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/1m10.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.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/1m10/1m10.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1m10.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1m10.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 Residue "B TYR 228": "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: 7468 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3250 Classifications: {'peptide': 199} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "B" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4218 Classifications: {'peptide': 267} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 246} Time building chain proxies: 1.60, per 1000 atoms: 0.21 Number of scatterers: 7468 At special positions: 0 Unit cell: (89.84, 89.84, 124.63, 90, 90, 120) Space group: P 61 (No. 169) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 682 8.00 N 628 7.00 C 2366 6.00 H 3778 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 695 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 209 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 264 " distance=2.04 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: 1.90 Conformation dependent library (CDL) restraints added in 230.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Time building geometry restraints manager: 2.18 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: 3777 1.15 - 1.32: 698 1.32 - 1.49: 1420 1.49 - 1.67: 1630 1.67 - 1.84: 19 Bond restraints: 7544 Sorted by residual: bond pdb=" N VAL B 256 " pdb=" H VAL B 256 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLU A 700 " pdb=" H GLU A 700 " 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 B 114 " pdb=" H SER B 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND1 HIS A 563 " pdb=" HD1 HIS A 563 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B 195 " pdb=" H HIS B 195 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7539 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 392 106.21 - 113.18: 8799 113.18 - 120.15: 2310 120.15 - 127.12: 2204 127.12 - 134.09: 31 Bond angle restraints: 13736 Sorted by residual: angle pdb=" N VAL B 78 " pdb=" CA VAL B 78 " pdb=" C VAL B 78 " ideal model delta sigma weight residual 112.43 120.71 -8.28 9.20e-01 1.18e+00 8.10e+01 angle pdb=" C LEU B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta sigma weight residual 119.84 130.41 -10.57 1.25e+00 6.40e-01 7.15e+01 angle pdb=" C LEU B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.56 127.99 -8.43 1.02e+00 9.61e-01 6.83e+01 angle pdb=" N ILE B 213 " pdb=" CA ILE B 213 " pdb=" C ILE B 213 " ideal model delta sigma weight residual 112.90 105.33 7.57 9.60e-01 1.09e+00 6.21e+01 angle pdb=" N ARG A 511 " pdb=" CA ARG A 511 " pdb=" C ARG A 511 " ideal model delta sigma weight residual 108.45 118.26 -9.81 1.26e+00 6.30e-01 6.06e+01 ... (remaining 13731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3167 17.57 - 35.14: 236 35.14 - 52.71: 102 52.71 - 70.28: 32 70.28 - 87.84: 4 Dihedral angle restraints: 3541 sinusoidal: 1982 harmonic: 1559 Sorted by residual: dihedral pdb=" CA LYS A 585 " pdb=" CB LYS A 585 " pdb=" CG LYS A 585 " pdb=" CD LYS A 585 " ideal model delta sinusoidal sigma weight residual -60.00 -118.49 58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN B 159 " pdb=" CB GLN B 159 " pdb=" CG GLN B 159 " pdb=" CD GLN B 159 " ideal model delta sinusoidal sigma weight residual 60.00 113.33 -53.33 