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/2jcl.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2jcl/2jcl.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2jcl/2jcl.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2jcl/2jcl.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2jcl.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2jcl.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 9180 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4576 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 262} Chain: "B" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4579 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Unusual residues: {'SO4': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.07, per 1000 atoms: 0.33 Number of scatterers: 9180 At special positions: 0 Unit cell: (95.93, 103.26, 121.49, 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 29 16.00 O 832 8.00 N 756 7.00 C 3022 6.00 H 4541 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.69 Conformation dependent library (CDL) restraints added in 1.2 seconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 4 sheets defined 36.3% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1091 through 1093 No H-bonds generated for 'chain 'A' and resid 1091 through 1093' Processing helix chain 'A' and resid 1115 through 1125 Processing helix chain 'A' and resid 1137 through 1154 removed outlier: 3.629A pdb=" N HIS A1142 " --> pdb=" O TYR A1139 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A1144 " --> pdb=" O GLU A1141 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU A1145 " --> pdb=" O HIS A1142 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A1149 " --> pdb=" O GLU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1212 removed outlier: 4.123A pdb=" N MET A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1217 No H-bonds generated for 'chain 'A' and resid 1214 through 1217' Processing helix chain 'A' and resid 1236 through 1238 No H-bonds generated for 'chain 'A' and resid 1236 through 1238' Processing helix chain 'A' and resid 1255 through 1257 No H-bonds generated for 'chain 'A' and resid 1255 through 1257' Processing helix chain 'A' and resid 1288 through 1307 Processing helix chain 'A' and resid 1315 through 1326 removed outlier: 3.538A pdb=" N LEU A1320 " --> pdb=" O GLU A1317 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A1321 " --> pdb=" O SER A1318 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A1323 " --> pdb=" O LEU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1337 No H-bonds generated for 'chain 'A' and resid 1335 through 1337' Processing helix chain 'A' and resid 1341 through 1343 No H-bonds generated for 'chain 'A' and resid 1341 through 1343' Processing helix chain 'B' and resid 2085 through 2087 No H-bonds generated for 'chain 'B' and resid 2085 through 2087' Processing helix chain 'B' and resid 2091 through 2093 No H-bonds generated for 'chain 'B' and resid 2091 through 2093' Processing helix chain 'B' and resid 2115 through 2125 Processing helix chain 'B' and resid 2137 through 2142 removed outlier: 3.898A pdb=" N HIS B2142 " --> pdb=" O TYR B2139 " (cutoff:3.500A) Processing helix chain 'B' and resid 2144 through 2154 removed outlier: 3.506A pdb=" N ASN B2152 " --> pdb=" O THR B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2170 through 2172 No H-bonds generated for 'chain 'B' and resid 2170 through 2172' Processing helix chain 'B' and resid 2191 through 2195 removed outlier: 3.592A pdb=" N TRP B2195 " --> pdb=" O GLU B2192 " (cutoff:3.500A) Processing helix chain 'B' and resid 2199 through 2212 removed outlier: 3.712A pdb=" N MET B2203 " --> pdb=" O SER B2199 " (cutoff:3.500A) Processing helix chain 'B' and resid 2214 through 2216 No H-bonds generated for 'chain 'B' and resid 2214 through 2216' Processing helix chain 'B' and resid 2236 through 2238 No H-bonds generated for 'chain 'B' and resid 2236 through 2238' Processing helix chain 'B' and resid 2248 through 2250 No H-bonds generated for 'chain 'B' and resid 2248 through 2250' Processing helix chain 'B' and resid 2255 through 2257 No H-bonds generated for 'chain 'B' and resid 2255 through 2257' Processing helix chain 'B' and resid 2288 through 2307 Processing helix chain 'B' and resid 2315 through 2326 removed outlier: 3.518A pdb=" N HIS B2319 " --> pdb=" O HIS B2315 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B2322 " --> pdb=" O SER B2318 " (cutoff:3.500A) Processing helix chain 'B' and resid 2335 through 2337 No H-bonds generated for 'chain 'B' and resid 2335 through 2337' Processing sheet with id= A, first strand: chain 'A' and resid 1106 