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/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+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/2jcl.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2jcl.pdb" 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" } 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: 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: 1.51, per 1000 atoms: 0.16 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: 2.32 Conformation dependent library (CDL) restraints added in 274.3 milliseconds 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. 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: 0.59 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: 1.91 Time building geometry restraints manager: 2.63 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2053 r_free=0.2492 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2053 r_free=0.2492 ========================= Local real-space refinement ========================= Before: r_work=0.2053 r_free=0.2492 159 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 101 time to evaluate : 0.694 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 29 residues processed: 58 average time/residue: 0.5010 time to fit residues: 37.5688 After: r_work=0.2120 r_free=0.2543 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.379469 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.284862 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 0.2279 0.2625 0.0346 0.003 0.6 6.8 0.2 5.8 0 0.125 0.2241 0.2613 0.0372 0.003 0.6 7.2 0.2 6.0 0 0.250 0.2181 0.2586 0.0404 0.003 0.6 7.7 0.2 5.6 0 0.500 0.2125 0.2540 0.0414 0.004 0.7 7.9 0.2 6.7 0 1.000 0.2054 0.2494 0.0440 0.006 0.8 8.9 0.2 6.7 0 2.000 0.2015 0.2472 0.0457 0.007 0.9 9.9 0.2 6.9 0 3.000 0.1987 0.2456 0.0469 0.009 1.0 11.8 0.2 7.9 0 4.000 0.1964 0.2456 0.0492 0.010 1.0 12.8 0.2 8.3 0 5.000 0.1945 0.2451 0.0505 0.012 1.1 14.4 0.2 8.5 0 6.000 0.1933 0.2444 0.0511 0.013 1.2 15.0 0.2 8.7 0 7.000 0.1920 0.2445 0.0525 0.014 1.3 16.1 0.2 9.5 0 8.000 0.1908 0.2436 0.0528 0.015 1.3 16.7 0.2 9.3 0 9.000 0.1898 0.2443 0.0545 0.016 1.4 17.7 0.2 9.5 0 10.000 0.1912 0.2444 0.0532 0.015 1.3 16.5 0.2 9.1 0 8.690 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2181 0.2586 0.0404 0.003 0.6 7.7 0.2 5.6 0 0.500 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2181 r_free=0.2586 146 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.924 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 3 residues processed: 28 average time/residue: 0.7650 time to fit residues: 30.9525 After: r_work=0.2238 r_free=0.2633 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.38 26.33 3.95 0.767 45.293 0.285 0.060 22.39 26.19 3.80 1.644 45.423 0.009 0.059 22.09 26.10 4.01 1.765 45.449 0.036 0.058 21.45 25.96 4.51 2.779 45.524 0.142 0.055 20.65 25.74 5.08 5.613 45.916 0.285 0.051 20.36 25.67 5.31 6.953 46.240 0.427 0.050 20.21 25.64 5.43 7.775 46.428 0.570 0.049 20.11 25.60 5.49 8.443 46.586 0.712 0.048 20.03 25.59 5.56 9.002 46.725 0.855 0.048 19.95 25.57 5.61 9.581 46.880 0.997 0.048 19.89 25.54 5.65 10.083 47.016 1.139 0.047 19.75 25.48 5.73 11.272 47.365 1.282 0.047 19.67 