Starting phenix.refine on Mon May 20 17:17:05 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.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=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.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 { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 5100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5082 Classifications: {'peptide': 320} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Modifications used: {'NH3': 1} Time building chain proxies: 1.84, per 1000 atoms: 0.36 Number of scatterers: 5100 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 476 8.00 N 427 7.00 C 1617 6.00 H 2569 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: 2.50 Conformation dependent library (CDL) restraints added in 432.6 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 565 1.05 - 1.25: 2357 1.25 - 1.44: 743 1.44 - 1.64: 1466 1.64 - 1.83: 20 Bond restraints: 5151 Sorted by residual: bond pdb=" NH2 ARG A 94 " pdb="HH22 ARG A 94 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" ND1 HIS A 117 " pdb=" HD1 HIS A 117 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 253 " pdb=" H ALA A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS A 168 " pdb=" HE2 HIS A 168 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LYS A 275 " pdb=" H LYS A 275 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 5146 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.38: 128 105.38 - 112.52: 5958 112.52 - 119.66: 1333 119.66 - 126.80: 1893 126.80 - 133.95: 34 Bond angle restraints: 9346 Sorted by residual: angle pdb=" N ALA A 280 " pdb=" CA ALA A 280 " pdb=" C ALA A 280 " ideal model delta sigma weight residual 113.38 99.63 13.75 1.23e+00 6.61e-01 1.25e+02 angle pdb=" N GLN A 279 " pdb=" CA GLN A 279 " pdb=" C GLN A 279 " ideal model delta sigma weight residual 114.09 99.75 14.34 1.55e+00 4.16e-01 8.56e+01 angle pdb=" N GLN A 145 " pdb=" CA GLN A 145 " pdb=" C GLN A 145 " ideal model delta sigma weight residual 110.97 101.49 9.48 1.09e+00 8.42e-01 7.57e+01 angle pdb=" N LEU A 186 " pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 113.72 103.13 10.59 1.30e+00 5.92e-01 6.64e+01 angle pdb=" N ALA A 253 " pdb=" CA ALA A 253 " pdb=" C ALA A 253 " ideal model delta sigma weight residual 113.41 104.47 8.94 1.22e+00 6.72e-01 5.37e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 2174 22.04 - 44.07: 165 44.07 - 66.11: 60 66.11 - 88.14: 7 88.14 - 110.18: 2 Dihedral angle restraints: 2408 sinusoidal: 1323 harmonic: 1085 Sorted by residual: dihedral pdb=" CG NVA A 900 " pdb=" CA NVA A 900 " pdb=" CB NVA A 900 " pdb=" HA NVA A 900 " ideal model delta sinusoidal sigma weight residual -62.82 47.36 -110.18 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" N GLN A 348 " pdb=" C GLN A 348 " pdb=" CA GLN A 348 " pdb=" CB GLN A 348 " ideal model delta harmonic sigma weight residual 122.80 114.22 8.58 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" CG ARG A 40 " pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " ideal model delta sinusoidal sigma weight residual -90.00 -43.56 -46.44 2 1.50e+01 4.44e-03 1.12e+01 ... (remaining 2405 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.077: 254 0.077 - 0.153: 94 0.153 - 0.229: 35 0.229 - 0.306: 10 0.306 - 0.382: 4 Chirality restraints: 397 Sorted by residual: chirality pdb=" CA TRP A 298 " pdb=" N TRP A 298 " pdb=" C TRP A 298 " pdb=" CB TRP A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN A 329 " pdb=" N ASN A 329 " pdb=" C