Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_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 amber.topology_file_name=4amber_2jcl.prmtop amber.coordinate_file_name=4amber_2jcl.rst7 amber.order_file_name=4amber_2jcl.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_2jcl.order 4amber_2jcl.rst7 4amber_2jcl.prmtop Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_2jcl.pdb" } default_model = "4phenix_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 { 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 } amber { use_amber = True topology_file_name = 4amber_2jcl.prmtop coordinate_file_name = 4amber_2jcl.rst7 order_file_name = 4amber_2jcl.order } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 9177 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: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4576 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: 1.26, per 1000 atoms: 0.14 Number of scatterers: 9177 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 4538 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: 1.65 Conformation dependent library (CDL) restraints added in 192.7 milliseconds 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: 0.55 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: 1.49 Time building geometry restraints manager: 1.88 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: 4532 1.15 - 1.32: 823 1.32 - 1.49: 2124 1.49 - 1.66: 1795 1.66 - 1.83: 42 Bond restraints: 9316 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 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=" N MET B2100 " pdb=" H MET B2100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N TYR B2260 " pdb=" H TYR B2260 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU A1118 " pdb=" H LEU A1118 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9311 not shown) Histogram of bond angle deviations from ideal: 93.01 - 104.72: 202 104.72 - 116.43: 11723 116.43 - 128.14: 4842 128.14 - 139.85: 68 139.85 - 151.56: 1 Bond angle restraints: 16836 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 16831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3775 17.65 - 35.30: 404 35.30 - 52.95: 149 52.95 - 70.60: 38 70.60 - 88.25: 14 Dihedral angle restraints: 4380 sinusoidal: 2288 harmonic: 2092 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 4377 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: 0.76 - 1.53: 46 1.53 - 2.30: 2273 2.30 - 3.07: 28936 3.07 - 3.83: 43380 3.83 - 4.60: 68834 Warning: very small nonbonded interaction distances. Nonbonded interactions: 143469 Sorted by model distance: nonbonded pdb=" HD1 HIS B2209 " pdb=" HE2 HIS B2213 " model vdw 0.763 2.100 nonbonded pdb="HE21 GLN B2231 " pdb=" HG SER B2355 " model vdw 0.819 2.100 nonbonded pdb="HD11 ILE B2283 " pdb=" HE1 MET B2354 " model vdw 0.877 2.440 nonbonded pdb=" HG SER B2150 " pdb=" H PHE B2230 " model vdw 0.996 2.100 nonbonded pdb=" HG1 THR B2101 " pdb=" H ALA B2105 " model vdw 1.030 2.100 ... (remaining 143464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_2jcl.prmtop atom order : 4amber_2jcl.order