Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1wl3.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.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_1wl3.prmtop amber.coordinate_file_name=4amber_1wl3.rst7 amber.order_file_name=4amber_1wl3.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_1wl3.order 4amber_1wl3.prmtop 4amber_1wl3.rst7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_1wl3.pdb" } default_model = "4phenix_1wl3.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.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_1wl3.prmtop coordinate_file_name = 4amber_1wl3.rst7 order_file_name = 4amber_1wl3.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: 8904 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4442 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 270} Chain: "B" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4462 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 271} Time building chain proxies: 0.98, per 1000 atoms: 0.11 Number of scatterers: 8904 At special positions: 0 Unit cell: (149.548, 149.548, 68.031, 90, 90, 90) Space group: P 4 21 2 (No. 90) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 823 8.00 N 729 7.00 C 2831 6.00 H 4497 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: 1.67 Conformation dependent library (CDL) restraints added in 182.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.515A pdb=" N PHE A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.888A pdb=" N LYS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 35' Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 61 through 85 removed outlier: 3.620A pdb=" N HIS A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 102 through 123 removed outlier: 3.560A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 149 Processing helix chain 'A' and resid 156 through 166 removed outlier: 3.736A pdb=" N GLY A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 187 through 211 Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 263 through 281 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'B' and resid 14 through 27 removed outlier: 3.646A pdb=" N PHE B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.528A pdb=" N LYS B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 34' Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 61 through 84 removed outlier: 3.626A pdb=" N HIS B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.513A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.568A pdb=" N GLN B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 166 removed outlier: 3.649A pdb=" N GLY B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 187 through 211 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 263 through 281 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' 281 hydrogen bonds defined for protein. 843 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: 1.56 Time building geometry restraints manager: 1.90 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: 4495 1.15 - 1.31: 769 1.31 - 1.48: 1661 1.48 - 1.64: 2002 1.64 - 1.81: 46 Bond restraints: 8973 Sorted by residual: bond pdb=" NE2 HIS B 118 " pdb=" HE2 HIS B 118 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER A 252 " pdb=" H SER A 252 " 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 A 39 " pdb=" H TYR A 39 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG A 259 " pdb=" HE ARG A 259 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 32 " pdb=" H ILE A 32 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 8968 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.54: 115 104.54 - 111.91: 10297 111.91 - 119.29: 2244 119.29 - 126.66: 3606 126.66 - 134.03: 30 Bond angle restraints: 16292 Sorted by residual: angle pdb=" N LEU B 38 " pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 111.11 124.42 -13.31 1.20e+00 6.94e-01 1.23e+02 angle pdb=" N GLU B 14 " pdb=" CA GLU B 14 " pdb=" C GLU B 14 " ideal model delta sigma weight residual 112.23 102.63 9.60 1.26e+00 6.30e-01 5.81e+01 angle pdb=" N ARG B 286 " pdb=" CA ARG B 286 " pdb=" C