Starting phenix.refine on Mon May 20 17:16:28 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fp9.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fp9.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fp9.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 7982 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7982 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 461} Time building chain proxies: 1.45, per 1000 atoms: 0.18 Number of scatterers: 7982 At special positions: 0 Unit cell: (104.913, 52.445, 104.908, 90, 96.42, 90) Space group: C 1 2 1 (No. 5) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 707 8.00 N 703 7.00 C 2641 6.00 H 3920 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 384.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Time building geometry restraints manager: 2.41 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: 3919 1.15 - 1.32: 661 1.32 - 1.48: 1834 1.48 - 1.65: 1688 1.65 - 1.82: 21 Bond restraints: 8123 Sorted by residual: bond pdb=" NH1 ARG A 84 " pdb="HH11 ARG A 84 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG A 476 " pdb="HH22 ARG A 476 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR A 399 " pdb=" H THR A 399 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG A 279 " pdb="HH22 ARG A 279 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE1 TRP A 159 " pdb=" HE1 TRP A 159 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8118 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 414 106.96 - 113.72: 8838 113.72 - 120.48: 2791 120.48 - 127.23: 2538 127.23 - 133.99: 74 Bond angle restraints: 14655 Sorted by residual: angle pdb=" OE1 GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 122.60 112.79 9.81 1.00e+00 1.00e+00 9.63e+01 angle pdb=" N THR A 391 " pdb=" CA THR A 391 " pdb=" C THR A 391 " ideal model delta sigma weight residual 111.36 102.64 8.72 1.09e+00 8.42e-01 6.40e+01 angle pdb=" CG GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 116.40 126.40 -10.00 1.50e+00 4.44e-01 4.44e+01 angle pdb=" N GLY A 21 " pdb=" CA GLY A 21 " pdb=" C GLY A 21 " ideal model delta sigma weight residual 114.90 124.70 -9.80 1.54e+00 4.22e-01 4.05e+01 angle pdb=" N GLY A 114 " pdb=" CA GLY A 114 " pdb=" C GLY A 114 " ideal model delta sigma weight residual 114.67 108.55 6.12 1.10e+00 8.26e-01 3.10e+01 ... (remaining 14650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 3435 14.82 - 29.65: 193 29.65 - 44.47: 97 44.47 - 59.29: 91 59.29 - 74.12: 23 Dihedral angle restraints: 3839 sinusoidal: 2018 harmonic: 1821 Sorted by residual: dihedral pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " pdb=" CZ ARG A 84 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " ideal model delta sinusoidal sigma weight residual 180.00 -129.53 -50.47 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " ideal model delta sinusoidal sigma weight residual 60.00 109.93 -49.93 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 3836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 255 0.056 - 0.112: 233 0.112 - 0.168: 47 0.168 - 0.224: 23 0.224 - 0.280: 6 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" C PRO A 469 " pdb=" CB PRO A 469 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA VAL A 349 " pdb=" N VAL A 349 " pdb=" C VAL A 349 " pdb=" CB VAL A 349 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL A 182 " pdb=" N VAL A 182 " pdb=" C VAL A 182 " pdb=" CB VAL A 182 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 561 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.051 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" CG TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.051 2.00e-02 2.50e+03 1.96e-02 1.15e+01 pdb=" CG TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 192 " 0.052 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" CG PHE A 192 