coordinates : 4amber_2jcl.rst7 ===================================== ... ===================================== ============================== 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 4538 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: 4538 of 9177 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 9177 n_use_u_iso = 9177 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 = 9177 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (9177 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 9177 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 } amber { use_amber = True topology_file_name = "4amber_2jcl.prmtop" coordinate_file_name = "4amber_2jcl.rst7" order_file_name = "4amber_2jcl.order" } } output { prefix = "4phenix_2jcl_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.29 - 25.82 A, n_refl.=18668 (all), 5.14 % free)------------| | | | r_work= 0.3573 r_free= 0.4495 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 6.005211 | | target function (ml) not normalized (work): 106340.282389 | | target function (ml) not normalized (free): 5849.782982 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.5457 0.6040 6.8078 7.0009| | 2: 6.27 - 4.99 1.00 2567 134 0.2968 0.4069 6.2477 6.2432| | 3: 4.99 - 4.36 1.00 2539 145 0.2825 0.3791 6.0252 6.1828| | 4: 4.36 - 3.96 1.00 2505 152 0.3252 0.4023 5.8945 5.9394| | 5: 3.96 - 3.68 1.00 2528 131 0.3402 0.4582 5.7786 5.8935| | 6: 3.68 - 3.46 1.00 2500 143 0.3410 0.4641 5.6931 5.8227| | 7: 3.46 - 3.29 0.98 2460 134 0.3282 0.4297 5.5432 5.6873| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 68.38 0.66 0.21 181598.40| | 2: 6.27 - 4.99 2567 134 0.53 49.27 1.03 0.40 83598.94| | 3: 4.99 - 4.36 2539 145 0.80 26.77 1.22 0.53 30480.49| | 4: 4.36 - 3.96 2505 152 0.82 25.01 1.35 0.59 23566.42| | 5: 3.96 - 3.68 2528 131 0.79 27.40 1.39 0.61 20515.44| | 6: 3.68 - 3.46 2500 143 0.77 29.89 1.34 0.59 18352.64| | 7: 3.46 - 3.29 2460 134 0.71 34.72 1.26 0.53 15754.67| |alpha: min = 0.21 max = 0.61 mean = 0.49| |beta: min = 15754.67 max = 181598.40 mean = 54286.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 89.99 mean = 37.55| |phase err.(test): min = 0.00 max = 89.90 mean = 36.15| |-----------------------------------------------------------------------------| ----------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= 0.3573 r_free= 0.4495 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 6.005211 | | target function (ml) not normalized (work): 106340.282389 | | target function (ml) not normalized (free): 5849.782982 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3622 0.3573 0.4495 n_refl.: 18668 re-set all scales: r(all,work,free)=0.3622 0.3573 0.4495 n_refl.: 18668 remove outliers: r(all,work,free)=0.3575 0.3523 0.4490 n_refl.: 18638 overall B=8.54 to atoms: r(all,work,free)=0.3867 0.3811 0.4835 n_refl.: 18638 bulk-solvent and scaling: r(all,work,free)=0.2083 0.2060 0.2508 n_refl.: 18638 remove outliers: r(all,work,free)=0.2079 0.2056 0.2498 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 0.6219 63.747 40.138 0.106 0.894 0.424 