | target function (ml) not normalized (work): 63005.877135 | | target function (ml) not normalized (free): 7073.885701 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2070 0.2017 0.2527 n_refl.: 11936 re-set all scales: r(all,work,free)=0.3954 0.3945 0.4034 n_refl.: 11936 remove outliers: r(all,work,free)=0.3954 0.3945 0.4034 n_refl.: 11936 overall B=0.39 to atoms: r(all,work,free)=0.3970 0.3962 0.4050 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2069 0.2016 0.2524 n_refl.: 11936 remove outliers: r(all,work,free)=0.2069 0.2016 0.2524 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 0.3194 513.271 475.041 1.248 1.091 0.387 15.606-12.533 99.01 92 8 0.1893 622.096 614.794 1.155 1.088 0.383 12.531-10.071 98.91 168 14 0.1819 664.535 652.070 1.095 1.082 0.382 10.061-8.090 99.71 322 26 0.1590 653.243 654.038 1.087 1.070 0.386 8.076-6.488 100.00 590 71 0.1861 453.927 444.049 1.006 1.054 0.387 6.485-5.210 100.00 1131 128 0.2216 339.406 326.607 0.902 1.029 0.386 5.208-4.183 99.96 2124 230 0.1740 406.662 394.575 0.951 0.992 0.348 4.182-3.358 99.96 4019 440 0.2038 323.475 310.777 1.116 0.934 0.137 3.358-3.102 99.68 2234 243 0.2511 215.487 199.342 1.123 0.882 0.089 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.1523 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2016 r_free=0.2524 After: r_work=0.2016 r_free=0.2524 ================================== NQH flips ================================== r_work=0.2016 r_free=0.2524 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 259 ASN B 235 GLN B 263 ASN B 276 GLN B 294 GLN Total number of N/Q/H flips: 6 r_work=0.2017 r_free=0.2520 ========================= Local real-space refinement ========================= Before: r_work=0.2017 r_free=0.2520 121 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.926 outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1980 time to fit residues: 1.6983 After: r_work=0.2017 r_free=0.2520 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.928062 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.065219 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 0.2014 0.2507 0.0493 0.005 0.6 2.8 0.0 0.5 0 0.125 0.2001 0.2506 0.0506 0.005 0.6 2.7 0.0 0.5 0 0.250 0.1960 0.2505 0.0545 0.008 0.7 2.8 0.0 0.5 0 0.500 0.1868 0.2496 0.0628 0.009 1.0 5.5 0.0 1.6 0 1.000 0.1810 0.2518 0.0708 0.013 1.4 7.4 0.0 1.9 0 2.000 0.1771 0.2541 0.0769 0.017 1.8 9.3 0.0 1.9 0 3.000 0.1772 0.2539 0.0767 0.020 1.7 11.1 0.0 3.9 0 4.000 0.1749 0.2573 0.0824 0.022 2.2 14.9 0.2 4.9 0 5.000 0.1720 0.2581 0.0861 0.029 2.5 15.4 0.2 5.6 0 6.000 0.1702 0.2597 0.0895 0.032 2.8 16.3 0.2 5.8 0 7.000 0.1693 0.2602 0.0909 0.033 3.0 16.5 0.2 6.7 0 8.000 0.1685 0.2624 0.0940 0.038 3.3 19.9 0.4 9.7 0 9.000 0.1678 0.2625 0.0947 0.038 3.4 20.1 0.4 8.8 0 10.000 0.1810 0.2517 0.0707 0.013 1.4 7.4 0.0 1.9 0 1.964 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2001 0.2506 0.0506 0.005 0.6 2.7 0.0 0.5 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2001 r_free=0.2506 119 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.680 revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2086 time to fit residues: 1.5391 After: r_work=0.2010 r_free=0.2521 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.10 