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 192 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 192 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 192 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 192 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 192 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 192 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 192 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 192 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 192 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 192 " 0.017 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 410 1.94 - 2.61: 9016 2.61 - 3.27: 26771 3.27 - 3.94: 35377 3.94 - 4.60: 53388 Nonbonded interactions: 124962 Sorted by model distance: nonbonded pdb=" O PRO A 215 " pdb="HH22 ARG A 279 " model vdw 1.279 1.850 nonbonded pdb=" HG2 ARG A 75 " pdb=" HD3 PRO A 76 " model vdw 1.320 2.440 nonbonded pdb=" HB3 GLN A 27 " pdb="HH21 ARG A 30 " model vdw 1.321 2.270 nonbonded pdb=" HG3 GLU A 334 " pdb=" HD3 PRO A 336 " model vdw 1.355 2.440 nonbonded pdb="HH22 ARG A 291 " pdb=" HE1 HIS A 394 " model vdw 1.358 2.100 ... (remaining 124957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 11 15.96 2 O 707 7.97 1 N 703 6.97 1 C 2641 5.97 2 H 3920 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: 3920 of 7982 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7982 n_use_u_iso = 7982 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 = 7982 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7982 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7982 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 { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1fp9_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3920 occupancy sum: 3920.00 (% of total atoms 49.11) Rotatable: count: 903 occupancy sum: 903.00 (% of total atoms 11.31) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 52.13 A, n_refl.=10132 (all), 10.01 % free)------------| | | | r_work= 0.4298 r_free= 0.5329 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.559026 | | target function (ml) not normalized (work): 50687.195951 | | target function (ml) not normalized (free): 5601.206097 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 52.13 - 5.93 0.97 1355 151 0.4603 0.4878 6.2066 6.1554| | 2: 5.93 - 4.71 0.96 1323 147 0.3547 0.4794 5.7546 5.7028| | 3: 4.71 - 4.11 0.96 1288 144 0.4084 0.5271 5.5696 5.4451| | 4: 4.11 - 3.74 0.96 1288 143 0.4551 0.5640 5.5142 5.619| | 5: 3.74 - 3.47 0.96 1281 142 0.4754 0.5967 5.4726 5.2661| | 6: 3.47 - 3.26 0.97 1282 142 0.4418 0.5860 5.2538 5.3947| | 7: 3.26 - 3.10 0.97 1301 145 0.4200 0.5257 5.1055 5.0481| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 52.13 - 5.93 1355 151 0.16 77.62 0.60 0.03 59863.03| | 2: 5.93 - 4.71 1323 147 0.58 46.10 1.30 0.17 26644.58| | 3: 4.71 - 4.11 1288 144 0.83 24.31 1.53 0.26 9202.68| | 4: 4.11 - 3.74 1288 143 0.82 25.71 1.67 0.28 8178.16| | 5: 3.74 - 3.47 1281 142 0.80 27.27 1.71 0.29 7239.08| | 6: 3.47 - 3.26 1282 142 0.77 30.37 1.60 0.27 6252.41| | 7: 3.26 - 3.10 1301 145 0.73 33.46 1.45 0.23 4577.34| |alpha: min = 0.03 max = 0.29 mean = 0.22| |beta: min = 4577.34 max = 59863.03 mean = 17766.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 90.00 mean = 38.16| |phase err.