ASN A 329 " pdb=" CB ASN A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ALA A 280 " pdb=" N ALA A 280 " pdb=" C ALA A 280 " pdb=" CB ALA A 280 " both_signs ideal model delta sigma weight residual False 2.48 2.80 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 394 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 298 " -0.117 2.00e-02 2.50e+03 3.53e-02 5.00e+01 pdb=" CG TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 298 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 298 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 298 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 298 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 298 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 298 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 298 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP A 298 " 0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP A 298 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP A 298 " 0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 298 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 298 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP A 298 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 193 " -0.080 2.00e-02 2.50e+03 2.41e-02 2.33e+01 pdb=" CG TRP A 193 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 193 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 193 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 193 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 193 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 193 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 193 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" HE3 TRP A 193 " 0.025 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 193 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 193 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 193 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 317 " 0.057 2.00e-02 2.50e+03 2.24e-02 1.51e+01 pdb=" CG TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 317 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 317 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 317 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 317 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 317 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 317 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR A 317 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 317 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 317 " -0.008 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.47: 38 1.47 - 2.25: 1195 2.25 - 3.03: 16091 3.03 - 3.82: 24076 3.82 - 4.60: 38651 Warning: very small nonbonded interaction distances. Nonbonded interactions: 80051 Sorted by model distance: nonbonded pdb=" HB3 ARG A 40 " pdb="HH11 ARG A 40 " model vdw 0.684 2.270 nonbonded pdb=" HG2 GLU A 87 " pdb=" HD1 HIS A 117 " model vdw 0.725 2.270 nonbonded pdb="HD13 ILE A 116 " pdb=" HB3 LEU A 124 " model vdw 0.838 2.440 nonbonded pdb=" HA ILE A 116 " pdb="HG21 VAL A 120 " model vdw 0.941 2.440 nonbonded pdb=" OE2 GLU A 122 " pdb=" HB3 PRO A 305 " model vdw sym.op. 0.998 2.620 z,x,y ... (remaining 80046 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 15.91 1 O 476 7.97 1 N 427 6.97 1 C 1617 5.97 1 H 2569 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: 2569 of 5100 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 5100 n_use_u_iso = 5100 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 = 5100 