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/3fm7.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.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 { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1598 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1609 Classifications: {'peptide': 104} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 23} Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1381 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Time building chain proxies: 1.41, per 1000 atoms: 0.21 Number of scatterers: 6838 At special positions: 0 Unit cell: (115.79, 115.79, 90.5004, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 666 8.00 N 569 7.00 C 2187 6.00 H 3394 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: 3.74 Conformation dependent library (CDL) restraints added in 294.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Time building geometry restraints manager: 3.99 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: 3382 1.15 - 1.31: 591 1.31 - 1.48: 1393 1.48 - 1.64: 1508 1.64 - 1.81: 32 Bond restraints: 6906 Sorted by residual: bond pdb=" NE2 GLN A 33 " pdb="HE21 GLN A 33 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ALA E 82 " pdb=" H ALA E 82 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE2 GLN F 27 " pdb="HE21 GLN F 27 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN D 116 " pdb="HE21 GLN D 116 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE F 86 " pdb=" H PHE F 86 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6901 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 230 107.50 - 114.12: 8500 114.12 - 120.73: 1545 120.73 - 127.35: 2144 127.35 - 133.97: 26 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C ASN F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta sigma weight residual 119.89 122.75 -2.86 1.02e+00 9.61e-01 7.84e+00 angle pdb=" N VAL E 7 " pdb=" CA VAL E 7 " pdb=" C VAL E 7 " ideal model delta sigma weight residual 106.72 111.14 -4.42 1.59e+00 3.96e-01 7.74e+00 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" C ASN C 119 " ideal model delta sigma weight residual 107.61 112.16 -4.55 1.74e+00 3.30e-01 6.84e+00 angle pdb=" N ASN E 10 " pdb=" CA ASN E 10 " pdb=" C ASN E 10 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" CA GLY A 72 " pdb=" C GLY A 72 " pdb=" N ALA A 73 " ideal model delta sigma weight residual 118.67 116.19 2.48 9.80e-01 1.04e+00 6.40e+00 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 2904 26.78 - 53.56: 289 53.56 - 80.34: 53 80.34 - 107.12: 5 107.12 - 133.91: 2 Dihedral angle restraints: 3253 sinusoidal: 1731 harmonic: 1522 Sorted by residual: dihedral pdb=" CA MET F 13 " pdb=" C MET F 13 " pdb=" N SER F 14 " pdb=" CA SER F 14 " ideal model delta harmonic sigma weight residual 180.00 46.09 133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA ASN C 114 " pdb=" C ASN C 114 " pdb=" N VAL C 115 " pdb=" CA VAL C 115 " ideal model delta harmonic sigma weight residual 180.00 52.83 127.17 0 5.00e+00 4.00e-02 6.47e+02 dihedral pdb=" CA MET E 13 " pdb=" C MET E 13 " pdb=" N SER E 14 " pdb=" CA SER E 14 " ideal model delta harmonic sigma weight residual -180.00 -75.18 -104.82 0 5.00e+00 4.00e-02 4.39e+02 ... (remaining 3250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 437 0.022 - 0.043: 11 0.043 - 0.065: 19 0.065 - 0.087: 59 0.087 - 0.108: 13 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA ASN D 114 " pdb=" N ASN D 114 " pdb=" C ASN D 114 " pdb=" CB ASN D 114 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.93e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.10e-01 