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" C HIS B 195 " pdb=" N HIS B 195 " pdb=" CA HIS B 195 " pdb=" CB HIS B 195 " ideal model delta harmonic sigma weight residual -122.60 -115.04 -7.56 0 2.50e+00 1.60e-01 9.15e+00 ... (remaining 3538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 349 0.080 - 0.160: 177 0.160 - 0.240: 54 0.240 - 0.320: 12 0.320 - 0.400: 4 Chirality restraints: 596 Sorted by residual: chirality pdb=" CA PRO B 2 " pdb=" N PRO B 2 " pdb=" C PRO B 2 " pdb=" CB PRO B 2 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN B 21 " pdb=" N GLN B 21 " pdb=" C GLN B 21 " pdb=" CB GLN B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA HIS B 195 " pdb=" N HIS B 195 " pdb=" C HIS B 195 " pdb=" CB HIS B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 593 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 44 " -0.125 2.00e-02 2.50e+03 5.17e-02 8.01e+01 pdb=" CG TYR B 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 44 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 44 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 44 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 44 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 44 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 44 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR B 44 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 44 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR B 44 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR B 44 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 600 " 0.122 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" CG TYR A 600 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 600 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 600 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 600 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 600 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 600 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 600 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 54 " 0.112 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" CG TYR B 54 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 54 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 54 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 54 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 54 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR B 54 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR B 54 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR B 54 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 54 " 0.006 2.00e-02 2.50e+03 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 115 1.73 - 2.45: 4531 2.45 - 3.17: 24552 3.17 - 3.88: 32886 3.88 - 4.60: 50977 Nonbonded interactions: 113061 Sorted by model distance: nonbonded pdb=" HA HIS A 559 " pdb=" HA ALA A 592 " model vdw 1.014 2.440 nonbonded pdb="HH22 ARG A 545 " pdb=" HG3 PRO A 703 " model vdw 1.092 2.270 nonbonded pdb=" HA ARG A 636 " pdb="HH11 ARG A 636 " model vdw 1.130 2.270 nonbonded pdb="HD22 LEU A 512 " pdb="HH21 ARG A 611 " model vdw 1.155 2.270 nonbonded pdb=" OE1 GLU A 613 " pdb=" H GLU A 613 " model vdw 1.278 1.850 ... (remaining 113056 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 14 15.96 2 O 682 7.97 1 N 628 6.97 1 C 2366 5.97 2 H 3778 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: 3778 of 7468 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7468 n_use_u_iso = 7468 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 = 7468 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7468 