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (5100 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 5100 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 { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1fb5_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2569 occupancy sum: 2569.00 (% of total atoms 50.55) Rotatable: count: 751 occupancy sum: 751.00 (% of total atoms 14.78) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.3934 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 7.070147 | | target function (ml) not normalized (work): 91155.402602 | | target function (ml) not normalized (free): 4891.182011 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2727 155 0.4383 0.4389 7.8547 7.6803| | 2: 5.98 - 4.75 0.97 2600 136 0.3400 0.3210 7.1228 7.1545| | 3: 4.75 - 4.15 0.98 2607 127 0.3675 0.3564 6.9337 6.9672| | 4: 4.15 - 3.77 0.95 2474 131 0.3917 0.3663 6.7408 6.855| | 5: 3.77 - 3.50 0.96 2485 141 0.4190 0.4058 6.6251 6.7013| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2727 155 0.56 45.31 0.74 0.54 772694.27| | 2: 5.98 - 4.75 2600 136 0.62 41.75 1.31 0.69 464297.85| | 3: 4.75 - 4.15 2607 127 0.77 28.66 1.48 0.80 250471.84| | 4: 4.15 - 3.77 2474 131 0.82 24.66 1.52 0.86 130060.96| | 5: 3.77 - 3.50 2485 141 0.79 27.72 1.54 0.87 102817.37| |alpha: min = 0.54 max = 0.87 mean = 0.75| |beta: min = 102817.37 max = 772694.27 mean = 352483.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 33.87| |phase err.(test): min = 0.00 max = 89.68 mean = 32.98| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.067 2582 Z= 0.581 Angle : 1.670 14.337 3492 Z= 1.077 Chirality : 0.099 0.382 397 Planarity : 0.008 0.083 441 Dihedral : 17.955 87.743 961 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 64.94 Ramachandran Plot: Outliers : 7.86 % Allowed : 20.75 % Favored : 71.38 % Rotamer: Outliers : 16.73 % Allowed : 15.64 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -6.37 (0.33), residues: 318 helix: -4.89 (0.20), residues: 119 sheet: -2.43 (0.57), residues: 57 loop : -4.35 (0.40), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 94 TYR 0.047 0.010 TYR A 317 PHE 0.031 0.012 PHE A 65 TRP 0.080 0.015 TRP A 298 HIS 0.003 0.001 HIS A 182 Individual atomic B min max mean iso aniso Overall: 9.34 143.19 50.12 1.69 2531 0 Protein: 9.34 143.19 50.12 1.69 2531 0 Chain A: 9.34 143.19 50.12 N/A 2531 0 Histogram: Values Number of atoms 9.34 - 22.73 309 22.73 - 36.11 663 36.11 - 49.50 541 49.50 - 62.88 410 62.88 - 76.27 277 76.27 - 89.65 96 89.65 - 103.03 41 103.03 - 116.42 41 116.42 - 129.81 78 129.81 - 143.19 75 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.3934 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 7.070147 | | target function (ml) not normalized (work): 91155.402602 | | target function (ml) not normalized (free): 4891.182011 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3926 0.3934 0.3841 n_refl.: 13583 re-set all scales: r(all,work,free)=0.3926 0.3934 0.3841 n_refl.: 13583 remove outliers: r(all,work,free)=0.3925 0.3933 0.3841 n_refl.: 13580 overall B=7.43 to atoms: r(all,work,free)=0.4217 0.4227 0.4091 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2182 0.2162 0.2544 n_refl.: 13580 remove outliers: r(all,work,free)=0.2181 0.2161 0.2544 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5432 2167.891 1699.946 1.237 1.215 0.394 19.362-15.234 92.45 91 7 0.4008 2001.516 1851.844 0.999 1.207 0.352 15.182-11.849 95.91 195 16 0.2182 2357.622 2247.797 1.016 1.196 0.346 11.824-9.235 95.44 396 