(test): min = 0.00 max = 89.99 mean = 38.55| |-----------------------------------------------------------------------------| ----------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 0.046 4203 Z= 0.321 Angle : 1.249 9.998 5718 Z= 0.861 Chirality : 0.082 0.280 564 Planarity : 0.005 0.040 750 Dihedral : 14.688 74.118 1524 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 1.81 % Allowed : 12.25 % Favored : 85.94 % Rotamer: Outliers : 2.24 % Allowed : 2.24 % Favored : 95.51 % 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: -5.15 (0.30), residues: 498 helix: -4.21 (0.20), residues: 229 sheet: -1.62 (0.66), residues: 60 loop : -2.83 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 279 TYR 0.043 0.007 TYR A 141 PHE 0.032 0.005 PHE A 192 TRP 0.033 0.006 TRP A 159 HIS 0.002 0.000 HIS A 384 Individual atomic B min max mean iso aniso Overall: 12.70 77.70 33.40 2.74 4062 0 Protein: 12.70 77.70 33.40 2.74 4062 0 Chain A: 12.70 77.70 33.40 N/A 4062 0 Histogram: Values Number of atoms 12.70 - 19.20 560 19.20 - 25.70 851 25.70 - 32.20 919 32.20 - 38.70 595 38.70 - 45.20 378 45.20 - 51.70 244 51.70 - 58.20 183 58.20 - 64.70 129 64.70 - 71.20 85 71.20 - 77.70 118 |-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: 3.10 - 52.13 A, n_refl.=10132 (all), 10.01 % free)------------| | | | r_work= 0.4298 r_free= 0.5329 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.559026 | | target function (ml) not normalized (work): 50687.195951 | | target function (ml) not normalized (free): 5601.206097 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4407 0.4298 0.5329 n_refl.: 10132 re-set all scales: r(all,work,free)=0.4407 0.4298 0.5329 n_refl.: 10132 remove outliers: r(all,work,free)=0.4160 0.4027 0.5329 n_refl.: 10127 overall B=3.30 to atoms: r(all,work,free)=0.4309 0.4168 0.5513 n_refl.: 10127 bulk-solvent and scaling: r(all,work,free)=0.2399 0.2398 0.2416 n_refl.: 10127 remove outliers: r(all,work,free)=0.2397 0.2397 0.2400 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2450 1487.728 1446.815 1.051 1.275 0.404 14.763-11.705 97.09 91 9 0.1774 1550.646 1541.206 0.930 1.260 0.398 11.688-9.266 96.82 191 22 0.1307 1812.092 1781.536 0.927 1.236 0.395 9.245-7.329 97.77 355 40 0.1746 1351.329 1327.100 0.906 1.200 0.392 7.324-5.801 97.35 727 80 0.2319 959.455 924.737 0.843 1.146 0.389 5.796-4.593 96.03 1414 157 0.2081 1149.827 1113.607 0.910 1.055 0.352 4.593-3.637 95.90 2818 313 0.2376 1063.229 1016.166 1.121 0.912 0.295 3.636-3.100 96.41 3429 381 0.2953 729.417 669.032 1.293 0.739 0.111 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8055 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.427336 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.301602 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 0.1978 0.2732 0.0754 0.013 1.2 22.8 1.8 3.2 0 6.714 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.78 27.32 7.54 1.968 36.488 0.302 0.047 20.20 27.27 7.06 3.991 37.016 0.009 0.049 19.76 27.29 7.53 3.923 36.964 0.038 0.047 18.70 27.45 8.75 4.365 36.875 0.151 0.042 18.12 27.59 9.47 5.270 36.939 0.302 0.039 17.77 27.68 9.91 6.259 37.147 0.452 0.038 17.59 27.76 10.17 6.918 37.277 0.603 0.037 17.47 27.82 10.36 7.454 37.394 0.754 0.037 17.38 27.88 10.50 7.895 37.495 0.905 0.036 17.31 27.92 10.61 8.266 37.583 1.056 0.036 17.26 27.97 10.71 8.580 37.658 1.206 0.036 17.14 28.05 10.91 9.339 37.879 1.357 0.035 17.07 28.10 11.02 9.822 38.015 1.508 0.035 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.038 Accepted refinement result: 19.76 27.29 7.53 3.923 36.964 0.038 0.047 Individual atomic B min max mean iso aniso Overall: 18.68 82.52 37.64 2.50 4062 0 Protein: 18.68 82.52 37.64 2.50 4062 0 Chain A: 18.68 82.52 37.64 N/A 4062 0 Histogram: Values Number of atoms 18.68 - 25.06 358 25.06 - 31.45 1144 31.45 - 37.83 1054 37.83 - 44.22 563 44.22 - 50.60 371 50.60 - 56.98 197 56.98 - 63.37 149 63.37 - 69.75 91 69.75 - 76.14 80 76.14 - 82.52 55 =========================== Idealize ADP of riding H ========================== r_work=0.1976 r_free=0.2729 r_work=0.1974 r_free=0.2722 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.1974 r_free= 0.2722 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ls_wunit_k1) (work): 0.046658 | | target function (ls_wunit_k1) not normalized (work): 425.148209 | | target function (ls_wunit_k1) not normalized (free): 95.239069 