through 1108 removed outlier: 3.717A pdb=" N GLN A1245 " --> pdb=" O ILE A1283 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A1283 " --> pdb=" O GLN A1245 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A1220 " --> pdb=" O THR A1128 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE A1134 " --> pdb=" O MET A1224 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU A1131 " --> pdb=" O PRO A1160 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A1162 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A1133 " --> pdb=" O ILE A1162 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR A1164 " --> pdb=" O VAL A1133 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA A1135 " --> pdb=" O TYR A1164 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N MET A1166 " --> pdb=" O ALA A1135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1228 through 1230 Processing sheet with id= C, first strand: chain 'B' and resid 2106 through 2108 Processing sheet with id= D, first strand: chain 'B' and resid 2283 through 2286 removed outlier: 4.211A pdb=" N PHE B2134 " --> pdb=" O MET B2224 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 354 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: 6.23 Time building geometry restraints manager: 5.65 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: 4535 1.15 - 1.32: 823 1.32 - 1.49: 2124 1.49 - 1.66: 1795 1.66 - 1.83: 42 Bond restraints: 9319 Sorted by residual: bond pdb=" C ASP B2197 " pdb=" N ILE B2198 " ideal model delta sigma weight residual 1.332 1.503 -0.171 1.36e-02 5.41e+03 1.58e+02 bond pdb=" NE1 TRP B2088 " pdb=" HE1 TRP B2088 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE1 TRP A1249 " pdb=" HE1 TRP A1249 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS B2209 " pdb=" HE2 HIS B2209 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B2319 " pdb=" H HIS B2319 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9314 not shown) Histogram of bond angle deviations from ideal: 93.01 - 104.72: 202 104.72 - 116.43: 11723 116.43 - 128.14: 4848 128.14 - 139.85: 68 139.85 - 151.56: 1 Bond angle restraints: 16842 Sorted by residual: angle pdb=" O ILE B2198 " pdb=" C ILE B2198 " pdb=" N SER B2199 " ideal model delta sigma weight residual 122.57 95.30 27.27 1.25e+00 6.40e-01 4.76e+02 angle pdb=" C ILE B2198 " pdb=" N SER B2199 " pdb=" CA SER B2199 " ideal model delta sigma weight residual 120.82 151.56 -30.74 1.50e+00 4.44e-01 4.20e+02 angle pdb=" CA ILE B2198 " pdb=" C ILE B2198 " pdb=" N SER B2199 " ideal model delta sigma weight residual 116.60 139.06 -22.46 1.45e+00 4.76e-01 2.40e+02 angle pdb=" O ASP B2197 " pdb=" C ASP B2197 " pdb=" N ILE B2198 " ideal model delta sigma weight residual 122.59 112.14 10.45 1.33e+00 5.65e-01 6.17e+01 angle pdb=" N GLN B2357 " pdb=" CA GLN B2357 " pdb=" C GLN B2357 " ideal model delta sigma weight residual 108.86 119.47 -10.61 1.41e+00 5.03e-01 5.67e+01 ... (remaining 16837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3762 17.65 - 35.30: 408 35.30 - 52.95: 154 52.95 - 70.60: 43 70.60 - 88.25: 16 Dihedral angle restraints: 4383 sinusoidal: 2288 harmonic: 2095 Sorted by residual: dihedral pdb=" CA ASP B2197 " pdb=" C ASP B2197 " pdb=" N ILE B2198 " pdb=" CA ILE B2198 " ideal model delta harmonic sigma weight residual -180.00 -148.71 -31.29 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" N HIS B2280 " pdb=" C HIS B2280 " pdb=" CA HIS B2280 " pdb=" CB HIS B2280 " ideal model delta harmonic sigma weight residual 122.80 108.29 14.51 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" C GLU A1192 " pdb=" N GLU A1192 " pdb=" CA GLU A1192 " pdb=" CB GLU A1192 " ideal model delta harmonic sigma weight residual -122.60 -135.18 12.58 0 2.50e+00 1.60e-01 2.53e+01 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 502 0.111 - 0.221: 143 0.221 - 0.332: 21 0.332 - 0.442: 5 0.442 - 0.553: 1 Chirality restraints: 672 Sorted by residual: chirality pdb=" CA ASN B2293 " pdb=" N ASN B2293 " pdb=" C ASN B2293 " pdb=" CB ASN B2293 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" CA GLN B2357 " pdb=" N GLN B2357 " pdb=" C GLN B2357 " pdb=" CB GLN B2357 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA GLU A1192 " pdb=" N GLU A1192 " pdb=" C GLU A1192 " pdb=" CB GLU A1192 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 669 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B2198 " 0.047 2.00e-02 2.50e+03 7.37e-02 5.43e+01 pdb=" C ILE B2198 " -0.127 2.00e-02 2.50e+03 pdb=" O ILE B2198 " 0.037 2.00e-02 2.50e+03 pdb=" N SER B2199 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B2197 " -0.040 2.00e-02 2.50e+03 7.13e-02 5.08e+01 pdb=" C ASP