ARG B 286 " ideal model delta sigma weight residual 112.87 104.22 8.65 1.20e+00 6.94e-01 5.20e+01 angle pdb=" N ARG A 286 " pdb=" CA ARG A 286 " pdb=" C ARG A 286 " ideal model delta sigma weight residual 110.80 125.14 -14.34 2.13e+00 2.20e-01 4.53e+01 angle pdb=" N GLY B 168 " pdb=" CA GLY B 168 " pdb=" C GLY B 168 " ideal model delta sigma weight residual 112.83 120.50 -7.67 1.22e+00 6.72e-01 3.96e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 3713 15.89 - 31.78: 224 31.78 - 47.67: 101 47.67 - 63.56: 79 63.56 - 79.45: 14 Dihedral angle restraints: 4131 sinusoidal: 2289 harmonic: 1842 Sorted by residual: dihedral pdb=" C ASP A 287 " pdb=" N ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual -122.60 -131.21 8.61 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual 122.80 131.25 -8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CG ARG A 243 " pdb=" CD ARG A 243 " pdb=" NE ARG A 243 " pdb=" CZ ARG A 243 " ideal model delta sinusoidal sigma weight residual -180.00 -137.85 -42.15 2 1.50e+01 4.44e-03 9.61e+00 ... (remaining 4128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 495 0.097 - 0.194: 152 0.194 - 0.291: 22 0.291 - 0.388: 1 0.388 - 0.485: 3 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA LEU B 38 " pdb=" N LEU B 38 " pdb=" C LEU B 38 " pdb=" CB LEU B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA ASP A 287 " pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CB ASP A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA ARG A 286 " pdb=" N ARG A 286 " pdb=" C ARG A 286 " pdb=" CB ARG A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 670 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 171 " -0.140 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG PHE A 171 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 171 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 171 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 171 " 0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 171 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 171 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 171 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 251 " 0.084 2.00e-02 2.50e+03 2.57e-02 2.63e+01 pdb=" CG TRP B 251 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 251 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 251 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 251 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 251 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 251 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 251 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP B 251 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP B 251 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 251 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 251 " 0.024 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 251 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 251 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 11 " 0.072 2.00e-02 2.50e+03 2.68e-02 2.16e+01 pdb=" CG TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 11 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 11 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 11 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 11 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR A 11 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 11 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 11 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 11 " 0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.75: 94 1.75 - 2.46: 4870 2.46 - 3.17: 29514 3.17 - 3.89: 38772 3.89 - 4.60: 58785 Nonbonded interactions: 132035 Sorted by model distance: nonbonded pdb=" HD2 PHE A 171 " pdb=" HA2 GLY A 197 " model vdw 1.033 2.270 nonbonded pdb=" HG SER B 229 " pdb=" HD2 PRO B 231 " model vdw 1.038 2.270 nonbonded pdb=" HE ARG B 19 " pdb=" HG SER B 65 " model vdw 1.203 2.100 nonbonded pdb=" HG SER A 48 " pdb="HD12 LEU A 177 " model vdw 1.262 2.270 nonbonded pdb=" HE3 LYS A 93 " pdb="HH22 ARG B 259 " model vdw sym.op. 1.356 2.270 y+1/2,-x+1/2,z ... (remaining 132030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1wl3.prmtop atom order : 4amber_1wl3.order coordinates : 4amber_1wl3.