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2049 0.1974 0.2722 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4216 0.4042 0.5540 n_refl.: 10125 remove outliers: r(all,work,free)=0.4216 0.4042 0.5540 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4216 0.4042 0.5540 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2047 0.1971 0.2736 n_refl.: 10125 remove outliers: r(all,work,free)=0.2047 0.1971 0.2736 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2089 811.495 794.890 1.131 1.203 0.408 14.763-11.705 97.09 91 9 0.1239 845.815 848.097 0.998 1.192 0.407 11.688-9.266 96.82 191 22 0.1042 988.423 972.682 0.970 1.173 0.400 9.245-7.329 97.77 355 40 0.1432 737.095 727.320 0.942 1.145 0.399 7.324-5.801 97.35 727 80 0.1907 523.344 513.377 0.869 1.103 0.390 5.796-4.593 96.03 1414 157 0.1712 627.184 618.397 0.918 1.032 0.360 4.593-3.637 95.90 2818 313 0.1941 579.948 568.700 1.098 0.918 0.270 3.636-3.100 96.41 3429 381 0.2459 397.867 377.979 1.258 0.782 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0185 b_overall=2.0957 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.938156 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.083872 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 0.2235 0.2726 0.0491 0.003 0.5 4.0 0.0 2.7 0 0.125 0.2172 0.2731 0.0559 0.004 0.6 5.1 0.2 2.5 0 0.250 0.2109 0.2765 0.0656 0.006 0.8 9.3 0.4 3.2 0 0.500 0.2040 0.2817 0.0777 0.010 1.1 16.4 1.4 5.0 0 1.000 0.1950 0.2869 0.0919 0.018 1.6 26.1 2.4 7.2 0 2.000 0.1894 0.2912 0.1018 0.024 2.0 32.8 4.6 10.5 0 3.000 0.1862 0.2931 0.1068 0.029 2.3 39.7 5.8 13.2 0 4.000 0.1835 0.2951 0.1116 0.034 2.6 43.4 6.4 14.0 0 5.000 0.1812 0.2991 0.1179 0.038 2.9 46.9 7.4 16.2 0 6.000 0.1793 0.3010 0.1217 0.043 3.1 51.5 8.2 18.7 0 7.000 0.1772 0.3022 0.1250 0.046 3.3 55.5 9.0 18.5 0 8.000 0.1757 0.3039 0.1282 0.050 3.6 59.6 9.8 18.7 1 9.000 0.1747 0.3058 0.1311 0.053 3.8 63.5 10.8 19.5 1 10.000 0.1994 0.2857 0.0863 0.014 1.3 21.9 2.2 6.2 0 1.469 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2235 0.2726 0.0491 0.003 0.5 4.0 0.0 2.7 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.35 27.26 4.91 5.766 41.288 0.084 6.377 23.39 27.78 4.38 6.403 43.301 0.003 6.411 22.19 27.30 5.11 6.011 41.188 0.010 6.370 21.72 27.36 5.64 6.302 41.041 0.042 6.356 20.65 27.76 7.11 8.407 41.221 0.084 6.326 20.36 27.89 7.54 9.275 41.604 0.126 6.320 20.16 28.01 7.85 10.073 41.912 0.168 6.316 20.02 28.12 8.09 10.782 42.163 0.210 6.314 19.92 28.21 8.29 11.407 42.372 0.252 6.313 19.85 28.29 8.44 11.954 42.550 0.294 6.312 19.79 28.35 8.55 12.409 42.695 0.335 6.311 19.75 28.41 8.66 12.822 42.824 0.377 6.311 19.72 28.46 8.74 13.185 42.935 0.419 6.310 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.010 Accepted refinement result: 22.19 27.30 5.11 6.011 41.188 0.010 6.370 Individual atomic B min max mean iso aniso Overall: 15.68 83.41 37.45 2.54 4062 0 Protein: 15.68 83.41 37.45 2.54 4062 0 Chain A: 15.68 83.41 37.45 N/A 4062 0 Histogram: Values Number of atoms 15.68 - 22.45 112 22.45 - 29.23 948 29.23 - 36.00 1245 36.00 - 42.77 724 42.77 - 49.55 450 49.55 - 56.32 219 56.32 - 63.09 162 63.09 - 69.87 89 69.87 - 76.64 72 76.64 - 83.41 41 =========================== Idealize ADP of riding H ========================== r_work=0.2219 r_free=0.2730 r_work=0.2218 r_free=0.2731 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.2218 r_free= 0.2731 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ml) (work): 6.369189 | | target function (ml) not normalized (work): 58036.053258 | | target function (ml) not normalized (free): 6577.752985 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2269 0.2218 0.2731 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4264 0.4098 0.5555 n_refl.: 10125 remove outliers: r(all,work,free)=0.4264 0.4098 0.5555 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4264 