chirality pdb=" CA ILE B 23 " pdb=" N ILE B 23 " pdb=" C ILE B 23 " pdb=" CB ILE B 23 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.04e-01 ... (remaining 536 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 40 " -0.000 2.00e-02 2.50e+03 7.01e-04 1.97e-02 pdb=" CG TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP B 40 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 40 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 46 " 0.000 2.00e-02 2.50e+03 7.99e-04 1.91e-02 pdb=" CG PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE F 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 54 " -0.000 2.00e-02 2.50e+03 6.55e-04 1.72e-02 pdb=" CG TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP E 54 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 54 " 0.000 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.52: 48 1.52 - 2.29: 1738 2.29 - 3.06: 20457 3.06 - 3.83: 30156 3.83 - 4.60: 47763 Warning: very small nonbonded interaction distances. Nonbonded interactions: 100162 Sorted by model distance: nonbonded pdb=" HA ASN C 114 " pdb="HG23 VAL C 115 " model vdw 0.746 2.440 nonbonded pdb=" HG3 GLN C 133 " pdb=" HB3 LYS F 36 " model vdw 0.848 2.440 nonbonded pdb=" HA GLN C 116 " pdb=" HB2 ALA C 117 " model vdw 0.871 2.440 nonbonded pdb=" HG2 ARG B 94 " pdb="HH11 ARG B 94 " model vdw 0.985 2.270 nonbonded pdb=" HA MET F 13 " pdb=" HB2 SER F 14 " model vdw 1.040 2.440 ... (remaining 100157 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 22 15.91 1 O 666 7.97 1 N 569 6.97 1 C 2187 5.97 1 H 3394 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: 3394 of 6838 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6838 n_use_u_iso = 6838 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 = 6838 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6838 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 6838 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 = "3fm7_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3394 occupancy sum: 3394.00 (% of total atoms 49.68) Rotatable: count: 1005 occupancy sum: 1005.00 (% of total atoms 14.71) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3573 r_free= 0.3825 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431057 | | target function (ml) not normalized (work): 50644.571594 | | target function (ml) not normalized (free): 5712.019596 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1358 142 0.4105 0.4302 7.4385 7.4058| | 2: 6.35 - 5.05 1.00 1326 136 0.3185 0.3402 6.6863 6.7637| | 3: 5.04 - 4.41 1.00 1320 143 0.3188 0.3218 6.3284 6.4613| | 4: 4.41 - 4.01 0.99 1291 153 0.3401 0.3699 6.1277 6.4141| | 5: 4.01 - 3.72 0.99 1285 148 0.3360 0.4071 5.9732 6.2399| | 6: 3.72 - 3.50 0.99 1295 148 0.3851 0.4177 5.9746 6.1601| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1358 142 0.52 50.23 0.82 0.72 437329.23| | 2: 6.35 - 5.05 1326 136 0.56 47.21 1.23 0.89 198795.77| | 3: 5.04 - 4.41 1320 143 0.78 29.03 1.38 1.01 71014.34| | 4: 4.41 - 4.01 1291 153 0.71 34.61 1.41 1.00 52577.48| | 5: 4.01 - 3.72 1285 148 0.62 42.28 1.34 0.96 45018.50| | 6: 3.72 - 3.50 1295 148 0.64 41.10 1.46 0.94 40633.46| |alpha: min = 0.72 max = 1.01 mean = 0.92| |beta: min = 40633.46 max = 437329.23 mean = 143438.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.64| |phase err.(work): min = 0.00 max = 89.98 mean = 40.81| |phase err.