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 24 15.91 1 O 823 7.97 1 N 729 6.97 1 C 2831 5.97 1 H 4497 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: 4497 of 8904 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8904 n_use_u_iso = 8904 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 = 8904 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8904 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8904 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 12 through 27 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 30 through 35 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 43 through 54 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 61 through 85 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 96 through 100 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 102 through 123 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 126 through 149 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 156 through 166 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 168 through 182 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 187 through 211 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 230 through 238 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 240 through 247 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 251 through 260 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 263 through 281 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 283 through 285 helix_type = alpha pi *3_10 unknown } helix { serial_number = "16" helix_identifier = "16" selection = chain 'B' and resid 14 through 27 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'B' and resid 30 through 34 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'B' and resid 43 through 54 } helix { serial_number = "19" helix_identifier = "19" selection = chain 'B' and resid 61 through 84 } helix { serial_number = "20" helix_identifier = "20" selection = chain 'B' and resid 96 through 100 } helix { serial_number = "21" helix_identifier = "21" selection = chain 'B' and resid 102 through 123 } helix { serial_number = "22" helix_identifier = "22" selection = chain 'B' and resid 126 through 149 } helix { serial_number = "23" helix_identifier = "23" selection = chain 'B' and resid 156 through 166 } helix { serial_number = "24" helix_identifier = "24" selection = chain 'B' and resid 168 through 182 } helix { serial_number = "25" helix_identifier = "25" selection = chain 'B' and resid 187 through 211 } helix { serial_number = "26" helix_identifier = "26" selection = chain 'B' and resid 230 through 238 } helix { serial_number = "27" helix_identifier = "27" selection = chain 'B' and resid 240 through 248 } helix { serial_number = "28" helix_identifier = "28" selection = chain 'B' and resid 251 through 261 } helix { serial_number = "29" helix_identifier = "29" selection = chain 'B' and resid 263 through 281 } helix { serial_number = "30" helix_identifier = "30" selection = chain 'B' and resid 283 through 285 helix_type = alpha pi *3_10 unknown } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_1wl3.prmtop" coordinate_file_name = "4amber_1wl3.rst7" order_file_name = "4amber_1wl3.order" } } output { prefix = "4phenix_1wl3_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: 3.50 - 41.75 A, n_refl.=9579 (all), 5.31 % free)-------------| | | | r_work= 0.4621 r_free= 0.4890 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 3.693379 | | target function (ml) not normalized (work): 33498.947427 | | target function (ml) not normalized (free): 2004.459357 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.75 - 5.55 0.98 2477 144 0.4990 0.4772 4.4926 5.1189| | 2: 5.55 - 4.41 0.96 2311 121 0.3864 0.4310 3.651 3.6315| | 3: 4.41 - 3.85 0.93 2220 112 0.4707 0.5137 3.3527 3.4439| | 4: 3.85 - 3.50 0.88 2062 132 0.4870 0.5652 3.1477 3.35| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 41.75 - 5.55 2477 144 0.45 54.83 0.83 0.03 996.05| | 2: 5.55 - 4.41 2311 121 0.45 55.13 1.34 0.02 444.87| | 3: 4.41 - 3.85 2220 112 0.63 41.18 1.62 0.03 154.97| | 4: 3.85 - 3.50 2062 132 0.56 47.35 1.53 0.03 126.33| |alpha: min = 0.02 max = 0.03 mean = 0.03| |beta: min = 126.33 max = 996.05 mean = 452.