0.4098 0.5555 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2260 0.2209 0.2715 n_refl.: 10125 remove outliers: r(all,work,free)=0.2260 0.2209 0.2715 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2092 811.495 799.592 1.242 1.183 0.406 14.763-11.705 97.09 91 9 0.1314 845.815 850.832 1.090 1.173 0.404 11.688-9.266 96.82 191 22 0.1123 988.423 975.189 1.060 1.157 0.404 9.245-7.329 97.77 355 40 0.1511 737.095 730.736 1.029 1.131 0.404 7.324-5.801 97.35 727 80 0.2071 523.344 512.025 0.952 1.092 0.403 5.796-4.593 96.03 1414 157 0.1898 627.184 613.534 0.969 1.027 0.390 4.593-3.637 95.90 2818 313 0.2234 579.948 558.770 1.117 0.923 0.310 3.636-3.100 96.41 3429 381 0.2761 397.867 369.347 1.251 0.800 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8440 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2209 r_free=0.2715 After: r_work=0.2209 r_free=0.2714 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.125913 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.085692 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 0.2208 0.2717 0.0509 0.003 0.5 4.3 0.0 2.5 0 0.125 0.2198 0.2718 0.0521 0.004 0.5 4.6 0.0 2.5 0 0.250 0.2160 0.2716 0.0556 0.007 0.6 4.9 0.0 2.5 0 0.500 0.2055 0.2740 0.0685 0.015 1.3 8.5 0.0 2.5 0 1.000 0.1981 0.2799 0.0819 0.018 1.9 23.7 1.0 3.7 0 2.000 0.1960 0.2799 0.0839 0.019 2.0 25.8 1.4 5.2 0 3.000 0.1924 0.2807 0.0882 0.023 2.2 26.8 1.8 5.2 0 4.000 0.1890 0.2866 0.0976 0.029 2.9 40.2 3.2 8.0 0 5.000 0.1851 0.2859 0.1008 0.041 3.5 38.5 2.0 4.5 0 6.000 0.1842 0.2861 0.1019 0.042 3.7 39.7 2.4 5.7 1 7.000 0.1824 0.2912 0.1087 0.044 4.0 48.9 3.4 9.7 1 8.000 0.1812 0.2931 0.1118 0.047 4.3 50.4 3.6 10.2 2 9.000 0.1802 0.2971 0.1170 0.050 4.6 59.0 6.6 16.2 4 10.000 0.2000 0.2790 0.0790 0.017 1.8 19.7 0.8 3.0 0 1.563 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2208 0.2717 0.0509 0.003 0.5 4.3 0.0 2.5 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.08 27.17 5.09 5.741 41.095 0.086 6.370 23.49 27.83 4.35 6.265 42.683 0.003 6.415 22.08 27.19 5.11 5.784 41.067 0.011 6.370 21.60 27.25 5.65 6.206 40.874 0.043 6.356 20.50 27.72 7.23 8.468 40.835 0.086 6.327 20.24 27.89 7.65 9.280 41.221 0.129 6.321 20.07 28.04 7.98 10.040 41.529 0.171 6.318 19.95 28.18 8.22 10.720 41.778 0.214 6.317 19.87 28.28 8.40 11.324 41.986 0.257 6.316 19.82 28.37 8.55 11.830 42.154 0.300 6.315 19.77 28.44 8.66 12.276 42.298 0.343 6.315 19.74 28.50 8.76 12.666 42.423 0.386 6.315 19.71 28.56 8.85 13.012 42.532 0.428 6.315 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.011 Accepted refinement result: 22.08 27.19 5.11 5.784 41.067 0.011 6.370 Individual atomic B min max mean iso aniso Overall: 15.98 83.57 37.39 2.53 4062 0 Protein: 15.98 83.57 37.39 2.53 4062 0 Chain A: 15.98 83.57 37.39 N/A 4062 0 Histogram: Values Number of atoms 15.98 - 22.74 130 22.74 - 29.50 980 29.50 - 36.26 1250 36.26 - 43.02 688 43.02 - 49.77 451 49.77 - 56.53 213 56.53 - 63.29 155 63.29 - 70.05 93 70.05 - 76.81 63 76.81 - 83.57 39 =========================== Idealize ADP of riding H ========================== r_work=0.2208 r_free=0.2719 r_work=0.2208 r_free=0.2719 ----------X-ray data---------- |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.2208 r_free= 0.2719 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ml) (work): 6.370183 | | target function (ml) not normalized (work): 58045.111097 | | target function (ml) not normalized (free): 6578.104355 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 52.13 - 5.93 0.97 1352 151 0.1644 0.2005 6.354 6.526| | 2: 5.93 - 4.71 0.96 1323 147 0.1934 0.2443 6.4097 6.5105| | 3: 4.71 - 4.11 0.96 1288 144 0.2058 0.2270 6.4942 6.5443| | 4: 4.11 - 3.74 0.96 1286 142 0.2287 0.3137 6.4631 6.7265| | 5: 3.74 - 3.47 0.96 1281 142 0.2621 0.3014 6.4411 6.457| | 6: 3.47 - 3.26 0.97 1281 142 0.2645 0.3452 6.291 6.5021| | 7: 3.26 - 