B2197 " 0.123 2.00e-02 2.50e+03 pdb=" O ASP B2197 " -0.045 2.00e-02 2.50e+03 pdb=" N ILE B2198 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1092 " -0.016 2.00e-02 2.50e+03 1.76e-02 9.34e+00 pdb=" CG PHE A1092 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A1092 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1092 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A1092 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A1092 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A1092 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A1092 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 PHE A1092 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE A1092 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A1092 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A1092 " -0.006 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 60 1.62 - 2.37: 3259 2.37 - 3.11: 29835 3.11 - 3.86: 43335 3.86 - 4.60: 67100 Warning: very small nonbonded interaction distances. Nonbonded interactions: 143589 Sorted by model distance: nonbonded pdb="HD11 ILE B2283 " pdb=" HE1 MET B2354 " model vdw 0.877 2.440 nonbonded pdb=" H GLU B2192 " pdb=" HG3 GLU B2192 " model vdw 1.263 2.270 nonbonded pdb=" HA LEU B2178 " pdb="HD23 LEU B2178 " model vdw 1.305 2.440 nonbonded pdb=" H ILE B2302 " pdb="HG13 ILE B2302 " model vdw 1.339 2.270 nonbonded pdb=" HB3 ASP B2197 " pdb=" HG3 MET B2200 " model vdw 1.346 2.440 ... (remaining 143584 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 29 15.96 2 O 832 7.97 1 N 756 6.97 1 C 3022 5.97 2 H 4541 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: 4541 of 9180 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 9180 n_use_u_iso = 9180 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 = 9180 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (9180 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 9180 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 1085 through 1087 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 1091 through 1093 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 1115 through 1125 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 1137 through 1154 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 1198 through 1212 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 1214 through 1217 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 1236 through 1238 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 1255 through 1257 helix_type = alpha pi *3_10 unknown } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 1288 through 1307 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 1315 through 1326 helix_type = alpha pi *3_10 unknown } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 1335 through 1337 helix_type = alpha pi *3_10 unknown } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 1341 through 1343 helix_type = alpha pi *3_10 unknown } helix { serial_number = "13" helix_identifier = "13" selection = chain 'B' and resid 2085 through 2087 helix_type = alpha pi *3_10 unknown } helix { serial_number = "14" helix_identifier = "14" selection = chain 'B' and resid 2091 through 2093 helix_type = alpha pi *3_10 unknown } helix { serial_number = "15" helix_identifier = "15" selection = chain 'B' and resid 2115 through 2125 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'B' and resid 2137 through 2142 helix_type = alpha pi *3_10 unknown } helix { serial_number = "17" helix_identifier = "17" selection = chain 'B' and resid 2144 through 2154 helix_type = alpha pi *3_10 unknown } helix { serial_number = "18" helix_identifier = "18" selection = chain 'B' and resid 2170 through 2172 helix_type = alpha pi *3_10 unknown } helix { serial_number = "19" helix_identifier = "19" selection = chain 'B' and resid 2191 through 2195 helix_type = alpha pi *3_10 unknown } helix { serial_number = "20" helix_identifier = "20" selection = chain 'B' and resid 2199 through 2212 } helix { serial_number = "21" helix_identifier = "21" selection = chain 'B' and resid 2214 through 2216 helix_type = alpha pi *3_10 unknown } helix { serial_number = "22" helix_identifier = "22" selection = chain 'B' and resid 2236 through 2238 helix_type = alpha pi *3_10 unknown } helix { serial_number = "23" helix_identifier = "23" selection = chain 'B' and resid 2248 through 2250 helix_type = alpha pi *3_10 unknown } helix { serial_number = "24" helix_identifier = "24" selection = chain 'B' and resid 2255 through 2257 helix_type = alpha pi *3_10 unknown } helix { serial_number = "25" helix_identifier = "25" selection = chain 'B' and resid 2288 through 2307 } helix { serial_number = "26" helix_identifier = "26" selection = chain 'B' and resid 2315 through 2326 } helix { serial_number = "27" helix_identifier = "27" selection = chain 'B' and resid 2335 through 2337 helix_type = alpha pi *3_10 unknown } sheet { first_strand = chain 'A' and resid 1106 through 1108 sheet_id = " A" strand { selection = chain 'A' and resid 1331 through 1333 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 1332 and name N bond_start_previous = chain 'A' and resid 1106 and name O } strand { selection = chain 'A' and resid 1242 through 1246 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 1244 and name N bond_start_previous = chain 'A' and resid 1331 and name O } strand { selection = chain 'A' and resid 1279 through 1286 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 1285 and name N bond_start_previous = chain 'A' and resid 1243 and name O } strand { selection = chain 'A' and resid 1220 through 1224 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 1223 and name N bond_start_previous = chain 'A' and resid 1284 and name O } strand { selection = chain 'A' and resid 1128 through 1135 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 1130 and name N bond_start_previous = chain 'A' and resid 1220 and name O } strand { selection = chain 'A' and resid 1160 through 1167 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 1160 and name N bond_start_previous = chain 'A' and resid 1129 and name O } strand { selection = chain 'A' and resid 1182 through 1188 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 1183 and name N bond_start_previous = chain 'A' and resid 1161 and name O } } sheet { first_strand = chain 'A' and resid 1228 through 1230 sheet_id = " B" strand { selection = chain 'A' and resid 1354 through 1356 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 1355 and name N bond_start_previous = chain 'A' and resid 1229 and name O } } sheet { first_strand = chain 'B' and resid 2106 through 2108 sheet_id = " C" strand { selection = chain 'B' and resid 2331 through 2333 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 2332 and name N bond_start_previous = chain 'B' and resid 2106 and name O } strand { selection = chain 'B' and resid 2243 through 2245 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 2244 and name N bond_start_previous = chain 'B' and resid 2331 and name O } } sheet { first_strand = chain 'B' and resid 2283 through 2286 sheet_id = " D" strand { selection = chain 'B' and resid 2220 through 2225 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 2223 and name N bond_start_previous = chain 'B' and resid 2284 and name O } strand { selection = chain 'B' and resid 2129 through 2135 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 2130 and name N bond_start_previous = chain 'B' and resid 2220 and name O } strand { selection = chain 'B' and resid 2161 through 2167 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 2162 and name N bond_start_previous = chain 'B' and resid 2129 and name O } strand { selection = chain 'B' and resid 2182 through 2188 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 2183 and name N bond_start_previous = chain 'B' and resid 2161 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2jcl_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4541 occupancy sum: 4541.00 (% of total atoms 49.50) Rotatable: count: 1174 occupancy sum: 1174.00 (% of total atoms 12.80) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.29 - 25.82 A, n_refl.=18668 (all), 5.14 % free)------------| | | | r_work= 0.3574 r_free= 0.4506 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 6.005759 | | target function (ml) not normalized (work): 106349.971859 | | target function (ml) not normalized (free): 5850.706034 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.82 - 6.27 0.96 2609 121 0.5460 0.6039 6.8079 7.0011| | 2: 6.27 - 4.99 1.00 2567 134 0.2965 0.4098 6.2482 6.2459| | 3: 4.99 - 4.36 1.00 2539 145 0.2829 0.3788 6.0268 6.1824| | 4: 4.36 - 3.96 1.00 2505 152 0.3257 0.4046 5.8953 5.9435| | 5: 3.96 - 3.68 1.00 2528 131 0.3404 0.4589 5.7793 5.8925| | 6: 3.68 - 3.46 1.00 2500 143 0.3408 0.4654 5.693 5.8233| | 7: 3.46 - 3.29 0.98 2460 134 0.3280 0.4313 5.5433 5.6874| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.82 - 6.27 2609 121 0.28 68.42 0.66 0.21 181754.43| | 2: 6.27 - 4.99 2567 134 0.53 49.33 1.03 0.40 83819.95| | 3: 4.99 - 4.36 2539 145 0.79 26.89 1.22 0.53 30673.89| | 4: 4.36 - 3.96 2505 152 0.82 25.11 1.35 0.59 23718.81| | 5: 3.96 - 3.68 2528 131 0.79 27.45 1.39 0.61 20566.81| | 6: 3.68 - 3.46 2500 143 0.77 29.89 1.34 0.59 18379.46| | 7: 3.46 - 3.29 2460 134 0.71 34.66 1.26 0.54 15754.19| |alpha: min = 0.21 max = 0.61 mean = 0.49| |beta: min = 15754.19 max = 181754.43 mean = 54402.34| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 89.99 mean = 37.59| |phase err.