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7468 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 = "1m10_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3778 occupancy sum: 3778.00 (% of total atoms 50.59) Rotatable: count: 1103 occupancy sum: 1103.00 (% of total atoms 14.77) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3804 r_free= 0.4305 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.437560 | | target function (ml) not normalized (work): 53940.591815 | | target function (ml) not normalized (free): 2943.016547 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.3660 0.4501 6.0037 5.8545| | 2: 4.90 - 3.90 1.00 2453 134 0.3747 0.3971 5.604 5.8298| | 3: 3.89 - 3.40 1.00 2476 150 0.4079 0.4323 5.2694 5.4009| | 4: 3.40 - 3.09 1.00 2461 127 0.3903 0.4710 4.8588 4.973| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.59 44.84 0.82 0.19 23753.52| | 2: 4.90 - 3.90 2453 134 0.66 39.62 1.40 0.30 15554.07| | 3: 3.89 - 3.40 2476 150 0.61 43.67 1.52 0.32 9054.65| | 4: 3.40 - 3.09 2461 127 0.53 49.92 1.29 0.25 4255.28| |alpha: min = 0.19 max = 0.32 mean = 0.27| |beta: min = 4255.28 max = 23753.52 mean = 13219.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.60| |phase err.(work): min = 0.00 max = 89.91 mean = 44.52| |phase err.(test): min = 0.00 max = 89.08 mean = 44.81| |-----------------------------------------------------------------------------| ----------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 0.119 3766 Z= 0.622 Angle : 1.710 10.944 5117 Z= 1.081 Chirality : 0.104 0.400 596 Planarity : 0.010 0.086 656 Dihedral : 15.487 87.844 1425 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 4.98 % Allowed : 12.77 % Favored : 82.25 % Rotamer: Outliers : 5.28 % Allowed : 6.24 % Favored : 88.49 % 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: -5.24 (0.31), residues: 462 helix: -4.51 (0.29), residues: 98 sheet: -2.23 (0.51), residues: 89 loop : -3.68 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 545 TYR 0.104 0.022 TYR B 44 PHE 0.051 0.010 PHE B 201 TRP 0.058 0.016 TRP B 219 HIS 0.003 0.001 HIS B 86 Individual atomic B min max mean iso aniso Overall: 15.65 95.55 52.24 1.37 3690 0 Protein: 15.65 95.55 52.24 1.37 3690 0 Chain A: 21.62 95.55 60.64 N/A 1602 0 Chain B: 15.65 77.97 45.80 N/A 2088 0 Histogram: Values Number of atoms 15.65 - 23.64 14 23.64 - 31.63 190 31.63 - 39.62 520 39.62 - 47.61 817 47.61 - 55.60 852 55.60 - 63.59 530 63.59 - 71.58 302 71.58 - 79.57 236 79.57 - 87.56 164 87.56 - 95.55 65 |-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: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3804 r_free= 0.4305 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.437560 | | target function (ml) not normalized (work): 53940.591815 | | target function (ml) not normalized (free): 2943.016547 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3828 0.3804 0.4305 n_refl.: 10454 re-set all scales: r(all,work,free)=0.3828 0.3804 0.4305 n_refl.: 10454 remove outliers: r(all,work,free)=0.3829 0.3805 0.4299 n_refl.: 10449 overall B=16.31 to atoms: r(all,work,free)=0.4448 0.4429 0.4826 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2288 0.2260 0.2819 n_refl.: 10449 remove outliers: r(all,work,free)=0.2288 0.2260 0.2819 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2311 1395.912 1343.970 1.051 1.212 0.395 14.512-11.594 100.00 95 5 0.1560 1328.531 1301.200 0.918 1.199 0.369 11.568-9.227 100.00 193 11 0.1404 1283.724 1248.849 0.929 1.180 0.359 9.162-7.352 100.00 368 15 0.2071 850.463 820.636 0.919 1.149 0.348 