14.999-13.060 76.79 85 1 0.6561 531.204 498.899 0.902 0.898 0.386 12.994-11.375 88.62 138 10 0.2668 977.029 933.685 1.253 0.895 0.384 11.369-9.901 99.22 240 13 0.1742 1062.970 1045.686 1.355 0.894 0.396 9.883-8.622 100.00 356 16 0.1649 1073.115 1055.150 1.313 0.892 0.400 8.618-7.507 99.82 546 20 0.1859 778.423 762.368 1.257 0.890 0.416 7.504-6.535 100.00 806 36 0.2234 611.703 592.658 1.181 0.888 0.411 6.532-5.692 100.00 1192 64 0.2027 610.094 587.894 1.149 0.884 0.373 5.690-4.954 99.95 1802 91 0.1951 639.573 618.824 1.081 0.880 0.361 4.954-4.314 100.00 2679 154 0.1715 728.342 711.950 1.134 0.873 0.334 4.314-3.756 100.00 4069 230 0.1850 628.257 609.006 1.193 0.865 0.254 3.756-3.291 98.98 5671 317 0.2543 453.052 424.873 1.168 0.854 0.168 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9564 b_overall=-3.1064 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.980550 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.294063 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 0.2394 0.2606 0.0212 0.014 2.0 1.4 1.1 7.5 0 0.125 0.2198 0.2542 0.0344 0.014 2.0 2.5 0.9 7.7 0 0.250 0.2059 0.2509 0.0451 0.014 2.1 3.4 1.3 8.1 0 0.500 0.1945 0.2457 0.0512 0.016 2.3 5.3 2.0 8.7 1 1.000 0.1849 0.2448 0.0598 0.019 2.7 7.0 2.0 9.9 3 2.000 0.1802 0.2459 0.0657 0.023 3.1 9.4 2.0 12.5 4 3.000 0.1770 0.2467 0.0697 0.026 3.5 12.4 2.2 13.1 7 4.000 0.1743 0.2481 0.0737 0.029 3.8 14.7 2.7 15.3 10 5.000 0.1721 0.2464 0.0743 0.032 4.1 15.5 2.9 15.9 12 6.000 0.1701 0.2466 0.0765 0.035 4.3 17.3 3.1 16.9 16 7.000 0.1693 0.2465 0.0772 0.037 4.7 19.4 3.1 19.2 22 8.000 0.1681 0.2460 0.0779 0.040 4.9 20.4 3.3 18.1 23 9.000 0.1672 0.2454 0.0783 0.042 5.0 22.0 3.1 18.8 25 10.000 0.1853 0.2463 0.0610 0.019 2.7 7.0 2.0 10.3 3 1.990 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2198 0.2542 0.0344 0.014 2.0 2.5 0.9 7.7 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.98 25.42 3.44 0.767 44.716 0.294 0.057 21.93 25.26 3.33 1.724 44.869 0.009 0.056 21.60 25.16 3.56 1.927 44.968 0.037 0.055 20.56 24.83 4.26 4.292 45.359 0.147 0.050 20.07 24.64 4.58 5.831 45.726 0.294 0.047 19.82 24.59 4.77 6.853 45.969 0.441 0.046 19.67 24.56 4.89 7.642 46.173 0.588 0.046 19.55 24.52 4.98 8.347 46.375 0.735 0.045 19.35 24.44 5.09 9.670 46.832 0.882 0.044 19.28 24.44 5.15 10.217 46.990 1.029 0.044 19.10 24.36 5.27 11.701 47.557 1.176 0.043 19.03 24.35 5.32 12.363 47.760 1.323 0.043 18.95 24.33 5.38 13.297 48.063 1.470 0.042 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.470 Accepted refinement result: 18.95 24.33 5.38 13.297 48.063 1.470 0.042 Individual atomic B min max mean iso aniso Overall: 17.83 158.49 51.56 12.71 4639 0 Protein: 17.83 129.24 51.19 12.66 4614 0 Other: 78.87 158.49 119.99 N/A 25 0 Chain A: 17.83 129.24 52.25 N/A 2307 0 Chain B: 19.23 158.49 50.88 N/A 2332 0 Histogram: Values Number of atoms 17.83 - 31.90 515 31.90 - 45.96 1522 45.96 - 60.03 1388 60.03 - 74.09 713 74.09 - 88.16 284 88.16 - 102.22 142 102.22 - 116.29 46 116.29 - 130.36 22 130.36 - 144.42 5 144.42 - 158.