(test): min = 0.00 max = 89.97 mean = 36.22| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.171 4778 Z= 1.031 Angle : 1.720 30.745 6478 Z= 1.107 Chirality : 0.105 0.553 672 Planarity : 0.006 0.074 810 Dihedral : 18.634 88.252 1734 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 2.91 % Allowed : 10.55 % Favored : 86.55 % Rotamer: Outliers : 11.69 % Allowed : 14.92 % Favored : 73.39 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.30), residues: 550 helix: -4.08 (0.23), residues: 171 sheet: -1.10 (0.46), residues: 102 loop : -2.50 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B2202 TYR 0.021 0.004 TYR B2251 PHE 0.041 0.004 PHE A1092 TRP 0.028 0.005 TRP B2195 HIS 0.008 0.003 HIS A1280 Individual atomic B min max mean iso aniso Overall: 13.23 125.66 36.40 1.07 4639 0 Protein: 13.23 96.11 36.04 1.07 4614 0 Other: 75.33 125.66 102.20 N/A 25 0 Chain A: 14.29 96.11 37.07 N/A 2307 0 Chain B: 13.23 125.66 35.73 N/A 2332 0 Histogram: Values Number of atoms 13.23 - 24.47 986 24.47 - 35.72 1683 35.72 - 46.96 899 46.96 - 58.20 780 58.20 - 69.44 154 69.44 - 80.69 49 80.69 - 91.93 53 91.93 - 103.17 25 103.17 - 114.42 5 114.42 - 125.66 5 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18668 (all), 5.14 % free)------------| | | | r_work= 0.3574 r_free= 0.4506 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 6.005759 | | target function (ml) not normalized (work): 106349.971859 | | target function (ml) not normalized (free): 5850.706034 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3624 0.3574 0.4506 n_refl.: 18668 re-set all scales: r(all,work,free)=0.3624 0.3574 0.4506 n_refl.: 18668 remove outliers: r(all,work,free)=0.3577 0.3525 0.4501 n_refl.: 18638 overall B=9.12 to atoms: r(all,work,free)=0.3890 0.3834 0.4867 n_refl.: 18638 bulk-solvent and scaling: r(all,work,free)=0.2080 0.2057 0.2502 n_refl.: 18638 remove outliers: r(all,work,free)=0.2076 0.2053 0.2492 n_refl.: 18632 ======================== 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 25.815-15.025 50.00 90 6 0.6251 63.748 40.141 0.096 1.038 0.433 14.999-13.060 76.79 85 1 0.6539 531.218 497.411 0.821 1.041 0.400 12.994-11.375 88.62 138 10 0.2683 977.054 929.700 1.098 1.037 0.394 11.369-9.901 99.22 240 13 0.1734 1062.997 1045.100 1.163 1.034 0.392 9.883-8.622 100.00 356 16 0.1658 1073.143 1054.776 1.123 1.031 0.389 8.618-7.507 99.82 546 20 0.1852 778.443 761.941 1.087 1.026 0.415 7.504-6.535 100.00 806 36 0.2240 611.718 592.471 1.024 1.020 0.410 6.532-5.692 100.00 1192 64 0.2011 610.109 588.519 1.005 1.013 0.376 5.690-4.954 99.95 1802 91 0.1944 639.590 618.957 0.948 1.002 0.359 4.954-4.314 100.00 2679 154 0.1716 728.361 712.094 1.005 0.988 0.341 4.314-3.756 100.00 4069 230 0.1848 628.274 609.098 1.067 0.970 0.251 3.756-3.291 98.98 5671 317 0.2536 453.064 424.909 1.060 0.947 0.166 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9563 b_overall=-3.3287 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.374438 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.288037 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 0.2271 0.2602 0.0330 0.003 0.6 6.4 2.4 8.3 0 0.125 0.2242 0.2588 0.0346 0.003 0.6 6.4 2.4 8.3 0 0.250 0.2170 0.2557 0.0387 0.004 0.6 6.5 2.0 8.3 0 0.500 0.2112 0.2527 0.0415 0.004 0.7 7.0 2.0 8.5 0 1.000 0.2051 0.2487 0.0436 0.006 0.8 8.8 2.0 9.3 0 2.000 0.2008 0.2483 0.0475 0.007 0.9 10.2 2.2 9.7 0 3.000 0.1982 0.2489 0.0507 0.009 1.0 11.7 2.4 10.1 0 4.000 0.1958 0.2479 0.0521 0.010 1.0 14.2 2.5 10.1 0 5.000 0.1939 0.2474 0.0535 0.012 1.1 15.3 2.7 10.3 0 6.000 0.1925 0.2468 0.0543 0.013 1.2 15.8 2.9 10.9 0 7.000 0.1911 0.2472 0.0561 0.014 1.3 16.6 2.7 11.3 0 8.000 0.1901 0.2462 0.0561 0.015 1.3 17.6 2.9 11.5 0 9.000 0.1888 0.2458 0.0570 0.016 1.4 17.6 2.9 11.9 0 10.000 0.1902 0.2461 0.0559 0.015 1.3 16.7 2.7 11.7 0 8.687 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2170 0.2557 0.0387 0.004 0.6 6.5 2.0 8.3 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.70 25.57 3.87 0.767 45.293 0.288 0.056 21.70 25.43 3.73 1.630 45.423 0.009 0.056 21.42 25.32 3.90 1.745 45.458 0.036 0.054 20.79 25.10 4.31 2.785 45.583 0.144 0.051 20.02 24.87 4.85 5.496 45.951 0.288 0.048 19.72 24.79 5.07 6.818 46.284 0.432 0.047 19.57 24.75 5.18 7.651 46.477 0.576 0.046 19.48 24.74 5.26 8.282 46.631 0.720 0.045 19.41 24.73 5.32 8.782 46.757 0.864 0.045 19.34 24.71 5.36 9.262 46.886 1.008 0.045 19.28 24.70 5.43 9.773 47.029 1.152 0.044 19.12 24.66 5.55 11.080 47.430 1.296 0.044 19.04 24.65 5.61 11.844 47.673 