7.349-5.862 100.00 740 33 0.2226 628.811 611.546 0.853 1.103 0.326 5.858-4.671 100.00 1425 79 0.1948 673.689 650.894 0.916 1.028 0.283 4.669-3.723 99.86 2790 156 0.2269 618.917 593.677 1.202 0.910 0.181 3.723-3.092 99.93 4210 230 0.2720 337.947 316.886 1.511 0.750 0.063 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-5.7724 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.787006 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.201646 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 0.2387 0.2755 0.0367 0.003 0.6 5.1 2.8 3.6 0 0.125 0.2357 0.2723 0.0366 0.003 0.6 4.7 2.6 3.6 0 0.250 0.2313 0.2727 0.0414 0.003 0.6 5.1 2.6 3.6 0 0.500 0.2250 0.2722 0.0472 0.004 0.7 5.9 2.2 3.6 0 1.000 0.2178 0.2703 0.0524 0.005 0.8 8.0 2.4 3.6 0 2.000 0.2136 0.2720 0.0584 0.007 0.9 10.3 3.2 4.1 0 3.000 0.2102 0.2747 0.0645 0.008 1.0 12.1 3.9 4.8 0 4.000 0.2073 0.2765 0.0691 0.010 1.1 13.4 4.1 5.5 0 5.000 0.2058 0.2766 0.0708 0.011 1.2 15.0 4.1 5.5 0 6.000 0.2048 0.2752 0.0704 0.012 1.3 17.3 4.5 5.8 0 7.000 0.2039 0.2752 0.0714 0.014 1.5 18.9 4.8 5.8 0 8.000 0.2024 0.2759 0.0735 0.015 1.5 19.8 4.8 6.5 0 9.000 0.2013 0.2760 0.0747 0.016 1.6 21.2 4.8 6.7 0 10.000 0.2039 0.2751 0.0713 0.014 1.4 18.4 4.8 5.8 0 7.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2357 0.2723 0.0366 0.003 0.6 4.7 2.6 3.6 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.57 27.23 3.66 0.970 68.287 0.202 0.061 23.75 27.28 3.53 1.903 68.386 0.006 0.062 23.37 27.20 3.82 1.889 68.427 0.025 0.060 22.58 27.06 4.48 2.921 68.587 0.101 0.056 21.54 26.91 5.38 6.176 69.192 0.202 0.051 21.23 26.86 5.63 7.327 69.486 0.302 0.050 20.92 26.90 5.98 8.682 69.932 0.403 0.048 20.77 26.90 6.13 9.421 70.142 0.504 0.047 20.66 26.93 6.27 10.034 70.320 0.605 0.047 20.53 26.94 6.41 10.798 70.565 0.706 0.046 20.46 26.95 6.50 11.260 70.701 0.807 0.046 20.39 26.98 6.58 11.663 70.821 0.907 0.046 20.13 26.98 6.85 13.447 71.432 1.008 0.045 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.302 Accepted refinement result: 21.23 26.86 5.63 7.327 69.486 0.302 0.050 Individual atomic B min max mean iso aniso Overall: 33.59 124.65 70.98 7.28 3690 0 Protein: 33.59 124.65 70.98 7.28 3690 0 Chain A: 35.98 124.65 78.67 N/A 1602 0 Chain B: 33.59 122.58 65.08 N/A 2088 0 Histogram: Values Number of atoms 33.59 - 42.70 53 42.70 - 51.80 303 51.80 - 60.91 697 60.91 - 70.02 916 70.02 - 79.12 683 79.12 - 88.23 446 88.23 - 97.33 318 97.33 - 106.44 210 106.44 - 115.55 56 115.55 - 124.65 8 =========================== Idealize ADP of riding H ========================== r_work=0.2123 r_free=0.2686 r_work=0.2097 r_free=0.2672 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2097 r_free= 0.2672 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ls_wunit_k1) (work): 0.048339 | | target function (ls_wunit_k1) not normalized (work): 479.334349 | | target function (ls_wunit_k1) not normalized (free): 43.733576 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2127 0.2097 0.2672 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4392 0.4376 0.4726 n_refl.: 10449 remove outliers: r(all,work,free)=0.4392 0.4376 0.4726 n_refl.: 10449 overall B=-2.00 to atoms: r(all,work,free)=0.4309 0.4292 0.4653 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2163 0.2132 0.2741 n_refl.: 10449 remove outliers: r(all,work,free)=0.2163 0.2132 0.2741 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2271 767.614 746.396 1.371 1.020 0.401 14.512-11.594 100.00 95 5 0.1429 730.561 728.083 1.157 1.020 0.367 11.568-9.227 100.00 193 11 0.1447 705.922 694.865 1.144 