23 0.1342 2602.458 2571.289 0.979 1.173 0.344 9.223-7.200 96.44 830 38 0.1832 1876.452 1853.962 0.974 1.135 0.330 7.195-5.615 96.35 1675 92 0.2488 1247.522 1185.861 0.934 1.073 0.276 5.612-4.379 97.24 3486 178 0.1919 1353.373 1301.390 0.987 0.969 0.222 4.378-3.502 95.73 6123 328 0.2280 1060.465 1008.484 1.225 0.812 0.131 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0575 b_overall=4.7221 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.303021 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254008 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 0.2396 0.2703 0.0307 0.003 0.8 10.8 1.6 15.6 0 0.125 0.2308 0.2622 0.0314 0.005 0.9 19.2 1.6 17.5 0 0.250 0.2330 0.2678 0.0348 0.004 0.8 10.8 1.6 16.0 0 0.500 0.2263 0.2637 0.0374 0.004 0.8 13.7 1.6 16.7 0 1.000 0.2196 0.2593 0.0398 0.006 0.9 20.2 1.6 17.5 0 2.000 0.2161 0.2565 0.0404 0.007 1.0 23.0 1.6 19.3 0 3.000 0.2132 0.2552 0.0420 0.009 1.1 25.7 1.6 19.3 0 4.000 0.2109 0.2527 0.0418 0.010 1.2 29.0 1.6 20.4 0 5.000 0.2091 0.2511 0.0420 0.011 1.3 31.2 1.9 21.5 0 6.000 0.2081 0.2513 0.0432 0.013 1.3 34.7 2.2 22.5 0 7.000 0.2065 0.2499 0.0435 0.014 1.4 34.7 2.2 22.5 0 8.000 0.2052 0.2488 0.0436 0.015 1.5 34.9 2.2 23.6 0 9.000 0.2043 0.2487 0.0444 0.016 1.6 35.7 2.2 24.4 0 10.000 0.2053 0.2481 0.0428 0.015 1.5 34.9 2.2 23.6 0 9.152 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2308 0.2622 0.0314 0.005 0.9 19.2 1.6 17.5 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.08 26.22 3.14 1.196 57.300 0.254 0.067 23.15 26.15 3.00 2.578 57.521 0.008 0.067 22.94 26.03 3.09 2.543 57.552 0.032 0.066 22.43 25.76 3.33 3.066 57.669 0.127 0.064 21.75 25.35 3.60 5.753 58.200 0.254 0.061 21.52 25.31 3.78 6.645 58.376 0.381 0.059 21.37 25.29 3.92 7.425 58.550 0.508 0.059 21.17 25.21 4.04 8.519 58.887 0.635 0.058 21.08 25.19 4.11 9.118 59.031 0.762 0.057 21.01 25.19 4.18 9.596 59.147 0.889 0.057 20.96 25.19 4.23 10.026 59.254 1.016 0.057 20.86 25.19 4.33 10.790 59.479 1.143 0.056 20.82 25.18 4.37 11.202 59.591 1.270 0.056 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.270 Accepted refinement result: 20.82 25.18 4.37 11.202 59.591 1.270 0.056 Individual atomic B min max mean iso aniso Overall: 11.77 166.08 62.17 10.19 2531 0 Protein: 11.77 166.08 62.17 10.19 2531 0 Chain A: 11.77 166.08 62.17 N/A 2531 0 Histogram: Values Number of atoms 11.77 - 27.20 114 27.20 - 42.63 607 42.63 - 58.06 624 58.06 - 73.50 538 73.50 - 88.93 261 88.93 - 104.36 147 104.36 - 119.79 66 119.79 - 135.22 73 135.22 - 150.65 77 150.65 - 166.08 24 =========================== Idealize ADP of riding H ========================== r_work=0.2082 r_free=0.2518 r_work=0.2057 r_free=0.2500 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2057 r_free= 0.2500 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ls_wunit_k1) (work): 0.054838 | | target function (ls_wunit_k1) not normalized (work): 706.812303 | | target function (ls_wunit_k1) not normalized (free): 56.361510 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2081 0.2057 0.2500 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4265 0.4274 0.4160 n_refl.: 13579 remove outliers: r(all,work,free)=0.4265 0.4274 0.4160 n_refl.: 13579 overall B=0.00 to atoms: r(all,work,free)=0.4265 0.4274 0.4160 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2094 0.2070 0.2511 n_refl.: 13579 remove outliers: r(all,work,free)=0.2094 0.2070 0.2511 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5516 1181.591 921.459 1.219 1.169 0.400 19.362-15.234 92.45 91 7 0.3826 