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1895 r_free=0.2433 r_work=0.1878 r_free=0.2430 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18632 (all), 5.14 % free)------------| | | | r_work= 0.1878 r_free= 0.2430 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.041550 | | target function (ls_wunit_k1) not normalized (work): 734.352063 | | target function (ls_wunit_k1) not normalized (free): 63.103851 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1907 0.1878 0.2430 n_refl.: 18632 re-set all scales: r(all,work,free)=0.3963 0.3901 0.5037 n_refl.: 18632 remove outliers: r(all,work,free)=0.3963 0.3901 0.5037 n_refl.: 18632 overall B=-0.97 to atoms: r(all,work,free)=0.3925 0.3864 0.4995 n_refl.: 18632 bulk-solvent and scaling: r(all,work,free)=0.1906 0.1877 0.2435 n_refl.: 18632 remove outliers: r(all,work,free)=0.1906 0.1877 0.2435 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 0.6072 37.385 26.829 0.109 1.015 0.440 14.999-13.060 76.79 85 1 0.6055 311.531 327.293 0.835 1.020 0.380 12.994-11.375 88.62 138 10 0.2214 572.991 564.215 1.132 1.017 0.384 11.369-9.901 99.22 240 13 0.1459 623.392 616.507 1.188 1.015 0.391 9.883-8.622 100.00 356 16 0.1449 629.342 624.343 1.170 1.013 0.398 8.618-7.507 99.82 546 20 0.1694 456.516 453.798 1.105 1.011 0.402 7.504-6.535 100.00 806 36 0.1840 358.741 354.086 1.033 1.007 0.402 6.532-5.692 100.00 1192 64 0.1845 357.797 350.496 1.014 1.003 0.372 5.690-4.954 99.95 1802 91 0.1817 375.086 366.910 0.952 0.996 0.363 4.954-4.314 100.00 2679 154 0.1580 427.146 421.213 1.001 0.987 0.334 4.314-3.756 100.00 4069 230 0.1768 368.449 361.937 1.054 0.976 0.271 3.756-3.291 98.98 5671 317 0.2285 265.698 254.655 1.051 0.961 0.153 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4696 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.894069 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.046310 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 0.1936 0.2435 0.0499 0.014 2.0 2.8 0.2 7.3 1 0.045 0.1860 0.2426 0.0566 0.014 2.0 2.2 0.9 7.7 0 0.134 0.1837 0.2413 0.0577 0.014 2.1 2.4 0.9 7.9 0 0.268 0.1816 0.2403 0.0587 0.015 2.1 2.5 0.9 7.9 0 0.402 0.1799 0.2395 0.0597 0.016 2.2 2.6 0.9 8.1 1 0.536 0.1756 0.2381 0.0625 0.020 2.5 3.2 0.9 8.3 2 0.671 0.1748 0.2377 0.0629 0.021 2.6 3.2 0.9 8.3 3 0.805 0.1739 0.2371 0.0632 0.023 2.7 3.3 0.9 8.3 3 0.939 0.1810 0.2399 0.0589 0.015 2.1 2.4 0.9 7.9 0 0.447 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1739 0.2371 0.0632 0.023 2.7 3.3 0.9 8.3 3 0.939 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.39 23.71 6.32 11.913 56.070 0.046 5.794 19.93 23.65 3.72 9.691 60.068 0.001 5.853 19.50 23.51 4.00 9.756 59.101 0.006 5.842 18.42 23.53 5.11 10.769 56.623 0.023 5.810 17.80 23.69 5.89 11.531 55.548 0.046 5.794 17.67 23.75 6.08 12.013 55.335 0.069 5.789 17.66 23.88 6.21 12.447 55.417 0.093 5.789 17.59 23.90 6.31 12.735 55.365 0.116 5.787 17.53 23.90 6.37 12.959 55.339 0.139 5.785 17.50 23.91 6.41 13.147 55.338 0.162 5.784 17.46 23.90 6.44 13.320 55.357 0.185 5.783 17.44 23.91 6.47 13.449 55.362 0.208 5.782 17.43 23.91 6.49 13.572 55.382 0.232 5.782 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 