1.440 0.043 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.440 Accepted refinement result: 19.04 24.65 5.61 11.844 47.673 1.440 0.043 Individual atomic B min max mean iso aniso Overall: 18.74 129.78 50.23 11.26 4639 0 Protein: 18.74 126.16 49.90 11.26 4614 0 Other: 80.79 129.78 111.58 N/A 25 0 Chain A: 20.09 126.16 51.12 N/A 2307 0 Chain B: 18.74 129.78 49.35 N/A 2332 0 Histogram: Values Number of atoms 18.74 - 29.85 418 29.85 - 40.95 1135 40.95 - 52.06 1252 52.06 - 63.16 910 63.16 - 74.26 504 74.26 - 85.37 214 85.37 - 96.47 106 96.47 - 107.58 55 107.58 - 118.68 34 118.68 - 129.78 11 =========================== Idealize ADP of riding H ========================== r_work=0.1904 r_free=0.2465 r_work=0.1884 r_free=0.2462 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18632 (all), 5.14 % free)------------| | | | r_work= 0.1884 r_free= 0.2462 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ls_wunit_k1) (work): 0.042471 | | target function (ls_wunit_k1) not normalized (work): 750.631938 | | target function (ls_wunit_k1) not normalized (free): 63.874153 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1913 0.1884 0.2462 n_refl.: 18632 re-set all scales: r(all,work,free)=0.3874 0.3813 0.4919 n_refl.: 18632 remove outliers: r(all,work,free)=0.3874 0.3813 0.4919 n_refl.: 18632 overall B=-1.01 to atoms: r(all,work,free)=0.3836 0.3775 0.4877 n_refl.: 18632 bulk-solvent and scaling: r(all,work,free)=0.1910 0.1880 0.2458 n_refl.: 18632 remove outliers: r(all,work,free)=0.1910 0.1880 0.2458 n_refl.: 18632 ======================== 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 25.815-15.025 50.00 90 6 0.6203 38.977 26.435 0.078 1.026 0.411 14.999-13.060 76.79 85 1 0.6399 324.797 331.809 0.873 1.029 0.399 12.994-11.375 88.62 138 10 0.2367 597.390 585.294 1.120 1.027 0.398 11.369-9.901 99.22 240 13 0.1619 649.938 642.783 1.163 1.024 0.398 9.883-8.622 100.00 356 16 0.1516 656.141 651.409 1.115 1.021 0.396 8.618-7.507 99.82 546 20 0.1768 475.956 471.501 1.060 1.018 0.395 7.504-6.535 100.00 806 36 0.2040 374.017 365.886 0.987 1.013 0.387 6.532-5.692 100.00 1192 64 0.1837 373.033 364.739 0.980 1.007 0.383 5.690-4.954 99.95 1802 91 0.1809 391.058 382.206 0.917 0.999 0.363 4.954-4.314 100.00 2679 154 0.1546 445.335 439.117 0.978 0.988 0.344 4.314-3.756 100.00 4069 230 0.1715 384.139 376.050 1.031 0.974 0.264 3.756-3.291 98.98 5671 317 0.2293 277.012 265.354 1.037 0.955 0.153 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.5232 ============================ 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 = 3.177885 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.050940 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 0.1903 0.2380 0.0478 0.003 0.6 6.0 1.3 7.1 0 0.125 0.1841 0.2385 0.0543 0.004 0.6 7.1 1.5 7.9 0 0.250 0.1804 0.2401 0.0597 0.006 0.8 8.0 1.5 8.7 0 0.500 0.1771 0.2413 0.0642 0.010 1.0 10.7 2.2 9.5 0 1.000 0.1743 0.2423 0.0680 0.016 1.3 14.9 2.5 10.3 0 2.000 0.1727 0.2433 0.0706 0.020 1.6 18.0 2.5 11.1 0 3.000 0.1717 0.2434 0.0717 0.024 1.8 19.8 2.4 12.1 0 4.000 0.1707 0.2441 0.0733 0.028 2.1 22.1 2.5 14.1 0 5.000 0.1699 0.2433 0.0734 0.031 2.3 23.6 2.4 14.1 0 6.000 0.1693 0.2436 0.0743 0.034 2.5 24.3 2.0 15.5 0 7.000 0.1689 0.2442 0.0753 0.037 2.6 25.3 2.4 16.1 0 8.000 0.1683 0.2442 0.0759 0.039 2.8 27.3 2.2 16.3 0 9.000 0.1681 0.2442 0.0760 0.042 2.9 28.4 2.4 17.1 0 10.000 0.1751 0.2417 0.0666 0.013 1.2 13.1 2.4 9.7 0 1.589 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1903 0.2380 0.0478 0.003 0.6 6.0 1.3 7.1 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.03 23.80 4.78 11.063 54.954 0.051 5.885 21.54 23.97 2.43 9.314 59.146 0.002 5.949 20.85 23.73 2.88 9.445 57.616 0.006 5.931 19.67 23.36 3.68 10.571 55.230 0.025 5.891 19.14 23.44 4.29 11.243 54.470 0.051 5.874 18.99 23.40 4.42 11.842 54.538 0.076 5.869 18.86 23.43 4.57 12.225 54.579 0.102 5.865 18.77 23.45 4.68 12.575 54.643 0.127 5.863 18.71 23.45 4.75 12.888 54.723 0.153 5.860 18.66 23.45 4.79 13.158 54.807 0.178 5.859 18.62 23.45 4.83 13.409 54.887 0.204 5.858 18.59 23.44 4.85 13.634 54.960 0.229 5.857 18.57 23.44 4.87 13.842 55.030 0.255 5.856 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.025 Accepted refinement result: 19.67 23.36 3.68 10.571 55.230 0.025 5.891 Individual atomic B min max mean iso aniso Overall: 19.08 123.78 49.77 7.25 4639 0 Protein: 19.08 120.56 49.46 7.23 4614 0 Other: 74.78 123.78 105.78 N/A 25 0 Chain A: 23.64 120.56 50.70 N/A 2307 0 Chain B: 19.08 123.78 48.85 N/A 2332 0 Histogram: Values Number of atoms 19.08 - 29.55 142 29.55 - 40.02 1281 40.02 - 50.49 1408 50.49 - 60.96 881 60.96 - 71.43 506 71.43 - 81.90 192 81.90 - 92.37 