1090.910 1028.684 0.996 1.165 0.345 15.182-11.849 95.91 195 16 0.2229 1285.002 1229.978 1.049 1.157 0.340 11.824-9.235 95.44 396 23 0.1394 1418.448 1403.110 1.018 1.138 0.335 9.223-7.200 96.44 830 38 0.1931 1022.745 1009.985 1.029 1.109 0.330 7.195-5.615 96.35 1675 92 0.2425 679.952 648.273 0.973 1.058 0.280 5.612-4.379 97.24 3486 178 0.1783 737.645 713.510 0.995 0.975 0.210 4.378-3.502 95.73 6123 328 0.2134 577.998 551.416 1.203 0.847 0.120 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.2779 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.750513 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.060713 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 0.2268 0.2630 0.0362 0.002 0.6 9.8 0.9 12.7 0 0.011 0.2224 0.2587 0.0363 0.002 0.6 9.6 0.9 13.5 0 0.032 0.2173 0.2550 0.0377 0.002 0.6 8.8 0.9 13.8 0 0.064 0.2135 0.2525 0.0390 0.003 0.7 10.0 0.9 14.9 0 0.095 0.2108 0.2506 0.0398 0.003 0.7 11.2 0.9 15.3 0 0.127 0.2083 0.2483 0.0400 0.003 0.7 10.8 0.9 15.3 0 0.159 0.2068 0.2472 0.0403 0.003 0.7 11.0 0.9 15.6 0 0.191 0.2058 0.2465 0.0407 0.003 0.7 11.4 0.9 16.0 0 0.223 0.2132 0.2519 0.0386 0.003 0.6 10.0 0.9 14.5 0 0.106 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2173 0.2550 0.0377 0.002 0.6 8.8 0.9 13.8 0 0.064 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.73 25.50 3.77 12.231 69.388 0.061 6.648 23.98 26.51 2.54 11.794 73.282 0.002 6.701 23.37 26.06 2.69 11.961 72.001 0.008 6.686 22.20 25.33 3.13 12.767 69.670 0.030 6.647 21.71 25.13 3.42 13.206 69.217 0.061 6.630 21.53 25.10 3.57 13.767 69.442 0.091 6.623 21.39 25.06 3.67 14.219 69.649 0.121 6.618 21.30 25.04 3.75 14.688 69.853 0.152 6.614 21.22 25.05 3.83 14.541 69.646 0.182 6.613 21.17 25.07 3.89 14.817 69.753 0.212 6.611 21.14 25.09 3.95 15.088 69.860 0.243 6.610 21.11 25.10 3.99 15.383 69.980 0.273 6.609 21.09 25.09 4.01 15.633 70.076 0.304 6.608 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.152 Accepted refinement result: 21.30 25.04 3.75 14.688 69.853 0.152 6.614 Individual atomic B min max mean iso aniso Overall: 8.87 176.11 63.10 14.13 2531 0 Protein: 8.87 176.11 63.10 14.13 2531 0 Chain A: 8.87 176.11 63.10 N/A 2531 0 Histogram: Values Number of atoms 8.87 - 25.60 80 25.60 - 42.32 662 42.32 - 59.04 680 59.04 - 75.77 456 75.77 - 92.49 248 92.49 - 109.21 136 109.21 - 125.94 97 125.94 - 142.66 81 142.66 - 159.38 71 159.38 - 176.11 20 =========================== Idealize ADP of riding H ========================== r_work=0.2130 r_free=0.2504 r_work=0.2135 r_free=0.2506 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2135 r_free= 0.2506 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ml) (work): 6.613538 | | target function (ml) not normalized (work): 85241.885012 | | target function (ml) not normalized (free): 4633.561557 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2155 0.2135 0.2506 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4245 0.4254 0.4130 n_refl.: 13579 remove outliers: r(all,work,free)=0.4245 0.4254 0.4130 n_refl.: 13579 overall B=0.00 to atoms: r(all,work,free)=0.4245 0.4254 0.4130 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2158 0.2138 0.2515 n_refl.: 13579 remove outliers: r(all,work,free)=0.2158 0.2138 0.2515 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5187 1181.591 964.512 1.337 1.093 0.400 19.362-15.234 92.45 91 7 0.3868 1090.910 1026.286 1.056 1.093 0.345 15.182-11.849 95.91 195 16 0.2276 1285.002 1235.385 1.153 1.090 0.340 11.824-9.235 95.44 396 23 0.1508 1418.448 1410.496 1.119 1.079 