19.50 23.51 4.00 9.756 59.101 0.006 5.842 Individual atomic B min max mean iso aniso Overall: 32.35 152.52 56.59 5.26 4639 0 Protein: 32.35 123.27 56.28 5.10 4614 0 Other: 72.91 152.52 114.29 N/A 25 0 Chain A: 32.92 123.27 57.23 N/A 2307 0 Chain B: 32.35 152.52 55.96 N/A 2332 0 Histogram: Values Number of atoms 32.35 - 44.36 846 44.36 - 56.38 1856 56.38 - 68.40 1163 68.40 - 80.41 472 80.41 - 92.43 171 92.43 - 104.45 71 104.45 - 116.47 42 116.47 - 128.48 12 128.48 - 140.50 5 140.50 - 152.52 1 =========================== Idealize ADP of riding H ========================== r_work=0.1950 r_free=0.2351 r_work=0.1978 r_free=0.2351 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18632 (all), 5.14 % free)------------| | | | r_work= 0.1978 r_free= 0.2351 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 5.851174 | | target function (ml) not normalized (work): 103413.651173 | | target function (ml) not normalized (free): 5700.843756 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1997 0.1978 0.2351 n_refl.: 18632 re-set all scales: r(all,work,free)=0.4204 0.4140 0.5308 n_refl.: 18632 remove outliers: r(all,work,free)=0.4204 0.4140 0.5308 n_refl.: 18632 overall B=-2.74 to atoms: r(all,work,free)=0.4098 0.4036 0.5186 n_refl.: 18632 bulk-solvent and scaling: r(all,work,free)=0.1991 0.1971 0.2366 n_refl.: 18632 remove outliers: r(all,work,free)=0.1991 0.1970 0.2366 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 0.6135 37.385 26.372 0.080 1.023 0.407 14.999-13.060 75.89 84 1 0.5587 314.636 330.423 0.811 1.027 0.381 12.994-11.375 88.62 138 10 0.2073 572.991 567.769 1.087 1.024 0.387 11.369-9.901 99.22 240 13 0.1384 623.392 619.218 1.134 1.022 0.392 9.883-8.622 100.00 356 16 0.1279 629.342 625.649 1.116 1.019 0.393 8.618-7.507 99.82 546 20 0.1559 456.516 454.041 1.071 1.016 0.404 7.504-6.535 100.00 806 36 0.1725 358.741 352.185 1.009 1.011 0.406 6.532-5.692 100.00 1192 64 0.1799 357.797 348.018 0.986 1.006 0.367 5.690-4.954 99.95 1802 91 0.1838 375.086 365.274 0.929 0.998 0.359 4.954-4.314 100.00 2679 154 0.1627 427.146 418.459 0.972 0.987 0.331 4.314-3.756 100.00 4069 230 0.1924 368.449 358.287 1.043 0.973 0.260 3.756-3.291 98.98 5671 317 0.2578 265.698 249.064 1.039 0.955 0.159 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.7847 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.791388 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.040986 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 0.2144 0.2452 0.0308 0.014 2.0 2.4 0.2 7.3 1 0.040 0.1993 0.2367 0.0374 0.015 2.2 2.8 0.9 7.9 0 0.119 0.1947 0.2362 0.0416 0.017 2.4 3.5 0.9 8.1 1 0.237 0.1921 0.2359 0.0438 0.020 2.6 4.0 0.9 8.1 2 0.356 0.1915 0.2354 0.0438 0.022 2.8 3.9 0.9 8.3 3 0.475 0.1937 0.2362 0.0425 0.023 2.7 3.9 0.9 8.3 3 0.594 0.1919 0.2355 0.0435 0.024 2.9 3.7 1.1 8.3 3 0.712 0.1961 0.2363 0.0402 0.023 2.7 3.3 0.9 8.3 3 0.831 0.1917 0.2360 0.0443 0.021 2.7 4.1 0.9 8.1 3 0.396 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2144 0.2452 0.0308 0.014 2.0 2.4 0.2 7.3 1 0.040 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.44 