(test): min = 0.00 max = 89.61 mean = 40.40| |-----------------------------------------------------------------------------| ----------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 : 0.003 0.016 3512 Z= 0.224 Angle : 0.846 4.753 4762 Z= 0.586 Chirality : 0.032 0.108 539 Planarity : 0.000 0.001 601 Dihedral : 23.554 133.906 1264 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 44.73 Ramachandran Plot: Outliers : 4.77 % Allowed : 13.60 % Favored : 81.62 % Rotamer: Outliers : 25.33 % Allowed : 17.15 % Favored : 57.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 2.64 % 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: -5.75 (0.30), residues: 419 helix: -4.63 (0.19), residues: 131 sheet: -1.47 (0.57), residues: 92 loop : -4.46 (0.27), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 60 TYR 0.001 0.000 TYR F 65 PHE 0.001 0.000 PHE F 46 TRP 0.001 0.000 TRP B 40 HIS 0.000 0.000 HIS A 76 Individual atomic B min max mean iso aniso Overall: 2.00 500.00 94.66 89.80 3444 0 Protein: 2.00 500.00 94.66 89.80 3444 0 Chain A: 2.00 500.00 114.65 N/A 807 0 Chain B: 2.00 458.88 97.81 N/A 813 0 Chain C: 2.00 495.15 104.99 N/A 215 0 Chain D: 2.00 500.00 119.77 N/A 215 0 Chain E: 2.00 478.28 71.82 N/A 697 0 Chain F: 2.00 403.25 79.76 N/A 697 0 Histogram: Values Number of atoms 2.00 - 51.80 934 51.80 - 101.60 1312 101.60 - 151.40 657 151.40 - 201.20 310 201.20 - 251.00 111 251.00 - 300.80 57 300.80 - 350.60 34 350.60 - 400.40 17 400.40 - 450.20 6 450.20 - 500.00 6 |-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 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3573 r_free= 0.3825 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431057 | | target function (ml) not normalized (work): 50644.571594 | | target function (ml) not normalized (free): 5712.019596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3589 0.3573 0.3825 n_refl.: 8745 re-set all scales: r(all,work,free)=0.3589 0.3573 0.3825 n_refl.: 8745 remove outliers: r(all,work,free)=0.3585 0.3571 0.3811 n_refl.: 8739 overall B=17.64 to atoms: r(all,work,free)=0.4218 0.4229 0.4187 n_refl.: 8739 bulk-solvent and scaling: r(all,work,free)=0.2240 0.2141 0.3139 n_refl.: 8739 remove outliers: r(all,work,free)=0.2235 0.2135 0.3139 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3558 1472.375 1342.545 1.239 0.973 0.325 15.490-12.512 99.01 89 11 0.2187 1306.036 1261.365 1.106 0.974 0.283 12.419-9.967 99.48 175 15 0.1814 1476.037 1437.608 1.169 0.977 0.280 9.933-7.985 99.73 337 34 0.1928 1108.226 1073.275 1.178 0.978 0.264 7.976-6.403 100.00 631 64 0.2456 609.809 575.118 1.094 0.979 0.229 6.399-5.132 99.93 1234 135 0.2161 578.066 550.281 0.973 0.981 0.174 5.129-4.115 99.81 2357 259 0.1739 559.520 545.409 0.991 0.984 0.113 4.114-3.501 98.83 2959 341 0.2478 337.971 323.299 1.036 0.987 0.037 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0046 b_overall=-0.2819 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.716293 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.127326 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 0.2288 0.3251 0.0962 0.003 0.6 5.6 3.3 15.3 0 0.125 0.2249 0.3248 0.0999 0.003 0.6 5.6 3.3 15.6 0 0.250 0.2192 0.3238 0.1046 0.003 0.6 5.6 3.3 16.1 0 0.500 0.2131 0.3242 0.1111 0.004 0.7 8.2 3.3 16.6 0 1.000 0.2050 0.3228 0.1178 0.005 0.7 9.7 3.3 17.9 0 2.000 0.2008 0.3234 0.1226 0.006 0.8 14.5 4.1 18.5 0 3.000 0.1972 0.3234 0.1262 0.008 0.9 17.0 4.3 19.5 0 4.000 0.1936 0.3219 0.1282 0.009 0.9 19.4 4.3 20.3 0 5.000 0.1919 0.3225 0.1307 0.010 1.0 21.3 5.0 20.8 0 6.000 0.1905 0.3226 0.1321 0.011 1.1 22.9 4.8 21.6 0 7.000 0.1887 0.3218 0.1330 0.012 1.1 23.9 4.8 22.2 0 8.000 0.1881 0.3217 0.1336 0.013 1.2 25.7 5.0 22.4 0 9.000 0.1876 0.3224 0.1347 0.014 1.3 28.6 5.0 22.7 0 10.000 0.1883 0.3220 0.1337 0.013 1.2 