0.340 9.223-7.200 96.44 830 38 0.2115 1022.745 1007.619 1.101 1.063 0.340 7.195-5.615 96.35 1675 92 0.2626 679.952 641.981 1.037 1.033 0.290 5.612-4.379 97.24 3486 178 0.1947 737.645 706.090 0.977 0.983 0.220 4.378-3.502 95.73 6123 328 0.2067 577.998 548.405 1.090 0.907 0.121 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.8575 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2138 r_free=0.2515 After: r_work=0.2138 r_free=0.2516 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.475112 wxc_scale = 0.027 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.057788 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 0.2139 0.2515 0.0376 0.002 0.7 9.6 0.9 13.8 0 0.012 0.2139 0.2515 0.0376 0.002 0.7 9.6 0.9 13.8 0 0.037 0.2138 0.2514 0.0376 0.002 0.7 9.6 0.9 13.8 0 0.073 0.2137 0.2513 0.0376 0.002 0.7 9.6 0.9 13.8 0 0.110 0.2135 0.2513 0.0377 0.002 0.7 9.8 0.9 14.2 0 0.147 0.2134 0.2510 0.0377 0.003 0.7 9.8 0.9 14.2 0 0.184 0.2132 0.2509 0.0377 0.003 0.7 10.0 0.9 14.2 0 0.220 0.2130 0.2508 0.0378 0.003 0.7 10.0 0.9 14.2 0 0.257 0.2137 0.2513 0.0376 0.002 0.7 9.6 0.9 13.8 0 0.122 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2137 0.2513 0.0376 0.002 0.7 9.6 0.9 13.8 0 0.110 0.2137 0.2513 0.0376 0.002 0.7 9.6 0.9 13.8 0 0.122 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.37 25.13 3.76 14.202 70.150 0.058 6.620 24.59 27.18 2.59 13.093 75.340 0.002 6.702 23.78 26.48 2.70 13.065 73.672 0.007 6.688 22.16 25.54 3.38 13.634 70.336 0.029 6.644 21.54 25.10 3.56 14.271 69.332 0.058 6.622 21.30 25.10 3.80 14.486 69.474 0.087 6.615 21.24 25.11 3.87 14.733 69.456 0.116 6.613 21.20 25.12 3.92 14.900 69.448 0.144 6.612 21.15 25.09 3.94 15.195 69.286 0.173 6.609 21.13 25.10 3.97 15.307 69.301 0.202 6.609 21.09 25.06 3.97 15.764 69.108 0.231 6.607 21.06 25.06 4.00 15.888 69.135 0.260 6.606 21.05 25.06 4.01 15.945 69.162 0.289 6.606 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.231 Accepted refinement result: 21.09 25.06 3.97 15.764 69.108 0.231 6.607 Individual atomic B min max mean iso aniso Overall: 7.92 178.50 61.00 15.60 2531 0 Protein: 7.92 178.50 61.00 15.60 2531 0 Chain A: 7.92 178.50 61.00 N/A 2531 0 Histogram: Values Number of atoms 7.92 - 24.98 140 24.98 - 42.04 701 42.04 - 59.10 678 59.10 - 76.16 394 76.16 - 93.21 227 93.21 - 110.27 130 110.27 - 127.33 98 127.33 - 144.39 75 144.39 - 161.45 69 161.45 - 178.50 19 =========================== Idealize ADP of riding H ========================== r_work=0.2109 r_free=0.2506 r_work=0.2106 r_free=0.2505 ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2106 r_free= 0.2505 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ml) (work): 6.605477 | | target function (ml) not normalized (work): 85137.989522 | | target function (ml) not normalized (free): 4630.986538 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2723 155 0.2340 0.2668 7.0451 7.1473| | 2: 5.98 - 4.75 0.97 2600 136 0.2174 0.2363 6.6876 6.749| | 3: 4.75 - 4.15 0.98 2607 127 0.1733 0.2328 6.5426 6.6747| | 4: 4.15 - 3.77 0.95 2474 131 0.1938 0.2221 6.4238 6.5214| | 5: 3.77 - 3.50 0.96 2485 141 0.2300 0.2900 6.2847 6.4063| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2723 155 0.79 25.98 1.01 0.88 210727.11| | 2: 5.98 - 4.75 2600 136 0.79 27.09 1.01 0.89 146127.16| | 3: 4.75 - 4.15 2607 127 0.86 20.59 1.00 0.88 98357.40| | 4: 4.15 - 3.77 2474 131 0.86 20.95 1.00 0.85 67147.94| | 5: 3.77 - 3.50 2485 141 0.84 23.13 0.94 0.82 52632.83| |alpha: min = 0.82 max = 0.89 mean = 0.86| |beta: min = 52632.83 max = 210727.11 mean = 116927.