24.52 3.08 8.960 59.426 0.041 5.912 22.65 25.16 2.52 7.704 63.271 0.001 5.951 21.52 24.85 3.33 8.795 61.875 0.005 5.918 21.00 24.45 3.45 9.125 59.252 0.020 5.897 20.29 24.35 4.06 10.150 59.288 0.041 5.871 20.11 24.35 4.23 10.454 59.537 0.061 5.865 20.00 24.34 4.34 10.756 59.736 0.082 5.862 19.95 24.35 4.40 10.924 59.819 0.102 5.860 19.89 24.37 4.48 11.161 59.954 0.123 5.859 19.84 24.39 4.54 11.373 60.062 0.143 5.858 19.80 24.39 4.58 11.577 60.161 0.164 5.857 19.78 24.40 4.62 11.732 60.233 0.184 5.856 19.75 24.41 4.65 11.910 60.313 0.205 5.855 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.082 Accepted refinement result: 20.00 24.34 4.34 10.756 59.736 0.082 5.862 Individual atomic B min max mean iso aniso Overall: 24.61 164.24 54.47 8.84 4639 0 Protein: 24.61 137.55 54.12 8.57 4614 0 Other: 65.17 164.24 118.45 N/A 25 0 Chain A: 25.87 137.55 55.15 N/A 2307 0 Chain B: 24.61 164.24 53.79 N/A 2332 0 Histogram: Values Number of atoms 24.61 - 38.57 677 38.57 - 52.54 1841 52.54 - 66.50 1204 66.50 - 80.46 555 80.46 - 94.43 210 94.43 - 108.39 97 108.39 - 122.35 34 122.35 - 136.32 14 136.32 - 150.28 6 150.28 - 164.24 1 =========================== Idealize ADP of riding H ========================== r_work=0.2000 r_free=0.2434 r_work=0.1992 r_free=0.2430 ----------X-ray data---------- |--(resolution: 3.29 - 25.82 A, n_refl.=18631 (all), 5.14 % free)------------| | | | r_work= 0.1992 r_free= 0.2430 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 5.858865 | | target function (ml) not normalized (work): 103543.713735 | | target function (ml) not normalized (free): 5719.908615 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1780 0.1915 5.9893 6.1057| | 2: 6.27 - 4.99 1.00 2567 134 0.1870 0.2545 5.8488 5.9787| | 3: 4.99 - 4.36 1.00 2539 145 0.1640 0.1800 5.8769 6.0162| | 4: 4.36 - 3.96 1.00 2505 152 0.1803 0.2321 5.8916 5.9514| | 5: 3.96 - 3.68 1.00 2528 131 0.2156 0.2605 5.8603 5.9693| | 6: 3.68 - 3.46 1.00 2500 143 0.2405 0.3088 5.828 5.9401| | 7: 3.46 - 3.29 0.98 2460 134 0.2848 0.3516 5.7108 5.8492| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.85 19.45 1.00 1.05 20674.66| | 2: 6.27 - 4.99 2567 134 0.86 20.02 1.00 1.01 20840.06| | 3: 4.99 - 4.36 2539 145 0.89 17.53 0.99 1.00 20886.40| | 4: 4.36 - 3.96 2505 152 0.88 18.60 1.02 1.01 21013.09| | 5: 3.96 - 3.68 2528 131 0.84 22.90 1.00 1.00 21940.31| | 6: 3.68 - 3.46 2500 143 0.79 27.81 1.03 0.95 22312.96| | 7: 3.46 - 3.29 2460 134 0.72 34.21 0.92 0.85 21931.61| |alpha: min = 0.85 max = 1.05 mean = 0.98| |beta: min = 20674.66 max = 22312.96 mean = 21364.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 89.98 mean = 22.87| |phase err.