3.10 0.97 1301 145 0.2938 0.3617 6.1404 6.1925| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 52.13 - 5.93 1352 151 0.88 18.02 0.99 0.95 56859.10| | 2: 5.93 - 4.71 1323 147 0.86 20.96 1.00 0.90 64877.72| | 3: 4.71 - 4.11 1288 144 0.86 21.63 1.00 0.88 70191.13| | 4: 4.11 - 3.74 1286 142 0.82 25.47 1.00 0.88 76683.87| | 5: 3.74 - 3.47 1281 142 0.78 28.78 1.05 0.90 74292.07| | 6: 3.47 - 3.26 1281 142 0.73 33.32 1.02 0.84 66114.80| | 7: 3.26 - 3.10 1301 145 0.69 36.98 0.92 0.70 48267.56| |alpha: min = 0.70 max = 0.95 mean = 0.87| |beta: min = 48267.56 max = 76683.87 mean = 65231.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.62 mean = 26.38| |phase err.(test): min = 0.00 max = 89.59 mean = 27.07| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2259 0.2208 0.2719 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4263 0.4098 0.5554 n_refl.: 10125 remove outliers: r(all,work,free)=0.4263 0.4098 0.5554 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4263 0.4098 0.5554 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2253 0.2202 0.2707 n_refl.: 10125 remove outliers: r(all,work,free)=0.2253 0.2202 0.2707 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2078 811.495 797.643 1.195 1.225 0.408 14.763-11.705 97.09 91 9 0.1328 845.815 848.166 1.050 1.213 0.407 11.688-9.266 96.82 191 22 0.1126 988.423 972.495 1.022 1.193 0.409 9.245-7.329 97.77 355 40 0.1506 737.095 728.901 0.993 1.163 0.410 7.324-5.801 97.35 727 80 0.2064 523.344 511.425 0.926 1.116 0.410 5.796-4.593 96.03 1414 157 0.1898 627.184 613.452 0.952 1.039 0.400 4.593-3.637 95.90 2818 313 0.2230 579.948 558.959 1.115 0.916 0.310 3.636-3.100 96.41 3429 381 0.2742 397.867 370.094 1.288 0.769 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.4402 ================= 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 : 0.4298 0.5329 0.005 1.249 12.7 77.7 33.4 0 0.000 1_bss: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_settarget: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_weight: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_xyzrec: 0.1978 0.2732 0.013 1.227 16.0 81.0 36.7 0 0.262 1_adp: 0.1976 0.2729 0.013 1.227 18.7 82.5 37.6 0 0.262 1_regHadp: 0.1974 0.2722 0.013 1.227 18.7 82.5 37.6 0 0.262 2_bss: 0.1971 0.2736 0.013 1.227 18.7 82.5 37.6 0 0.262 2_settarget: 0.1971 0.2736 0.013 1.227 18.7 82.5 37.6 0 0.262 2_updatecdl: 0.1971 0.2736 0.013 1.271 18.7 82.5 37.6 0 0.262 2_weight: 0.1971 0.2736 0.013 1.271 18.7 82.5 37.6 0 0.262 2_xyzrec: 0.2235 0.2726 0.003 0.520 18.7 82.5 37.6 0 0.244 2_adp: 0.2219 0.2730 0.003 0.520 15.7 83.4 37.4 0 0.244 2_regHadp: 0.2218 0.2731 0.003 0.520 15.7 83.4 37.4 0 0.244 3_bss: 0.2209 0.2715 0.003 0.520 15.7 83.4 37.4 0 0.244 3_settarget: 0.2209 0.2715 0.003 0.520 15.7 83.4 37.4 0 0.244 3_updatecdl: 0.2209 0.2715 0.003 0.588 15.7 83.4 37.4 0 0.244 3_setrh: 0.2209 0.2714 0.003 0.588 15.7 83.4 37.4 0 0.244 3_weight: 0.2209 0.2714 0.003 0.588 15.7 83.4 37.4 0 0.244 3_xyzrec: 0.2208 0.2717 0.003 0.526 15.7 83.4 37.4 0 0.243 3_adp: 0.2208 0.2719 0.003 0.526 16.0 83.6 37.4 0 0.243 3_regHadp: 0.2208 0.2719 0.003 0.526 16.0 83.6 37.4 0 0.243 end: 0.2202 0.2707 0.003 0.526 16.0 83.6 37.4 0 0.243 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1fp9_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1fp9_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 9.9000 Refinement macro-cycles (run) : 310.9600 Write final files (write_after_run_outputs) : 27.6400 Total : 348.5000 Total CPU time: 6.32 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:08 PDT -0700 (1716251648.95 s) Start R-work = 0.2397, R-free = 0.2400 Final R-work = 0.2202, R-free = 0.2707 =============================================================================== Job complete usr+sys time: 405.77 seconds wall clock time: 18 minutes 11.91 seconds (1091.91 seconds total)