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.52| |phase err.(work): min = 0.00 max = 89.99 mean = 49.86| |phase err.(test): min = 0.00 max = 89.91 mean = 48.89| |-----------------------------------------------------------------------------| ----------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 : 0.005 0.085 4476 Z= 0.343 Angle : 1.323 14.340 6012 Z= 0.928 Chirality : 0.095 0.485 673 Planarity : 0.005 0.053 772 Dihedral : 15.841 79.450 1703 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 2.36 % Allowed : 5.26 % Favored : 92.38 % Rotamer: Outliers : 3.40 % Allowed : 7.43 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.05 (0.27), residues: 551 helix: -2.44 (0.18), residues: 445 sheet: None (None), residues: 0 loop : -2.62 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 161 TYR 0.056 0.011 TYR A 11 PHE 0.085 0.007 PHE A 171 TRP 0.056 0.008 TRP B 251 HIS 0.001 0.000 HIS B 118 Individual atomic B min max mean iso aniso Overall: 21.36 100.34 56.13 1.48 4407 0 Protein: 21.36 100.34 56.13 1.48 4407 0 Chain A: 24.53 91.36 59.78 N/A 2198 0 Chain B: 21.36 100.34 52.50 N/A 2209 0 Histogram: Values Number of atoms 21.36 - 29.26 126 29.26 - 37.16 321 37.16 - 45.05 629 45.05 - 52.95 817 52.95 - 60.85 833 60.85 - 68.75 769 68.75 - 76.65 497 76.65 - 84.54 290 84.54 - 92.44 121 92.44 - 100.34 4 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9579 (all), 5.31 % free)-------------| | | | r_work= 0.4621 r_free= 0.4890 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 3.693379 | | target function (ml) not normalized (work): 33498.947427 | | target function (ml) not normalized (free): 2004.459357 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4641 0.4621 0.4890 n_refl.: 9579 re-set all scales: r(all,work,free)=0.4641 0.4621 0.4890 n_refl.: 9579 remove outliers: r(all,work,free)=0.4620 0.4600 0.4849 n_refl.: 9561 overall B=23.61 to atoms: r(all,work,free)=0.5307 0.5280 0.5616 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2590 0.2574 0.2867 n_refl.: 9561 remove outliers: r(all,work,free)=0.2590 0.2574 0.2867 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.4372 1220.043 1226.624 1.159 1.120 0.405 16.951-13.495 94.17 95 2 0.3097 1758.187 1725.711 0.958 1.115 0.377 13.466-10.728 99.01 188 12 0.2304 2173.375 2116.852 1.047 1.101 0.368 10.715-8.517 98.92 348 19 0.1963 2052.424 2021.663 1.054 1.086 0.350 8.515-6.766 98.37 689 37 0.2416 1366.049 1306.590 0.989 1.055 0.326 6.761-5.374 96.29 1294 80 0.2751 856.125 812.076 0.873 1.008 0.279 5.373-4.268 96.39 2549 123 0.2285 952.144 913.444 0.996 0.932 0.222 4.267-3.500 89.96 3807 225 0.2936 675.491 628.139 1.237 0.835 0.129 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.4216 ============================ 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 = 3.295157 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168777 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2512 0.2825 0.0312 0.014 2.0 0.7 1.1 3.0 0 0.125 0.2370 0.2807 0.0437 0.014 2.0 0.3 1.1 2.5 0 0.250 0.2251 0.2796 0.0545 0.015 2.1 1.0 0.9 2.1 0 0.500 0.2133 0.2835 0.0703 0.016 2.3 2.6 0.7 2.3 0 1.000 0.2044 0.2883 0.0839 0.020 2.8 4.2 0.5 3.0 1 2.000 0.1993 0.2881 0.0888 0.024 3.2 6.3 1.1 4.5 4 3.000 0.2063 0.2894 0.0831 0.028 3.2 8.8 1.8 3.4 0 4.000 0.1933 0.2942 0.1009 0.031 4.1 9.2 2.9 5.9 15 5.000 0.1920 0.2943 0.1023 0.034 4.3 13.4 5.3 12.3 16 6.000 0.1895 0.2954 0.1059 0.037 4.6 16.9 6.7 13.0 21 7.000 0.1886 0.2967 0.1082 0.039 4.8 17.9 7.1 14.2 25 8.000 0.1991 0.2895 0.0904 0.041 4.0 13.7 2.2 3.6 5 9.000 0.1992 0.2894 0.0903 0.042 4.1 14.4 2.2 3.6 5 10.000 0.2072 0.2907 0.0835 0.019 2.7 3.8 1.1 5.1 2 1.648 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2251 0.2796 0.0545 0.015 2.1 1.0 0.9 2.1 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.51 27.96 5.45 1.045 79.397 