119 92.37 - 102.84 52 102.84 - 113.31 42 113.31 - 123.78 16 =========================== Idealize ADP of riding H ========================== r_work=0.1967 r_free=0.2336 r_work=0.1981 r_free=0.2338 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18632 (all), 5.14 % free)------------| | | | r_work= 0.1981 r_free= 0.2338 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.894699 | | target function (ml) not normalized (work): 104182.917497 | | target function (ml) not normalized (free): 5744.573258 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2000 0.1981 0.2338 n_refl.: 18632 re-set all scales: r(all,work,free)=0.3916 0.3859 0.4923 n_refl.: 18632 remove outliers: r(all,work,free)=0.3916 0.3859 0.4923 n_refl.: 18632 overall B=-0.66 to atoms: r(all,work,free)=0.3891 0.3835 0.4895 n_refl.: 18632 bulk-solvent and scaling: r(all,work,free)=0.1998 0.1980 0.2330 n_refl.: 18632 remove outliers: r(all,work,free)=0.1997 0.1979 0.2330 n_refl.: 18631 ======================== 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 25.815-15.025 50.00 90 6 0.6097 38.977 26.646 0.079 1.021 0.415 14.999-13.060 75.89 84 1 0.5767 328.034 332.683 0.936 1.027 0.405 12.994-11.375 88.62 138 10 0.2242 597.390 588.562 1.163 1.024 0.400 11.369-9.901 99.22 240 13 0.1571 649.938 645.731 1.214 1.021 0.401 9.883-8.622 100.00 356 16 0.1525 656.141 650.623 1.162 1.018 0.401 8.618-7.507 99.82 546 20 0.1731 475.956 473.308 1.115 1.016 0.401 7.504-6.535 100.00 806 36 0.2051 374.017 364.418 1.034 1.011 0.401 6.532-5.692 100.00 1192 64 0.1941 373.033 362.824 1.001 1.006 0.382 5.690-4.954 99.95 1802 91 0.1817 391.058 380.885 0.940 0.998 0.372 4.954-4.314 100.00 2679 154 0.1632 445.335 436.555 0.991 0.988 0.363 4.314-3.756 100.00 4069 230 0.1871 384.139 373.273 1.043 0.975 0.283 3.756-3.291 98.98 5671 317 0.2476 277.012 260.700 1.030 0.958 0.172 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-2.2719 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1979 r_free=0.2330 After: r_work=0.1979 r_free=0.2329 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.077186 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.048083 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 0.1979 0.2331 0.0352 0.003 0.6 6.3 1.3 7.1 0 0.125 0.1973 0.2327 0.0354 0.003 0.6 6.2 1.3 6.9 0 0.250 0.1934 0.2314 0.0380 0.007 0.7 6.7 1.3 6.7 0 0.500 0.1840 0.2299 0.0459 0.014 1.4 12.1 1.3 7.9 0 1.000 0.1811 0.2309 0.0498 0.017 1.5 14.5 1.6 9.7 0 2.000 0.1779 0.2336 0.0558 0.021 1.9 18.4 2.2 10.3 0 3.000 0.1765 0.2339 0.0574 0.026 2.1 19.6 2.2 10.5 0 4.000 0.1763 0.2358 0.0595 0.028 2.4 23.3 2.7 12.5 0 5.000 0.1745 0.2370 0.0626 0.033 2.9 25.7 3.3 13.5 0 6.000 0.1736 0.2378 0.0643 0.037 3.3 28.2 3.1 12.7 1 7.000 0.1726 0.2367 0.0641 0.039 3.5 27.5 2.7 12.3 1 8.000 0.1721 0.2371 0.0650 0.042 3.7 28.2 2.7 12.7 1 9.000 0.1731 0.2383 0.0653 0.042 3.7 31.1 4.2 16.3 1 10.000 0.1819 0.2316 0.0497 0.015 1.5 15.5 1.6 9.1 0 1.539 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1973 0.2327 0.0354 0.003 0.6 6.2 1.3 6.9 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.73 23.27 3.54 9.020 54.408 0.048 5.892 22.04 24.07 2.03 8.081 57.919 0.001 5.964 21.88 24.09 2.21 8.829 57.230 0.006 5.964 19.72 23.25 3.53 8.990 54.224 0.024 5.891 19.53 23.21 3.68 9.279 54.163 0.048 5.884 19.45 23.20 3.75 9.448 54.125 0.072 5.881 19.16 23.16 3.99 10.213 53.901 0.096 5.870 18.96 23.15 4.19 11.069 54.026 0.120 5.862 18.89 23.16 4.27 11.346 54.168 0.144 5.860 18.85 23.18 4.32 11.538 54.267 0.168 5.858 18.83 23.19 4.35 11.628 54.317 0.192 5.858 18.81 23.20 4.39 11.776 54.389 0.216 5.857 18.79 23.22 4.42 11.889 54.442 0.240 5.857 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.120 Accepted refinement result: 18.96 23.15 4.19 11.069 54.026 0.120 5.862 Individual atomic B min max mean iso aniso Overall: 16.15 131.60 48.36 10.32 4639 0 Protein: 16.15 131.60 48.05 10.27 4614 0 Other: 69.13 130.78 104.78 N/A 25 0 Chain A: 18.76 131.60 49.31 N/A 2307 0 Chain B: 16.15 130.78 47.41 N/A 2332 0 Histogram: Values Number of atoms 16.15 - 27.69 307 27.69 - 39.24 1305 39.24 - 50.78 1357 50.78 - 62.33 835 62.33 - 73.87 429 73.87 - 85.42 196 85.42 - 96.96 107 96.96 - 108.51 60 108.51 - 120.05 28 120.05 - 131.60 15 =========================== Idealize ADP of riding H ========================== r_work=0.1896 r_free=0.2315 r_work=0.1890 r_free=0.2319 ----------X-ray data---------- |--(resolution: 3.29 - 25.82 A, n_refl.