25.46 5.79 12.029 47.594 1.424 0.046 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.424 Accepted refinement result: 19.67 25.46 5.79 12.029 47.594 1.424 0.046 Individual atomic B min max mean iso aniso Overall: 18.74 137.44 50.07 11.41 4639 0 Protein: 18.74 137.44 49.73 11.40 4614 0 Other: 79.60 131.59 112.87 N/A 25 0 Chain A: 20.13 137.44 50.89 N/A 2307 0 Chain B: 18.74 131.59 49.27 N/A 2332 0 Histogram: Values Number of atoms 18.74 - 30.61 499 30.61 - 42.48 1303 42.48 - 54.35 1275 54.35 - 66.22 797 66.22 - 78.09 421 78.09 - 89.96 176 89.96 - 101.83 91 101.83 - 113.70 45 113.70 - 125.57 24 125.57 - 137.44 8 =========================== Idealize ADP of riding H ========================== r_work=0.1967 r_free=0.2546 r_work=0.1944 r_free=0.2540 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18632 (all), 5.14 % free)------------| | | | r_work= 0.1944 r_free= 0.2540 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ls_wunit_k1) (work): 0.045197 | | target function (ls_wunit_k1) not normalized (work): 798.817202 | | target function (ls_wunit_k1) not normalized (free): 67.720568 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1975 0.1944 0.2540 n_refl.: 18632 re-set all scales: r(all,work,free)=0.3868 0.3807 0.4918 n_refl.: 18632 remove outliers: r(all,work,free)=0.3868 0.3807 0.4918 n_refl.: 18632 overall B=-1.08 to atoms: r(all,work,free)=0.3828 0.3767 0.4873 n_refl.: 18632 bulk-solvent and scaling: r(all,work,free)=0.1971 0.1940 0.2538 n_refl.: 18632 remove outliers: r(all,work,free)=0.1971 0.1940 0.2538 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 0.6132 39.241 27.465 0.082 1.025 0.420 14.999-13.060 76.79 85 1 0.6446 326.998 332.917 0.892 1.029 0.402 12.994-11.375 88.62 138 10 0.2514 601.439 587.118 1.121 1.026 0.399 11.369-9.901 99.22 240 13 0.1719 654.342 646.423 1.167 1.023 0.398 9.883-8.622 100.00 356 16 0.1674 660.588 654.467 1.122 1.021 0.393 8.618-7.507 99.82 546 20 0.1953 479.181 472.219 1.063 1.018 0.392 7.504-6.535 100.00 806 36 0.2128 376.552 366.336 0.990 1.013 0.392 6.532-5.692 100.00 1192 64 0.1940 375.561 365.588 0.974 1.007 0.373 5.690-4.954 99.95 1802 91 0.1873 393.708 384.703 0.915 0.999 0.353 4.954-4.314 100.00 2679 154 0.1590 448.353 442.029 0.983 0.988 0.334 4.314-3.756 100.00 4069 230 0.1764 386.742 378.384 1.038 0.973 0.264 3.756-3.291 98.98 5671 317 0.2314 278.890 266.393 1.044 0.954 0.143 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.8446 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1940 r_free=0.2538 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1209 HIS A1293 ASN A1327 ASN B2196 GLN B2293 ASN Total number of N/Q/H flips: 5 r_work=0.1944 r_free=0.2542 ========================= Local real-space refinement ========================= Before: r_work=0.1944 r_free=0.2542 138 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.516 outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 2.4631 time to fit residues: 9.6614 After: r_work=0.1944 r_free=0.2542 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.449080 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.052376 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 0.1913 0.2431 0.0518 