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 89.93 mean = 23.60| |phase err.(test): min = 0.00 max = 87.45 mean = 23.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2127 0.2106 0.2505 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4118 0.4126 0.4023 n_refl.: 13579 remove outliers: r(all,work,free)=0.4118 0.4126 0.4023 n_refl.: 13579 overall B=6.43 to atoms: r(all,work,free)=0.4386 0.4395 0.4257 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2137 0.2115 0.2521 n_refl.: 13579 remove outliers: r(all,work,free)=0.2137 0.2115 0.2521 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5190 1181.591 967.471 1.342 1.042 0.399 19.362-15.234 92.45 91 7 0.3868 1090.910 1027.479 1.058 1.044 0.343 15.182-11.849 95.91 195 16 0.2282 1285.002 1236.894 1.153 1.045 0.337 11.824-9.235 95.44 396 23 0.1520 1418.448 1411.590 1.117 1.039 0.335 9.223-7.200 96.44 830 38 0.2117 1022.745 1008.046 1.100 1.031 0.332 7.195-5.615 96.35 1675 92 0.2631 679.952 641.697 1.042 1.016 0.288 5.612-4.379 97.24 3486 178 0.1923 737.645 705.441 0.960 0.989 0.206 4.378-3.502 95.73 6123 328 0.2022 577.998 549.071 1.064 0.948 0.108 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0417 b_overall=2.4122 ================= 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 : 0.3934 0.3841 0.010 1.670 9.3 143.2 50.1 0 0.000 1_bss: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_settarget: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_updatephipsi: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_weight: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_xyzrec: 0.2308 0.2622 0.005 0.917 16.8 150.6 57.6 0 0.168 1_adp: 0.2082 0.2518 0.005 0.917 11.8 166.1 62.2 0 0.168 1_regHadp: 0.2057 0.2500 0.005 0.917 11.8 166.1 62.2 0 0.168 2_bss: 0.2070 0.2511 0.005 0.917 11.8 166.1 62.2 0 0.168 2_settarget: 0.2070 0.2511 0.005 0.917 11.8 166.1 62.2 0 0.168 2_updatephipsi: 0.2070 0.2511 0.005 0.917 11.8 166.1 62.2 0 0.168 2_updatecdl: 0.2070 0.2511 0.005 0.958 11.8 166.1 62.2 0 0.168 2_weight: 0.2070 0.2511 0.005 0.958 11.8 166.1 62.2 0 0.168 2_xyzrec: 0.2173 0.2550 0.002 0.637 11.8 166.1 62.2 0 0.266 2_adp: 0.2130 0.2504 0.002 0.637 8.9 176.1 63.1 0 0.266 2_regHadp: 0.2135 0.2506 0.002 0.637 8.9 176.1 63.1 0 0.266 3_bss: 0.2138 0.2515 0.002 0.637 8.9 176.1 63.1 0 0.266 3_settarget: 0.2138 0.2515 0.002 0.637 8.9 176.1 63.1 0 0.266 3_updatephipsi: 0.2138 0.2515 0.002 0.637 8.9 176.1 63.1 0 0.266 3_updatecdl: 0.2138 0.2515 0.003 0.662 8.9 176.1 63.1 0 0.266 3_setrh: 0.2138 0.2516 0.003 0.662 8.9 176.1 63.1 0 0.266 3_weight: 0.2138 0.2516 0.003 0.662 8.9 176.1 63.1 0 0.266 3_xyzrec: 0.2137 0.2513 0.002 0.652 8.9 176.1 63.1 0 0.266 3_adp: 0.2109 0.2506 0.002 0.652 7.9 178.5 61.0 0 0.266 3_regHadp: 0.2106 0.2505 0.002 0.652 7.9 178.5 61.0 0 0.266 end: 0.2115 0.2521 0.002 0.652 14.4 184.9 67.4 0 0.266 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1fb5_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1fb5_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.4200 Refinement macro-cycles (run) : 297.3300 Write final files (write_after_run_outputs) : 18.5600 Total : 323.3100 Total CPU time: 6.06 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:57 PDT -0700 (1716251757.68 s) Start R-work = 0.2161, R-free = 0.2544 Final R-work = 0.2115, R-free = 0.2521 =============================================================================== Job complete usr+sys time: 387.14 seconds wall clock time: 19 minutes 18.67 seconds (1158.67 seconds total)