1.017 0.362 9.162-7.352 100.00 368 15 0.1824 467.671 461.145 1.106 1.012 0.363 7.349-5.862 100.00 740 33 0.2036 345.784 340.459 0.963 1.007 0.334 5.858-4.671 100.00 1425 79 0.1840 370.463 360.099 0.942 0.997 0.275 4.669-3.723 99.93 2790 156 0.2029 340.343 331.691 1.105 0.981 0.185 3.723-3.092 100.00 4210 230 0.2727 185.837 176.609 1.181 0.959 0.042 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-6.1945 ============================ 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 = 3.581437 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.042084 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 0.2082 0.2693 0.0611 0.002 0.5 4.2 1.7 2.2 0 0.125 0.2039 0.2684 0.0645 0.003 0.6 5.2 2.2 2.9 0 0.250 0.2001 0.2696 0.0695 0.005 0.7 6.0 2.2 3.4 0 0.500 0.1963 0.2732 0.0769 0.008 1.0 9.5 2.6 5.0 0 1.000 0.1929 0.2762 0.0833 0.014 1.4 15.1 3.2 6.0 0 2.000 0.1895 0.2787 0.0892 0.019 1.7 18.1 3.5 5.5 0 3.000 0.1879 0.2781 0.0902 0.024 1.9 20.0 3.7 5.5 0 4.000 0.1861 0.2767 0.0905 0.027 2.1 25.1 4.8 11.0 0 5.000 0.1851 0.2779 0.0929 0.030 2.4 29.7 5.2 13.7 0 6.000 0.1843 0.2783 0.0940 0.033 2.6 31.6 5.6 14.1 0 7.000 0.1835 0.2782 0.0946 0.036 2.8 33.0 6.1 15.1 0 8.000 0.1825 0.2791 0.0966 0.039 3.0 34.4 6.3 14.6 0 9.000 0.1817 0.2794 0.0977 0.041 3.1 35.2 6.5 16.8 0 10.000 0.1934 0.2758 0.0824 0.013 1.3 14.9 3.2 6.2 0 1.791 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2039 0.2684 0.0645 0.003 0.6 5.2 2.2 2.9 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.39 26.84 6.45 11.520 76.260 0.042 5.728 23.76 28.53 4.78 9.010 80.970 0.001 5.793 22.83 27.58 4.75 10.419 78.825 0.005 5.775 20.52 26.79 6.27 11.580 76.046 0.021 5.723 20.33 26.81 6.47 11.845 75.960 0.042 5.719 20.18 26.79 6.61 12.307 75.745 0.063 5.712 19.92 26.67 6.75 13.311 75.606 0.084 5.700 19.83 26.67 6.84 13.444 75.710 0.105 5.699 19.77 26.67 6.91 13.551 75.798 0.126 5.697 19.72 26.69 6.97 13.645 75.871 0.147 5.697 19.68 26.70 7.02 13.723 75.932 0.168 5.696 19.65 26.71 7.05 13.793 75.984 0.189 5.696 19.63 26.71 7.08 13.854 76.028 0.210 5.695 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 22.83 27.58 4.75 10.419 78.825 0.005 5.775 Individual atomic B min max mean iso aniso Overall: 35.80 143.15 74.17 4.41 3690 0 Protein: 35.80 143.15 74.17 4.41 3690 0 Chain A: 39.76 143.15 81.29 N/A 1602 0 Chain B: 35.80 123.50 68.70 N/A 2088 0 Histogram: Values Number of atoms 35.80 - 46.54 16 46.54 - 57.27 299 57.27 - 68.01 899 68.01 - 78.74 1283 78.74 - 89.48 637 89.48 - 100.21 467 100.21 - 110.95 79 110.95 - 121.68 7 121.68 - 132.42 2 132.42 - 143.15 1 =========================== Idealize ADP of riding H ========================== r_work=0.2283 r_free=0.2758 r_work=0.2312 r_free=0.2765 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2312 r_free= 0.2765 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ml) (work): 5.782268 | | target function (ml) not normalized (work): 57336.968016 | | target function (ml) not normalized (free): 3156.593117 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2334 0.2312 0.2765 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4627 0.4611 0.4937 n_refl.: 10449 remove outliers: r(all,work,free)=0.4627 0.4611 0.4937 n_refl.: 10449 overall B=-1.88 to atoms: r(all,work,free)=0.4549 0.4533 0.4863 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2320 0.2299 0.2719 n_refl.: 10449 remove outliers: r(all,work,free)=0.2320 0.2299 0.2719 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.1883 767.614 758.320 1.291 1.030 0.403 14.512-11.594 100.00 95 5 0.1260 730.561 