0.003 0.5 5.6 0.0 1.4 0 0.125 0.1866 0.2420 0.0554 0.004 0.6 6.7 0.0 2.2 0 0.250 0.1825 0.2427 0.0602 0.006 0.7 8.2 0.0 3.4 0 0.500 0.1790 0.2431 0.0641 0.010 0.9 10.6 0.0 6.2 0 1.000 0.1757 0.2429 0.0671 0.015 1.2 14.0 0.0 7.9 0 2.000 0.1739 0.2436 0.0698 0.020 1.5 16.6 0.2 8.9 0 3.000 0.1725 0.2430 0.0706 0.024 1.8 17.7 0.2 9.5 0 4.000 0.1717 0.2427 0.0710 0.027 2.0 20.5 0.2 11.5 0 5.000 0.1709 0.2421 0.0712 0.031 2.2 20.8 0.2 11.9 0 6.000 0.1701 0.2424 0.0723 0.033 2.4 21.9 0.2 14.5 0 7.000 0.1696 0.2428 0.0732 0.036 2.5 23.2 0.2 14.9 0 8.000 0.1691 0.2430 0.0739 0.039 2.7 24.4 0.4 15.7 0 9.000 0.1687 0.2429 0.0742 0.041 2.8 26.3 0.4 16.1 0 10.000 0.1762 0.2429 0.0667 0.014 1.2 13.5 0.0 7.7 0 1.725 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1913 0.2431 0.0518 0.003 0.5 5.6 0.0 1.4 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1913 r_free=0.2431 151 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.280 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.5152 time to fit residues: 5.6022 After: r_work=0.1918 r_free=0.2433 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.18 24.33 5.15 11.159 54.816 0.052 5.899 21.44 24.34 2.90 9.427 58.528 0.002 5.955 20.96 24.16 3.20 9.580 57.572 0.007 5.942 19.79 24.05 4.26 10.782 55.101 0.026 5.905 19.26 24.14 4.89 11.424 54.309 0.052 5.888 19.08 24.14 5.06 11.910 54.227 0.079 5.883 19.01 24.17 5.17 12.468 54.446 0.105 5.880 18.93 24.22 5.29 12.807 54.514 0.131 5.878 18.86 24.24 5.37 13.116 54.610 0.157 5.876 18.82 24.23 5.41 13.388 54.698 0.183 5.874 18.79 24.23 5.44 13.652 54.790 0.210 5.873 18.76 24.23 5.46 13.880 54.867 0.236 5.873 18.74 24.24 5.50 14.091 54.939 0.262 5.872 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.026 Accepted refinement result: 19.79 24.05 4.26 10.782 55.101 0.026 5.905 Individual atomic B min max mean iso aniso Overall: 21.23 131.36 49.56 7.60 4639 0 Protein: 21.23 131.36 49.25 7.58 4614 0 Other: 73.53 125.51 106.97 N/A 25 0 Chain A: 21.61 131.36 50.35 N/A 2307 0 Chain B: 21.23 125.51 48.78 N/A 2332 0 Histogram: Values Number of atoms 21.23 - 32.24 441 32.24 - 43.26 1514 43.26 - 54.27 1238 54.27 - 65.28 781 65.28 - 76.30 338 76.30 - 87.31 151 87.31 - 98.32 95 98.32 - 109.34 44 109.34 - 120.35 27 120.35 - 131.36 10 =========================== Idealize ADP of riding H ========================== r_work=0.1979 r_free=0.2405 r_work=0.1994 r_free=0.2408 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18632 (all), 5.14 % free)------------| | | | r_work= 0.1994 r_free= 0.2408 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 5.908405 | | target function (ml) not normalized (work): 104425.157647 | | target function (ml) not normalized (free): 5760.809001 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2015 0.1994 0.2408 n_refl.: 18632 re-set all scales: r(all,work,free)=0.3902 0.3845 0.4923 n_refl.: 18632 remove outliers: r(all,work,free)=0.3902 0.3845 0.4923 n_refl.: 18632 overall B=-0.60 to atoms: r(all,work,free)=0.3880 0.3823 0.4897 n_refl.: 18632 bulk-solvent and scaling: r(all,work,free)=0.2012 0.1991 0.2398 n_refl.: 18632 remove outliers: r(all,work,free)=0.2011 0.1990 0.2398 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 