=18631 (all), 5.14 % free)------------| | | | r_work= 0.1890 r_free= 0.2319 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 5.860183 | | target function (ml) not normalized (work): 103567.014474 | | target function (ml) not normalized (free): 5738.486821 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.82 - 6.27 0.95 2574 119 0.1905 0.1937 6.0833 6.186| | 2: 6.27 - 4.99 1.00 2567 134 0.1804 0.2454 5.8713 5.9949| | 3: 4.99 - 4.36 1.00 2539 145 0.1540 0.1785 5.8725 6.0558| | 4: 4.36 - 3.96 1.00 2505 152 0.1675 0.2235 5.8743 5.9928| | 5: 3.96 - 3.68 1.00 2528 131 0.1919 0.2421 5.8214 5.9566| | 6: 3.68 - 3.46 1.00 2500 143 0.2193 0.2819 5.8023 5.9345| | 7: 3.46 - 3.29 0.98 2460 134 0.2617 0.3210 5.6867 5.8291| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.82 - 6.27 2574 119 0.84 20.50 1.00 0.97 25153.91| | 2: 6.27 - 4.99 2567 134 0.86 20.39 1.00 0.94 23254.95| | 3: 4.99 - 4.36 2539 145 0.89 17.21 1.00 0.94 22170.90| | 4: 4.36 - 3.96 2505 152 0.89 18.09 1.02 0.94 21639.89| | 5: 3.96 - 3.68 2528 131 0.85 21.75 1.00 0.95 21919.26| | 6: 3.68 - 3.46 2500 143 0.82 25.52 1.03 0.90 21133.92| | 7: 3.46 - 3.29 2460 134 0.76 30.44 0.92 0.80 19545.72| |alpha: min = 0.80 max = 0.97 mean = 0.92| |beta: min = 19545.72 max = 25153.91 mean = 22139.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 21.94| |phase err.(test): min = 0.00 max = 88.83 mean = 21.61| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1912 0.1890 0.2319 n_refl.: 18631 re-set all scales: r(all,work,free)=0.3806 0.3749 0.4819 n_refl.: 18631 remove outliers: r(all,work,free)=0.3806 0.3749 0.4819 n_refl.: 18631 overall B=-0.30 to atoms: r(all,work,free)=0.3795 0.3738 0.4806 n_refl.: 18631 bulk-solvent and scaling: r(all,work,free)=0.1911 0.1889 0.2320 n_refl.: 18631 remove outliers: r(all,work,free)=0.1911 0.1889 0.2320 n_refl.: 18631 ======================== 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 25.815-15.025 50.00 90 6 0.6033 38.977 26.896 0.083 1.018 0.416 14.999-13.060 75.89 84 1 0.5836 328.034 341.789 0.950 1.024 0.400 12.994-11.375 88.62 138 10 0.2236 597.390 588.011 1.168 1.022 0.400 11.369-9.901 99.22 240 13 0.1577 649.938 644.724 1.218 1.019 0.400 9.883-8.622 100.00 356 16 0.1517 656.141 650.428 1.168 1.016 0.400 8.618-7.507 99.82 546 20 0.1723 475.956 473.580 1.121 1.014 0.401 7.504-6.535 100.00 806 36 0.2030 374.017 364.286 1.035 1.010 0.401 6.532-5.692 100.00 1192 64 0.1886 373.033 362.926 1.006 1.005 0.391 5.690-4.954 99.95 1802 91 0.1763 391.058 380.939 0.932 0.998 0.371 4.954-4.314 100.00 2679 154 0.1538 445.335 437.429 0.977 0.988 0.361 4.314-3.756 100.00 4069 230 0.1720 384.139 374.230 1.033 0.976 0.277 3.756-3.291 98.98 5671 317 0.2367 277.012 261.445 1.008 0.960 0.161 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-1.0635 ================= 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 : 0.3574 0.4506 0.016 1.720 13.2 125.7 36.4 0 0.000 1_bss: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_settarget: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_weight: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_xyzrec: 0.2170 0.2557 0.004 0.642 22.4 134.8 45.5 0 0.177 1_adp: 0.1904 0.2465 0.004 0.642 18.7 129.8 50.2 0 0.177 1_regHadp: 0.1884 0.2462 0.004 0.642 18.7 129.8 50.2 0 0.177 2_bss: 0.1880 0.2458 0.004 0.642 17.7 128.8 49.2 0 0.177 2_settarget: 0.1880 0.2458 0.004 0.642 17.7 128.8 49.2 0 0.177 2_updatecdl: 0.1880 0.2458 0.004 0.705 17.7 128.8 49.2 0 0.177 2_weight: 0.1880 0.2458 0.004 0.705 17.7 128.8 49.2 0 0.177 2_xyzrec: 0.1903 0.2380 0.003 0.575 17.7 128.8 49.2 0 0.250 2_adp: 0.1967 0.2336 0.003 0.575 19.1 123.8 49.8 0 0.250 2_regHadp: 0.1981 0.2338 0.003 0.575 19.1 123.8 49.8 0 0.250 3_bss: 0.1979 0.2330 0.003 0.575 18.4 123.1 49.1 0 0.250 3_settarget: 0.1979 0.2330 0.003 0.575 18.4 123.1 49.1 0 0.250 3_updatecdl: 0.1979 0.2330 0.003 0.615 18.4 123.1 49.1 0 0.250 3_setrh: 0.1979 0.2329 0.003 0.615 18.4 123.1 49.1 0 0.250 3_weight: 0.1979 0.2329 0.003 0.615 18.4 123.1 49.1 0 0.250 3_xyzrec: 0.1973 0.2327 0.003 0.596 18.4 123.1 49.1 0 0.250 3_adp: 0.1896 0.2315 0.003 0.596 16.1 131.6 48.4 0 0.250 3_regHadp: 0.1890 0.2319 0.003 0.596 16.1 131.6 48.4 0 0.250 end: 0.1889 0.2320 0.003 0.596 15.8 131.3 48.1 0 0.250 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2jcl_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2jcl_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 15.0500 Refinement macro-cycles (run) : 329.4900 Write final files (write_after_run_outputs) : 19.6400 Total : 364.1800 Total CPU time: 6.97 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:36:38 PDT -0700 (1716251798.28 s) Start R-work = 0.2053, R-free = 0.2492 Final R-work = 0.1889, R-free = 0.2320 =============================================================================== Job complete usr+sys time: 442.12 seconds wall clock time: 19 minutes 29.13 seconds (1169.13 seconds total)