729.597 1.098 1.028 0.375 11.568-9.227 100.00 193 11 0.1278 705.922 698.060 1.086 1.024 0.372 9.162-7.352 100.00 368 15 0.1741 467.671 460.925 1.055 1.017 0.373 7.349-5.862 100.00 740 33 0.2146 345.784 338.529 0.934 1.008 0.334 5.858-4.671 100.00 1425 79 0.1993 370.463 358.269 0.931 0.993 0.275 4.669-3.723 99.93 2790 156 0.2300 340.343 327.683 1.106 0.968 0.165 3.723-3.092 100.00 4210 230 0.2988 185.837 172.323 1.210 0.934 0.021 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.4691 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2299 r_free=0.2719 After: r_work=0.2299 r_free=0.2720 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.289018 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.039610 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 0.2302 0.2722 0.0421 0.003 0.6 5.5 2.2 2.9 0 0.125 0.2296 0.2723 0.0427 0.003 0.6 5.4 2.2 2.9 0 0.250 0.2270 0.2724 0.0454 0.006 0.7 5.9 1.9 3.1 0 0.500 0.2183 0.2740 0.0557 0.015 1.2 9.9 1.9 3.4 0 1.000 0.2120 0.2783 0.0663 0.016 1.9 20.5 2.6 5.3 0 2.000 0.2063 0.2783 0.0720 0.023 2.5 23.6 2.6 5.5 0 3.000 0.2034 0.2795 0.0761 0.029 2.9 25.5 2.6 6.7 0 4.000 0.2017 0.2799 0.0782 0.031 3.1 27.6 2.8 7.7 0 5.000 0.1994 0.2839 0.0845 0.034 3.6 36.2 5.0 11.5 0 6.000 0.1982 0.2828 0.0845 0.043 3.7 28.9 2.8 7.4 0 7.000 0.1958 0.2845 0.0887 0.041 4.1 39.7 5.8 11.8 2 8.000 0.1953 0.2839 0.0885 0.043 4.2 41.0 5.6 11.5 1 9.000 0.1943 0.2846 0.0904 0.046 4.5 44.5 6.3 13.7 2 10.000 0.2122 0.2782 0.0660 0.017 1.9 17.5 1.9 4.3 0 1.645 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2296 0.2723 0.0427 0.003 0.6 5.4 2.2 2.9 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.96 27.23 4.27 11.113 79.848 0.040 5.784 25.04 29.45 4.42 10.770 83.153 0.001 5.844 22.73 27.15 4.41 11.054 79.803 0.005 5.778 22.46 27.09 4.62 11.225 79.720 0.020 5.769 20.99 26.57 5.58 12.521 80.037 0.040 5.723 20.77 26.53 5.76 12.876 80.359 0.059 5.716 20.65 26.54 5.88 13.167 80.567 0.079 5.712 20.57 26.55 5.98 13.457 80.749 0.099 5.709 20.49 26.57 6.08 13.775 80.930 0.119 5.706 20.43 26.58 6.15 14.049 81.074 0.139 5.705 20.38 26.59 6.21 14.291 81.192 0.158 5.703 20.35 26.60 6.26 14.512 81.295 0.178 5.702 20.32 26.62 6.31 14.706 81.384 0.198 5.701 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.059 Accepted refinement result: 20.77 26.53 5.76 12.876 80.359 0.059 5.716 Individual atomic B min max mean iso aniso Overall: 28.92 147.32 73.32 9.11 3690 0 Protein: 28.92 147.32 73.32 9.11 3690 0 Chain A: 45.10 137.21 80.22 N/A 1602 0 Chain B: 28.92 147.32 68.03 N/A 2088 0 Histogram: Values Number of atoms 28.92 - 40.76 13 40.76 - 52.60 260 52.60 - 64.44 914 64.44 - 76.28 1131 76.28 - 88.12 731 88.12 - 99.96 371 99.96 - 111.80 186 111.80 - 123.64 65 123.64 - 135.48 16 135.48 - 147.32 3 =========================== Idealize ADP of riding H ========================== r_work=0.2077 r_free=0.2653 r_work=0.2063 r_free=0.2663 ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2063 r_free= 0.2663 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ml) (work): 5.712657 | | target function (ml) not normalized (work): 56646.709104 | | target function (ml) not normalized (free): 3150.472073 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.1757 0.2240 5.9822 6.0667| | 2: 4.90 - 3.90 1.00 2451 133 0.1890 0.2499 5.8699 6.2111| | 3: 3.89 - 3.40 1.00 2475 150 0.2373 0.2925 5.6811 5.886| | 4: 3.40 - 3.09 1.00 2460 127 0.2858 0.3680 5.3106 5.4748| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.85 22.20 0.99 0.94 27430.43| | 2: 4.90 - 3.90 2451 133 0.83 23.56 1.02 0.99 24166.06| | 3: 3.89 - 3.40 2475 150 0.74 32.10 1.04 0.94 18650.86| | 4: 3.40 - 3.09 2460 127 0.67 38.95 0.90 0.79 10884.84| |alpha: min = 0.79 max = 0.99 mean = 0.92| |beta: min = 10884.84 max = 27430.43 mean = 20327.51| |figures of merit: min = 0.01 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.61 mean = 29.16| |phase err.