25.21 5.11 8.352 48.043 0.065 5.853 23.31 26.38 3.07 7.425 52.372 0.002 5.935 22.25 25.35 3.10 7.412 50.247 0.008 5.908 20.43 24.94 4.51 8.010 47.787 0.033 5.857 19.97 25.15 5.18 8.458 47.926 0.065 5.848 19.81 25.20 5.39 8.789 47.845 0.098 5.845 19.30 25.12 5.82 9.769 47.913 0.130 5.833 19.14 25.17 6.03 10.291 48.045 0.163 5.830 18.91 25.26 6.35 11.336 48.343 0.196 5.827 18.85 25.33 6.48 11.750 48.489 0.228 5.827 18.73 25.50 6.77 12.910 48.960 0.261 5.828 18.70 25.56 6.85 13.315 49.110 0.293 5.829 18.68 25.61 6.93 13.680 49.242 0.326 5.829 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.033 Accepted refinement result: 20.43 24.94 4.51 8.010 47.787 0.033 5.857 Individual atomic B min max mean iso aniso Overall: 18.57 95.29 43.34 5.46 3919 0 Protein: 18.57 95.29 43.34 5.46 3919 0 Chain A: 21.17 90.50 43.85 N/A 1976 0 Chain B: 18.57 95.29 42.82 N/A 1943 0 Histogram: Values Number of atoms 18.57 - 26.24 89 26.24 - 33.91 844 33.91 - 41.58 1080 41.58 - 49.26 885 49.26 - 56.93 503 56.93 - 64.60 248 64.60 - 72.27 142 72.27 - 79.94 76 79.94 - 87.61 43 87.61 - 95.29 9 =========================== Idealize ADP of riding H ========================== r_work=0.2043 r_free=0.2494 r_work=0.2050 r_free=0.2494 ----------X-ray data---------- |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.2050 r_free= 0.2494 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 5.858767 | | target function (ml) not normalized (work): 63057.913394 | | target function (ml) not normalized (free): 7062.518123 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1916 0.2316 6.2317 6.3649| | 2: 6.19 - 4.92 1.00 1344 158 0.2097 0.2377 5.92 6.0087| | 3: 4.92 - 4.30 1.00 1355 145 0.1732 0.2119 5.8951 6.07| | 4: 4.30 - 3.91 1.00 1321 156 0.1881 0.2238 5.9005 6.0703| | 5: 3.91 - 3.63 1.00 1335 128 0.2025 0.2461 5.854 6.0451| | 6: 3.63 - 3.41 1.00 1341 144 0.2264 0.3023 5.7705 6.0426| | 7: 3.41 - 3.24 1.00 1293 151 0.2409 0.2981 5.6641 5.74| | 8: 3.24 - 3.10 0.99 1320 139 0.2661 0.3183 5.5917 5.8123| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.82 22.05 1.00 0.95 39179.14| | 2: 6.19 - 4.92 1344 158 0.79 26.06 1.01 0.96 28577.04| | 3: 4.92 - 4.30 1355 145 0.86 20.03 0.99 0.97 23430.05| | 4: 4.30 - 3.91 1321 156 0.84 21.77 1.03 0.99 23817.13| | 5: 3.91 - 3.63 1335 128 0.84 22.67 1.02 0.97 23343.46| | 6: 3.63 - 3.41 1341 144 0.80 26.45 0.97 0.94 21662.27| | 7: 3.41 - 3.24 1293 151 0.75 31.13 1.00 0.92 19431.98| | 8: 3.24 - 3.10 1320 139 0.70 35.47 0.96 0.91 18280.88| |alpha: min = 0.91 max = 0.99 mean = 0.95| |beta: min = 18280.88 max = 39179.14 mean = 24905.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.88 mean = 25.62| |phase err.(test): min = 0.00 max = 89.23 mean = 24.02| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2091 0.2046 0.2484 n_refl.: 11936 re-set all scales: r(all,work,free)=0.3961 0.3953 0.4032 n_refl.: 11936 remove outliers: r(all,work,free)=0.3961 0.3953 0.4032 n_refl.: 11936 overall B=0.42 to atoms: r(all,work,free)=0.3979 0.3971 0.4049 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2096 0.2051 0.2490 n_refl.: 11936 remove outliers: r(all,work,free)=0.2096 0.2051 0.2490 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 0.3183 513.271 475.063 1.282 1.068 