0.169 0.055 22.65 27.70 5.06 3.368 79.645 0.005 0.055 22.10 27.69 5.59 3.450 79.731 0.021 0.053 20.99 27.80 6.81 4.702 80.063 0.084 0.048 20.47 27.92 7.46 6.008 80.382 0.169 0.046 20.20 28.00 7.80 6.973 80.653 0.253 0.045 19.93 28.07 8.15 8.094 81.045 0.338 0.044 19.80 28.07 8.27 8.617 81.197 0.422 0.044 19.71 28.12 8.41 9.083 81.331 0.506 0.043 19.56 28.18 8.62 9.917 81.626 0.591 0.043 19.50 28.22 8.72 10.293 81.736 0.675 0.042 19.35 28.30 8.95 11.299 82.089 0.759 0.042 19.25 28.37 9.13 12.103 82.357 0.844 0.041 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.021 Accepted refinement result: 22.10 27.69 5.59 3.450 79.731 0.021 0.053 Individual atomic B min max mean iso aniso Overall: 54.48 121.11 80.42 2.14 4407 0 Protein: 54.48 121.11 80.42 2.14 4407 0 Chain A: 54.48 113.06 83.70 N/A 2198 0 Chain B: 55.00 121.11 77.15 N/A 2209 0 Histogram: Values Number of atoms 54.48 - 61.15 236 61.15 - 67.81 526 67.81 - 74.47 797 74.47 - 81.13 819 81.13 - 87.80 794 87.80 - 94.46 562 94.46 - 101.12 386 101.12 - 107.79 210 107.79 - 114.45 70 114.45 - 121.11 7 =========================== Idealize ADP of riding H ========================== r_work=0.2210 r_free=0.2769 r_work=0.2211 r_free=0.2769 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2211 r_free= 0.2769 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ls_wunit_k1) (work): 0.052978 | | target function (ls_wunit_k1) not normalized (work): 479.664199 | | target function (ls_wunit_k1) not normalized (free): 41.179596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2241 0.2211 0.2769 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5297 0.5258 0.5753 n_refl.: 9561 remove outliers: r(all,work,free)=0.5297 0.5258 0.5753 n_refl.: 9561 overall B=5.33 to atoms: r(all,work,free)=0.5471 0.5431 0.5928 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2232 0.2202 0.2751 n_refl.: 9561 remove outliers: r(all,work,free)=0.2232 0.2202 0.2751 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.3644 486.896 486.665 1.187 1.108 0.409 16.951-13.495 94.17 95 2 0.2383 701.660 705.011 0.914 1.104 0.363 13.466-10.728 99.01 188 12 0.1863 867.353 853.918 1.018 1.091 0.357 10.715-8.517 98.92 348 19 0.1518 819.084 813.748 1.052 1.076 0.339 8.515-6.766 98.37 689 37 0.1877 545.165 534.796 1.005 1.046 0.332 6.761-5.374 96.29 1294 80 0.2424 341.664 332.183 0.901 1.001 0.270 5.373-4.268 96.39 2549 123 0.2044 379.983 369.076 1.024 0.927 0.217 4.267-3.500 89.96 3807 225 0.2547 269.576 256.216 1.258 0.834 0.110 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.6642 ============================ 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 = 0.924660 wxc_scale = 0.129 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044969 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2566 0.2770 0.0204 0.014 2.0 0.4 0.5 3.4 0 0.012 0.2384 0.2737 0.0354 0.014 2.0 0.2 0.7 2.5 0 0.036 0.2243 0.2694 0.0450 0.014 2.0 0.6 0.7 2.5 0 0.072 0.2189 0.2722 0.0533 0.014 2.1 1.5 0.5 2.8 0 0.107 0.2142 0.2731 0.0589 0.014 2.2 1.3 0.5 3.0 0 0.143 0.2182 0.2751 0.0569 0.015 2.2 1.0 0.9 2.1 0 0.179 0.2188 0.2755 0.0567 0.015 2.1 1.0 0.9 2.1 0 0.215 0.2195 0.2753 0.0558 0.015 2.1 1.0 0.9 2.1 0 0.251 0.2175 0.2730 0.0556 0.014 2.2 1.3 0.5 2.8 0 0.119 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2384 0.2737 0.0354 0.014 2.0 0.2 0.7 2.5 0 0.036 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.84 27.37 3.54 11.565 93.605 0.045 6.065 24.73 28.08 3.35 11.789 94.645 0.001 6.087 23.79 27.36 3.57 11.599 93.591 0.006 6.063 23.05 27.25 4.20 12.080 93.444 0.022 6.038 21.60 27.05 5.44 13.499 94.900 0.045 5.991 21.40 27.02 5.62 13.770 95.053 0.067 5.985 21.34 27.08 5.75 13.987 95.125 0.090 5.985 21.25 27.13 5.88 14.367 95.323 0.112 5.983 21.17 27.18 6.00 14.774 95.523 0.135 5.981 21.12 27.20 6.09 15.137 95.690 0.157 5.980 21.11 27.22 6.11 15.203 95.719 0.180 5.980 21.03 27.26 6.23 15.785 95.970 0.202 5.978 21.01 27.28 6.27 15.997 96.057 0.225 5.977 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.067 Accepted refinement result: 21.40 27.02 5.62 13.770 95.053 0.067 5.985 Individual atomic