0.6088 39.241 27.281 0.106 0.906 0.430 14.999-13.060 75.89 84 1 0.5793 330.257 333.460 1.048 0.911 0.407 12.994-11.375 88.62 138 10 0.2319 601.439 589.044 1.289 0.908 0.400 11.369-9.901 99.22 240 13 0.1598 654.342 649.333 1.359 0.906 0.401 9.883-8.622 100.00 356 16 0.1550 660.588 654.082 1.310 0.904 0.397 8.618-7.507 99.82 546 20 0.1827 479.181 474.128 1.251 0.901 0.398 7.504-6.535 100.00 806 36 0.2080 376.552 365.636 1.156 0.897 0.397 6.532-5.692 100.00 1192 64 0.1940 375.561 364.380 1.131 0.893 0.392 5.690-4.954 99.95 1802 91 0.1840 393.708 383.120 1.051 0.886 0.362 4.954-4.314 100.00 2679 154 0.1643 448.353 439.392 1.111 0.877 0.352 4.314-3.756 100.00 4069 230 0.1869 386.742 376.074 1.172 0.865 0.273 3.756-3.291 98.98 5671 317 0.2474 278.890 262.290 1.158 0.849 0.172 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-2.0659 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1990 r_free=0.2398 After: r_work=0.1990 r_free=0.2398 ================================== NQH flips ================================== r_work=0.1990 r_free=0.2398 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1196 GLN Total number of N/Q/H flips: 1 r_work=0.1991 r_free=0.2399 ========================= Local real-space refinement ========================= Before: r_work=0.1991 r_free=0.2399 146 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 0.686 outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.9766 time to fit residues: 3.9981 After: r_work=0.1991 r_free=0.2399 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.169906 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049478 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 0.1984 0.2393 0.0409 0.003 0.6 6.1 0.0 0.6 0 0.125 0.1979 0.2391 0.0412 0.003 0.6 6.0 0.0 0.6 0 0.250 0.1940 0.2381 0.0440 0.007 0.7 6.3 0.0 0.6 0 0.500 0.1854 0.2360 0.0506 0.014 1.3 12.0 0.0 0.8 0 1.000 0.1810 0.2384 0.0574 0.017 1.7 17.7 0.0 4.2 0 2.000 0.1799 0.2378 0.0580 0.019 1.7 16.7 0.2 5.0 0 3.000 0.1769 0.2392 0.0623 0.026 2.3 21.3 0.5 5.8 0 4.000 0.1765 0.2394 0.0629 0.030 2.4 21.7 0.9 7.7 0 5.000 0.1757 0.2390 0.0634 0.033 2.7 22.1 1.1 8.5 0 6.000 0.1747 0.2400 0.0653 0.036 2.9 24.6 1.1 9.9 0 7.000 0.1745 0.2400 0.0655 0.038 3.1 25.7 1.3 10.9 0 8.000 0.1743 0.2402 0.0659 0.041 3.3 27.4 1.6 11.7 1 9.000 0.1738 0.2399 0.0662 0.044 3.5 27.5 2.0 13.3 1 10.000 0.1827 0.2366 0.0539 0.015 1.4 15.8 0.0 3.6 0 1.585 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1979 0.2391 0.0412 0.003 0.6 6.0 0.0 0.6 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1979 r_free=0.2391 145 residues out of total 496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 0.368 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.3883 time to fit residues: 1.7073 After: r_work=0.1979 r_free=0.2391 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.79 23.91 4.12 9.170 54.303 0.049 5.903 22.09 24.59 2.51 8.323 57.800 0.001 5.972 21.58 24.38 2.80 8.666 56.810 0.006 5.961 19.77 23.80 4.03 9.166 54.061 0.025 5.901 19.58 23.77 4.19 9.397 54.067 0.049 5.894 19.44 23.77 4.33 9.718 53.941 0.074 5.889 19.20 23.72 4.52 10.376 53.748 0.099 5.880 18.99 23.69 4.70 11.288 53.839 0.124 