0.387 15.606-12.533 99.01 92 8 0.1893 622.096 613.946 1.176 1.066 0.383 12.531-10.071 98.91 168 14 0.1804 664.535 654.022 1.115 1.062 0.382 10.061-8.090 99.71 322 26 0.1567 653.243 655.528 1.110 1.052 0.386 8.076-6.488 100.00 590 71 0.1862 453.927 444.468 1.021 1.039 0.387 6.485-5.210 100.00 1131 128 0.2219 339.406 326.977 0.910 1.021 0.385 5.208-4.183 99.96 2124 230 0.1770 406.662 394.570 0.950 0.993 0.348 4.182-3.358 99.96 4019 440 0.2096 323.475 310.549 1.098 0.949 0.137 3.358-3.102 99.68 2234 243 0.2577 215.487 199.110 1.086 0.909 0.089 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.1624 ================= 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_updatephipsi: 0.2372 0.2694 0.007 1.418 30.9 56.9 40.9 0 0.000 1_nqh: 0.2372 0.2694 0.007 1.418 30.9 56.9 40.9 0 0.000 1_realsrl: 0.2422 0.2712 0.007 1.418 30.9 56.9 40.9 0 0.034 1_weight: 0.2422 0.2712 0.007 1.418 30.9 56.9 40.9 0 0.034 1_xyzrec: 0.2499 0.2732 0.003 0.558 30.9 56.9 40.9 0 0.206 1_realsrl2: 0.2528 0.2755 0.003 0.558 30.9 56.9 40.9 0 0.214 1_adp: 0.2214 0.2681 0.003 0.558 25.9 90.0 42.6 0 0.214 1_regHadp: 0.2187 0.2678 0.003 0.558 25.9 90.0 42.6 0 0.214 2_bss: 0.2177 0.2664 0.003 0.558 26.7 90.8 43.4 0 0.214 2_settarget: 0.2177 0.2664 0.003 0.558 26.7 90.8 43.4 0 0.214 2_updatephipsi: 0.2177 0.2664 0.003 0.558 26.7 90.8 43.4 0 0.214 2_updatecdl: 0.2177 0.2664 0.003 0.580 26.7 90.8 43.4 0 0.214 2_nqh: 0.2180 0.2670 0.003 0.580 26.7 90.8 43.4 0 0.218 2_realsrl: 0.2180 0.2665 0.003 0.580 26.7 90.8 43.4 0 0.219 2_weight: 0.2180 0.2665 0.003 0.580 26.7 90.8 43.4 0 0.219 2_xyzrec: 0.2084 0.2606 0.002 0.501 26.7 90.8 43.4 0 0.245 2_realsrl2: 0.2095 0.2624 0.002 0.501 26.7 90.8 43.4 0 0.247 2_adp: 0.2018 0.2534 0.002 0.501 21.7 95.7 43.5 0 0.247 2_regHadp: 0.2017 0.2527 0.002 0.501 21.7 95.7 43.5 0 0.247 3_bss: 0.2016 0.2524 0.002 0.501 22.1 96.1 43.8 0 0.247 3_settarget: 0.2016 0.2524 0.002 0.501 22.1 96.1 43.8 0 0.247 3_updatephipsi: 0.2016 0.2524 0.002 0.501 22.1 96.1 43.8 0 0.247 3_updatecdl: 0.2016 0.2524 0.002 0.522 22.1 96.1 43.8 0 0.247 3_setrh: 0.2016 0.2524 0.002 0.522 22.1 96.1 43.8 0 0.247 3_nqh: 0.2017 0.2520 0.002 0.522 22.1 96.1 43.8 0 0.251 3_realsrl: 0.2017 0.2520 0.002 0.522 22.1 96.1 43.8 0 0.251 3_weight: 0.2017 0.2520 0.002 0.522 22.1 96.1 43.8 0 0.251 3_xyzrec: 0.2001 0.2506 0.005 0.566 22.1 96.1 43.8 0 0.252 3_realsrl2: 0.2010 0.2521 0.005 0.566 22.1 96.1 43.8 0 0.252 3_adp: 0.2043 0.2494 0.005 0.566 18.6 95.3 43.3 0 0.252 3_regHadp: 0.2050 0.2494 0.005 0.566 18.6 95.3 43.3 0 0.252 end: 0.2051 0.2490 0.005 0.566 19.0 95.7 43.8 0 0.252 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2etc_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2etc_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.0500 Refinement macro-cycles (run) : 409.3700 Write final files (write_after_run_outputs) : 24.3400 Total : 439.7600 Total CPU time: 7.77 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:11 PDT -0700 (1716251711.75 s) Start R-work = 0.2372, R-free = 0.2694 Final R-work = 0.2051, R-free = 0.2490 =============================================================================== Job complete usr+sys time: 486.69 seconds wall clock time: 20 minutes 7.55 seconds (1207.55 seconds total)