B min max mean iso aniso Overall: 54.81 172.46 88.67 10.43 4407 0 Protein: 54.81 172.46 88.67 10.43 4407 0 Chain A: 54.81 155.36 91.79 N/A 2198 0 Chain B: 55.34 172.46 85.56 N/A 2209 0 Histogram: Values Number of atoms 54.81 - 66.57 318 66.57 - 78.34 1076 78.34 - 90.10 1221 90.10 - 101.87 854 101.87 - 113.63 497 113.63 - 125.40 265 125.40 - 137.17 128 137.17 - 148.93 40 148.93 - 160.70 7 160.70 - 172.46 1 =========================== Idealize ADP of riding H ========================== r_work=0.2140 r_free=0.2702 r_work=0.2125 r_free=0.2705 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2125 r_free= 0.2705 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 5.981058 | | target function (ml) not normalized (work): 54152.497475 | | target function (ml) not normalized (free): 3115.136517 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2157 0.2125 0.2705 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5509 0.5470 0.5909 n_refl.: 9561 remove outliers: r(all,work,free)=0.5509 0.5470 0.5909 n_refl.: 9561 overall B=1.69 to atoms: r(all,work,free)=0.5567 0.5529 0.5966 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2133 0.2099 0.2719 n_refl.: 9561 remove outliers: r(all,work,free)=0.2133 0.2099 0.2719 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.3859 486.896 493.997 1.145 1.139 0.419 16.951-13.495 94.17 95 2 0.2491 701.660 692.805 0.884 1.133 0.364 13.466-10.728 99.01 188 12 0.1961 867.353 848.231 0.969 1.116 0.359 10.715-8.517 98.92 348 19 0.1578 819.084 811.019 1.005 1.096 0.341 8.515-6.766 98.37 689 37 0.1929 545.165 529.805 0.969 1.060 0.331 6.761-5.374 96.29 1294 80 0.2632 341.664 324.906 0.919 1.004 0.267 5.373-4.268 96.39 2549 123 0.1924 379.983 367.147 1.027 0.913 0.196 4.267-3.500 89.96 3807 225 0.2168 269.576 256.060 1.285 0.795 0.094 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.3069 ============================ 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 = 1.058800 wxc_scale = 0.181 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.046919 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2240 0.2724 0.0485 0.014 1.9 0.3 0.5 3.8 0 0.019 0.2064 0.2698 0.0634 0.014 2.0 0.6 0.5 3.0 0 0.057 0.2097 0.2719 0.0621 0.014 1.9 0.2 0.7 2.5 0 0.115 0.2098 0.2720 0.0622 0.014 1.9 0.2 0.7 2.5 0 0.172 0.2098 0.2719 0.0622 0.014 1.9 0.2 0.7 2.5 0 0.230 0.2097 0.2720 0.0623 0.014 1.9 0.2 0.7 2.5 0 0.287 0.2096 0.2720 0.0624 0.014 1.9 0.2 0.7 2.5 0 0.345 0.2095 0.2721 0.0625 0.014 1.9 0.2 0.7 2.5 0 0.402 0.2098 0.2719 0.0622 0.014 1.9 0.2 0.7 2.5 0 0.191 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2240 0.2724 0.0485 0.014 1.9 0.3 0.5 3.8 0 0.019 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.40 27.24 4.85 14.739 99.113 0.047 6.028 26.50 28.81 2.31 11.158 106.126 0.001 6.117 24.92 28.13 3.21 11.298 104.111 0.006 6.086 22.50 27.29 4.79 14.571 99.856 0.023 6.032 21.76 27.40 5.64 15.290 99.548 0.047 6.014 21.31 27.61 6.29 15.768 100.030 0.070 6.005 21.17 27.63 6.47 16.091 100.054 0.094 6.001 21.08 27.69 6.61 16.395 100.163 0.117 5.999 20.99 27.77 6.78 16.761 100.381 0.141 5.998 20.93 27.83 6.91 17.092 100.570 0.164 5.997 20.89 27.87 6.98 17.342 100.696 0.188 5.997 20.85 27.92 7.07 17.590 100.826 0.211 5.996 20.82 27.95 7.13 17.815 100.940 0.235 5.996 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.023 Accepted refinement result: 22.50 27.29 4.79 14.571 99.856 0.023 6.032 Individual atomic B min max mean iso aniso Overall: 53.32 183.28 91.86 8.30 4407 0 Protein: 53.32 183.28 91.86 8.30 4407 0 Chain A: 53.32 161.68 95.27 N/A 2198 0 Chain B: 53.94 183.28 88.46 N/A 2209 0 Histogram: Values Number of atoms 53.32 - 66.32 173 66.32 - 79.31 1062 79.31 - 92.31 1302 92.31 - 105.31 931 105.31 - 118.30 533 118.30 - 131.30 256 131.30 - 144.30 105 144.30 - 157.29 38 157.29 - 170.29 5 170.29 - 183.