(test): min = 0.00 max = 88.92 mean = 29.60| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2093 0.2063 0.2663 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4471 0.4455 0.4787 n_refl.: 10449 remove outliers: r(all,work,free)=0.4471 0.4455 0.4787 n_refl.: 10449 overall B=-1.78 to atoms: r(all,work,free)=0.4395 0.4379 0.4715 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2071 0.2041 0.2634 n_refl.: 10449 remove outliers: r(all,work,free)=0.2071 0.2041 0.2634 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.1907 767.614 755.201 1.221 1.119 0.404 14.512-11.594 100.00 95 5 0.1280 730.561 725.885 1.027 1.110 0.371 11.568-9.227 100.00 193 11 0.1274 705.922 694.539 1.023 1.099 0.365 9.162-7.352 100.00 368 15 0.1621 467.671 459.729 1.001 1.079 0.362 7.349-5.862 100.00 740 33 0.2005 345.784 337.755 0.902 1.051 0.323 5.858-4.671 100.00 1425 79 0.1812 370.463 359.595 0.938 1.005 0.275 4.669-3.723 99.93 2790 156 0.1966 340.343 330.781 1.169 0.933 0.175 3.723-3.092 100.00 4210 230 0.2607 185.837 174.972 1.346 0.836 0.031 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-6.3659 ================= 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 : 0.3804 0.4305 0.010 1.710 15.7 95.5 52.2 0 0.000 1_bss: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_settarget: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_weight: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_xyzrec: 0.2357 0.2723 0.003 0.568 32.0 111.9 68.6 0 0.184 1_adp: 0.2123 0.2686 0.003 0.568 33.6 124.7 71.0 0 0.184 1_regHadp: 0.2097 0.2672 0.003 0.568 33.6 124.7 71.0 0 0.184 2_bss: 0.2132 0.2741 0.003 0.568 31.6 122.6 69.0 0 0.184 2_settarget: 0.2132 0.2741 0.003 0.568 31.6 122.6 69.0 0 0.184 2_updatecdl: 0.2132 0.2741 0.003 0.641 31.6 122.6 69.0 0 0.184 2_weight: 0.2132 0.2741 0.003 0.641 31.6 122.6 69.0 0 0.184 2_xyzrec: 0.2039 0.2684 0.003 0.602 31.6 122.6 69.0 0 0.222 2_adp: 0.2283 0.2758 0.003 0.602 35.8 143.2 74.2 0 0.222 2_regHadp: 0.2312 0.2765 0.003 0.602 35.8 143.2 74.2 0 0.222 3_bss: 0.2299 0.2719 0.003 0.602 33.9 141.3 72.3 0 0.222 3_settarget: 0.2299 0.2719 0.003 0.602 33.9 141.3 72.3 0 0.222 3_updatecdl: 0.2299 0.2719 0.003 0.647 33.9 141.3 72.3 0 0.222 3_setrh: 0.2299 0.2720 0.003 0.647 33.9 141.3 72.3 0 0.222 3_weight: 0.2299 0.2720 0.003 0.647 33.9 141.3 72.3 0 0.222 3_xyzrec: 0.2296 0.2723 0.003 0.614 33.9 141.3 72.3 0 0.222 3_adp: 0.2077 0.2653 0.003 0.614 28.9 147.3 73.3 0 0.222 3_regHadp: 0.2063 0.2663 0.003 0.614 28.9 147.3 73.3 0 0.222 end: 0.2041 0.2634 0.003 0.614 27.1 145.5 71.5 0 0.222 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1m10_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1m10_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 8.6800 Refinement macro-cycles (run) : 263.9400 Write final files (write_after_run_outputs) : 25.7700 Total : 298.3900 Total CPU time: 5.42 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:33:55 PDT -0700 (1716251635.89 s) Start R-work = 0.2260, R-free = 0.2819 Final R-work = 0.2041, R-free = 0.2634 =============================================================================== Job complete usr+sys time: 351.29 seconds wall clock time: 17 minutes 59.08 seconds (1079.08 seconds total)