5.872 18.94 23.69 4.76 11.519 53.960 0.148 5.871 18.90 23.70 4.81 11.721 54.061 0.173 5.870 18.87 23.72 4.85 11.886 54.143 0.198 5.869 18.85 23.72 4.88 12.034 54.214 0.223 5.868 18.83 23.74 4.91 12.173 54.278 0.247 5.868 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.124 Accepted refinement result: 18.99 23.69 4.70 11.288 53.839 0.124 5.872 Individual atomic B min max mean iso aniso Overall: 16.02 135.64 48.05 10.61 4639 0 Protein: 16.02 135.64 47.73 10.57 4614 0 Other: 72.48 131.76 105.40 N/A 25 0 Chain A: 16.02 135.64 48.94 N/A 2307 0 Chain B: 16.35 131.76 47.16 N/A 2332 0 Histogram: Values Number of atoms 16.02 - 27.98 396 27.98 - 39.94 1390 39.94 - 51.90 1289 51.90 - 63.86 811 63.86 - 75.83 368 75.83 - 87.79 204 87.79 - 99.75 88 99.75 - 111.71 60 111.71 - 123.67 24 123.67 - 135.64 9 =========================== Idealize ADP of riding H ========================== r_work=0.1899 r_free=0.2369 r_work=0.1893 r_free=0.2370 ----------X-ray data---------- |--(resolution: 3.29 - 25.82 A, n_refl.=18631 (all), 5.14 % free)------------| | | | r_work= 0.1893 r_free= 0.2370 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.870474 | | target function (ml) not normalized (work): 103748.887985 | | target function (ml) not normalized (free): 5749.620977 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1930 0.1991 6.0989 6.2162| | 2: 6.27 - 4.99 1.00 2567 134 0.1791 0.2554 5.8812 6.0231| | 3: 4.99 - 4.36 1.00 2539 145 0.1548 0.1762 5.8816 6.0446| | 4: 4.36 - 3.96 1.00 2505 152 0.1668 0.2230 5.8841 5.9839| | 5: 3.96 - 3.68 1.00 2528 131 0.1925 0.2501 5.8321 5.9847| | 6: 3.68 - 3.46 1.00 2500 143 0.2198 0.2925 5.8123 5.9487| | 7: 3.46 - 3.29 0.98 2460 134 0.2609 0.3321 5.6936 5.8368| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 21.01 1.01 0.98 26254.18| | 2: 6.27 - 4.99 2567 134 0.86 20.63 1.00 0.95 24127.49| | 3: 4.99 - 4.36 2539 145 0.89 17.33 1.00 0.94 22678.36| | 4: 4.36 - 3.96 2505 152 0.89 18.13 1.02 0.94 21883.15| | 5: 3.96 - 3.68 2528 131 0.85 21.99 1.00 0.94 22509.10| | 6: 3.68 - 3.46 2500 143 0.81 25.92 1.03 0.90 22045.59| | 7: 3.46 - 3.29 2460 134 0.76 30.93 0.92 0.81 20516.27| |alpha: min = 0.81 max = 0.98 mean = 0.92| |beta: min = 20516.27 max = 26254.18 mean = 22882.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.92 mean = 22.23| |phase err.(test): min = 0.00 max = 89.69 mean = 22.31| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1918 0.1893 0.2370 n_refl.: 18631 re-set all scales: r(all,work,free)=0.3788 0.3730 0.4822 n_refl.: 18631 remove outliers: r(all,work,free)=0.3788 0.3730 0.4822 n_refl.: 18631 overall B=-0.26 to atoms: r(all,work,free)=0.3779 0.3720 0.4811 n_refl.: 18631 bulk-solvent and scaling: r(all,work,free)=0.1915 0.1890 0.2369 n_refl.: 18631 remove outliers: r(all,work,free)=0.1915 0.1890 0.2369 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 0.6024 39.241 27.445 0.093 1.028 0.423 14.999-13.060 75.89 84 1 0.5853 330.257 343.970 0.963 1.034 0.399 12.994-11.375 88.62 138 10 0.2323 601.439 589.452 1.182 1.031 0.399 11.369-9.901 99.22 240 13 0.1588 654.342 648.820 1.250 1.028 0.399 9.883-8.622 100.00 356 16 0.1530 660.588 654.418 1.210 1.025 0.400 8.618-7.507 99.82 546 