(test): min = 0.00 max = 88.96 mean = 23.07| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2015 0.1992 0.2430 n_refl.: 18631 re-set all scales: r(all,work,free)=0.4110 0.4049 0.5157 n_refl.: 18631 remove outliers: r(all,work,free)=0.4110 0.4049 0.5157 n_refl.: 18631 overall B=-0.74 to atoms: r(all,work,free)=0.4082 0.4021 0.5123 n_refl.: 18631 bulk-solvent and scaling: r(all,work,free)=0.2013 0.1990 0.2421 n_refl.: 18631 remove outliers: r(all,work,free)=0.2012 0.1989 0.2421 n_refl.: 18630 ======================== 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 0.6221 37.385 26.251 0.088 1.020 0.416 14.999-13.060 75.00 83 1 0.5491 317.723 336.576 0.900 1.025 0.390 12.994-11.375 88.62 138 10 0.2157 572.991 563.956 1.129 1.022 0.390 11.369-9.901 99.22 240 13 0.1425 623.392 619.578 1.183 1.020 0.391 9.883-8.622 100.00 356 16 0.1367 629.342 625.163 1.155 1.017 0.391 8.618-7.507 99.82 546 20 0.1662 456.516 452.181 1.101 1.015 0.392 7.504-6.535 100.00 806 36 0.1843 358.741 350.889 1.032 1.010 0.390 6.532-5.692 100.00 1192 64 0.1910 357.797 347.623 1.017 1.005 0.377 5.690-4.954 99.95 1802 91 0.1846 375.086 364.881 0.955 0.997 0.372 4.954-4.314 100.00 2679 154 0.1644 427.146 417.941 0.982 0.987 0.333 4.314-3.756 100.00 4069 230 0.1898 368.449 357.840 1.058 0.973 0.276 3.756-3.291 98.98 5671 317 0.2578 265.698 248.849 1.040 0.956 0.173 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-2.9047 ================= 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 : 0.3573 0.4495 0.016 1.720 13.2 125.7 36.4 0 0.000 1_bss: 0.2056 0.2498 0.016 1.720 21.8 134.2 44.9 0 0.000 1_settarget: 0.2056 0.2498 0.016 1.720 21.8 134.2 44.9 0 0.000 1_weight: 0.2056 0.2498 0.016 1.720 21.8 134.2 44.9 0 0.000 1_xyzrec: 0.2198 0.2542 0.014 1.986 21.8 134.2 44.9 0 0.309 1_adp: 0.1895 0.2433 0.014 1.986 17.8 158.5 51.6 0 0.309 1_regHadp: 0.1878 0.2430 0.014 1.986 17.8 158.5 51.6 0 0.309 2_bss: 0.1877 0.2435 0.014 1.986 16.9 157.5 50.6 0 0.309 2_settarget: 0.1877 0.2435 0.014 1.986 16.9 157.5 50.6 0 0.309 2_updatecdl: 0.1877 0.2435 0.014 1.983 16.9 157.5 50.6 0 0.309 2_weight: 0.1877 0.2435 0.014 1.983 16.9 157.5 50.6 0 0.309 2_xyzrec: 0.1739 0.2371 0.023 2.673 16.9 157.5 50.6 0 0.301 2_adp: 0.1950 0.2351 0.023 2.673 32.3 152.5 56.6 0 0.301 2_regHadp: 0.1978 0.2351 0.023 2.673 32.3 152.5 56.6 0 0.301 3_bss: 0.1970 0.2366 0.023 2.673 29.6 149.8 53.9 0 0.301 3_settarget: 0.1970 0.2366 0.023 2.673 29.6 149.8 53.9 0 0.301 3_updatecdl: 0.1970 0.2366 0.023 2.673 29.6 149.8 53.9 0 0.301 3_setrh: 0.1970 0.2366 0.023 2.673 29.6 149.8 53.9 0 0.301 3_weight: 0.1970 0.2366 0.023 2.673 29.6 149.8 53.9 0 0.301 3_xyzrec: 0.2144 0.2452 0.014 1.983 29.6 149.8 53.9 0 0.380 3_adp: 0.2000 0.2434 0.014 1.983 24.6 164.2 54.5 0 0.380 3_regHadp: 0.1992 0.2430 0.014 1.983 24.6 164.2 54.5 0 0.380 end: 0.1989 0.2421 0.014 1.983 23.9 163.5 53.7 0 0.380 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2jcl_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2jcl_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.8800 Refinement macro-cycles (run) : 235.6600 Write final files (write_after_run_outputs) : 15.2200 Total : 256.7600 Total CPU time: 4.90 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:40:13 PDT -0700 (1723221613.63 s) Start R-work = 0.2056, R-free = 0.2498 Final R-work = 0.1989, R-free = 0.2421 =============================================================================== Job complete usr+sys time: 310.63 seconds wall clock time: 8 minutes 54.25 seconds (534.25 seconds total)