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.2250 r_free=0.2729 r_work=0.2258 r_free=0.2736 ----------X-ray data---------- |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2258 r_free= 0.2736 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 6.034999 | | target function (ml) not normalized (work): 54640.883748 | | target function (ml) not normalized (free): 3131.072336 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.75 - 5.55 0.97 2463 143 0.2270 0.2718 6.4144 6.5276| | 2: 5.55 - 4.41 0.96 2310 121 0.2150 0.2406 6.0728 6.1196| | 3: 4.41 - 3.85 0.93 2220 112 0.2172 0.2656 5.8821 6.061| | 4: 3.85 - 3.50 0.88 2061 131 0.2544 0.3312 5.704 5.9413| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 41.75 - 5.55 2463 143 0.75 29.39 1.00 1.02 65698.51| | 2: 5.55 - 4.41 2310 121 0.78 28.09 1.01 1.03 40180.34| | 3: 4.41 - 3.85 2220 112 0.79 27.49 1.03 1.00 25535.17| | 4: 3.85 - 3.50 2061 131 0.71 34.49 0.97 0.94 21762.98| |alpha: min = 0.94 max = 1.03 mean = 1.00| |beta: min = 21762.98 max = 65698.51 mean = 39338.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.76| |phase err.(work): min = 0.00 max = 89.96 mean = 29.75| |phase err.(test): min = 0.00 max = 89.83 mean = 29.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2285 0.2258 0.2736 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5670 0.5630 0.6084 n_refl.: 9561 remove outliers: r(all,work,free)=0.5670 0.5630 0.6084 n_refl.: 9561 overall B=-0.77 to atoms: r(all,work,free)=0.5643 0.5603 0.6059 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2313 0.2286 0.2758 n_refl.: 9561 remove outliers: r(all,work,free)=0.2313 0.2286 0.2758 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.3842 486.896 498.792 1.340 1.015 0.420 16.951-13.495 94.17 95 2 0.2558 701.660 699.903 1.052 1.019 0.372 13.466-10.728 99.01 188 12 0.1939 867.353 853.469 1.099 1.013 0.357 10.715-8.517 98.92 348 19 0.1689 819.084 815.625 1.107 1.009 0.331 8.515-6.766 98.37 689 37 0.2004 545.165 535.014 1.061 0.998 0.331 6.761-5.374 96.29 1294 80 0.2799 341.664 323.921 0.961 0.982 0.261 5.373-4.268 96.39 2549 123 0.2127 379.983 363.170 0.990 0.956 0.182 4.267-3.500 89.96 3807 225 0.2456 269.576 254.529 1.132 0.929 0.081 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-2.7543 ================= 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 : 0.4621 0.4890 0.005 1.323 21.4 100.3 56.1 0 0.000 1_bss: 0.2574 0.2867 0.005 1.323 45.0 124.0 79.7 0 0.000 1_settarget: 0.2574 0.2867 0.005 1.323 45.0 124.0 79.7 0 0.000 1_weight: 0.2574 0.2867 0.005 1.323 45.0 124.0 79.7 0 0.000 1_xyzrec: 0.2251 0.2796 0.015 2.121 45.0 124.0 79.7 0 0.307 1_adp: 0.2210 0.2769 0.015 2.121 54.5 121.1 80.4 0 0.307 1_regHadp: 0.2211 0.2769 0.015 2.121 54.5 121.1 80.4 0 0.307 2_bss: 0.2202 0.2751 0.015 2.121 59.8 126.4 85.7 0 0.307 2_settarget: 0.2202 0.2751 0.015 2.121 59.8 126.4 85.7 0 0.307 2_updatecdl: 0.2202 0.2751 0.015 2.116 59.8 126.4 85.7 0 0.307 2_weight: 0.2202 0.2751 0.015 2.116 59.8 126.4 85.7 0 0.307 2_xyzrec: 0.2384 0.2737 0.014 1.952 59.8 126.4 85.7 0 0.399 2_adp: 0.2140 0.2702 0.014 1.952 54.8 172.5 88.7 0 0.399 2_regHadp: 0.2125 0.2705 0.014 1.952 54.8 172.5 88.7 0 0.399 3_bss: 0.2099 0.2719 0.014 1.952 56.5 174.2 90.4 0 0.399 3_settarget: 0.2099 0.2719 0.014 1.952 56.5 174.2 90.4 0 0.399 3_updatecdl: 0.2099 0.2719 0.014 1.943 56.5 174.2 90.4 0 0.399 3_setrh: 0.2099 0.2719 0.014 1.943 56.5 174.2 90.4 0 0.399 3_weight: 0.2099 0.2719 0.014 1.943 56.5 174.2 90.4 0 0.399 3_xyzrec: 0.2240 0.2724 0.014 1.950 56.5 174.2 90.4 0 0.475 3_adp: 0.2250 0.2729 0.014 1.950 53.3 183.3 91.9 0 0.475 3_regHadp: 0.2258 0.2736 0.014 1.950 53.3 183.3 91.9 0 0.475 end: 0.2286 0.2758 0.014 1.950 52.6 182.5 91.1 0 0.475 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1wl3_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1wl3_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.3000 Refinement macro-cycles (run) : 316.3800 Write final files (write_after_run_outputs) : 11.9900 Total : 333.6700 Total CPU time: 6.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:47:02 PDT -0700 (1723222022.90 s) Start R-work = 0.2574, R-free = 0.2867 Final R-work = 0.2286, R-free = 0.2758 =============================================================================== Job complete usr+sys time: 391.31 seconds wall clock time: 15 minutes 35.83 seconds (935.83 seconds total)