20 0.1782 479.181 475.241 1.155 1.021 0.400 7.504-6.535 100.00 806 36 0.2026 376.552 365.967 1.067 1.016 0.401 6.532-5.692 100.00 1192 64 0.1870 375.561 364.949 1.037 1.010 0.390 5.690-4.954 99.95 1802 91 0.1749 393.708 383.747 0.969 1.001 0.381 4.954-4.314 100.00 2679 154 0.1546 448.353 440.231 1.013 0.989 0.361 4.314-3.756 100.00 4069 230 0.1719 386.742 376.787 1.070 0.973 0.281 3.756-3.291 98.98 5671 317 0.2362 278.890 262.915 1.053 0.952 0.161 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.7265 ================= 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_updatephipsi: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_nqh: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_realsrl: 0.2120 0.2543 0.016 1.720 22.4 134.8 45.5 0 0.038 1_weight: 0.2120 0.2543 0.016 1.720 22.4 134.8 45.5 0 0.038 1_xyzrec: 0.2181 0.2586 0.003 0.641 22.4 134.8 45.5 0 0.215 1_realsrl2: 0.2238 0.2633 0.003 0.641 22.4 134.8 45.5 0 0.231 1_adp: 0.1967 0.2546 0.003 0.641 18.7 137.4 50.1 0 0.231 1_regHadp: 0.1944 0.2540 0.003 0.641 18.7 137.4 50.1 0 0.231 2_bss: 0.1940 0.2538 0.003 0.641 17.7 136.4 49.0 0 0.231 2_settarget: 0.1940 0.2538 0.003 0.641 17.7 136.4 49.0 0 0.231 2_updatephipsi: 0.1940 0.2538 0.003 0.641 17.7 136.4 49.0 0 0.231 2_updatecdl: 0.1940 0.2538 0.004 0.674 17.7 136.4 49.0 0 0.231 2_nqh: 0.1944 0.2542 0.004 0.674 17.7 136.4 49.0 0 0.235 2_realsrl: 0.1944 0.2542 0.004 0.674 17.7 136.4 49.0 0 0.235 2_weight: 0.1944 0.2542 0.004 0.674 17.7 136.4 49.0 0 0.235 2_xyzrec: 0.1913 0.2431 0.003 0.543 17.7 136.4 49.0 0 0.291 2_realsrl2: 0.1918 0.2433 0.003 0.543 17.7 136.4 49.0 0 0.292 2_adp: 0.1979 0.2405 0.003 0.543 21.2 131.4 49.6 0 0.292 2_regHadp: 0.1994 0.2408 0.003 0.543 21.2 131.4 49.6 0 0.292 3_bss: 0.1990 0.2398 0.003 0.543 20.6 130.8 49.0 0 0.292 3_settarget: 0.1990 0.2398 0.003 0.543 20.6 130.8 49.0 0 0.292 3_updatephipsi: 0.1990 0.2398 0.003 0.543 20.6 130.8 49.0 0 0.292 3_updatecdl: 0.1990 0.2398 0.003 0.566 20.6 130.8 49.0 0 0.292 3_setrh: 0.1990 0.2398 0.003 0.566 20.6 130.8 49.0 0 0.291 3_nqh: 0.1991 0.2399 0.003 0.566 20.6 130.8 49.0 0 0.292 3_realsrl: 0.1991 0.2399 0.003 0.566 20.6 130.8 49.0 0 0.292 3_weight: 0.1991 0.2399 0.003 0.566 20.6 130.8 49.0 0 0.292 3_xyzrec: 0.1979 0.2391 0.003 0.559 20.6 130.8 49.0 0 0.292 3_realsrl2: 0.1979 0.2391 0.003 0.559 20.6 130.8 49.0 0 0.292 3_adp: 0.1899 0.2369 0.003 0.559 16.0 135.6 48.0 0 0.292 3_regHadp: 0.1893 0.2370 0.003 0.559 16.0 135.6 48.0 0 0.292 end: 0.1890 0.2369 0.003 0.559 15.8 135.4 47.8 0 0.292 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2jcl_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2jcl_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.3800 Refinement macro-cycles (run) : 468.8900 Write final files (write_after_run_outputs) : 20.6500 Total : 496.9200 Total CPU time: 8.78 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:36:34 PDT -0700 (1716251794.82 s) Start R-work = 0.2053, R-free = 0.2492 Final R-work = 0.1890, R-free = 0.2369 =============================================================================== Job complete usr+sys time: 551.01 seconds wall clock time: 21 minutes 34.16 seconds (1294.16 seconds total)