26.0 5.0 22.2 0 8.858 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1881 0.3217 0.1336 0.013 1.2 25.7 5.0 22.4 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.81 32.17 13.36 64.040 110.958 0.127 0.042 24.82 32.49 7.67 46.622 120.195 0.004 0.068 24.49 32.34 7.84 46.707 120.014 0.016 0.066 23.38 31.92 8.54 47.093 119.384 0.064 0.061 22.31 31.51 9.20 47.588 118.843 0.127 0.056 21.61 31.28 9.67 47.952 118.636 0.191 0.053 20.97 31.10 10.13 48.480 118.190 0.255 0.051 20.46 30.95 10.49 48.989 117.808 0.318 0.049 20.03 30.83 10.80 49.485 117.463 0.382 0.047 19.69 30.74 11.05 49.915 117.223 0.446 0.046 19.43 30.66 11.23 50.272 117.089 0.509 0.045 19.71 30.85 11.14 50.080 118.327 0.573 0.046 19.43 30.81 11.37 50.497 117.964 0.637 0.045 max suggested for this run: 22.19 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.004 Accepted refinement result: 24.82 32.49 7.67 46.622 120.195 0.004 0.068 Individual atomic B min max mean iso aniso Overall: 64.82 512.64 130.64 57.58 3444 0 Protein: 64.82 512.64 130.64 57.58 3444 0 Chain A: 79.23 512.64 152.13 N/A 807 0 Chain B: 78.78 471.52 133.55 N/A 813 0 Chain C: 75.34 507.79 144.22 N/A 215 0 Chain D: 80.39 512.64 154.92 N/A 215 0 Chain E: 64.82 490.92 106.50 N/A 697 0 Chain F: 72.71 415.89 114.84 N/A 697 0 Histogram: Values Number of atoms 64.82 - 109.60 1488 109.60 - 154.39 1264 154.39 - 199.17 400 199.17 - 243.95 144 243.95 - 288.73 63 288.73 - 333.51 36 333.51 - 378.29 26 378.29 - 423.08 14 423.08 - 467.86 3 467.86 - 512.64 6 =========================== Idealize ADP of riding H ========================== r_work=0.2482 r_free=0.3249 r_work=0.2574 r_free=0.3251 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2574 r_free= 0.3251 coordinate error (max.-lik. estimate): 0.16 A | | | | normalized target function (ls_wunit_k1) (work): 0.072436 | | target function (ls_wunit_k1) not normalized (work): 570.001347 | | target function (ls_wunit_k1) not normalized (free): 107.947020 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2640 0.2574 0.3251 n_refl.: 8738 re-set all scales: r(all,work,free)=0.5133 0.5159 0.4914 n_refl.: 8738 remove outliers: r(all,work,free)=0.5133 0.5159 0.4914 n_refl.: 8738 overall B=-31.08 to atoms: r(all,work,free)=0.4029 0.4037 0.4012 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2302 0.2216 0.3090 n_refl.: 8738 remove outliers: r(all,work,free)=0.2302 0.2216 0.3090 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.2860 655.850 626.526 1.343 0.959 0.331 15.490-12.512 99.01 89 11 0.1634 581.757 568.772 1.228 0.960 0.302 12.419-9.967 99.48 175 15 0.1359 657.482 645.216 1.228 0.965 0.277 9.933-7.985 99.73 337 34 0.1441 493.645 485.147 1.242 0.967 0.266 7.976-6.403 100.00 631 64 0.2164 271.632 262.277 1.120 0.972 0.234 6.399-5.132 99.93 1234 135 0.2118 257.492 247.983 0.999 0.978 0.192 5.129-4.115 99.81 2357 259 0.2022 249.231 243.814 0.998 0.988 0.132 4.114-3.501 98.83 2959 341 0.3051 150.545 143.024 1.008 0.999 0.052 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.3304 ============================ 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 = 6.424890 wxc_scale = 0.043 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.038782 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 0.2380 0.3124 0.0744 0.003 0.7 8.5 3.3 17.7 0 0.028 0.2355 0.3108 0.0753 0.003 0.6 7.8 3.3 17.2 0 0.083 0.2318 0.3096 0.0778 0.003 0.6 8.2 2.9 16.6 0 0.165 0.2293 0.3086 0.0793 0.003 0.6 8.9 2.9 16.6 0 0.248 0.2277 0.3082 0.0805 0.004 0.7 10.1 3.1 18.2 0 0.331 0.2246 0.3072 0.0826 0.004 0.7 9.8 2.9 18.2 0 0.414 0.2233 0.3058 0.0825 0.004 0.7 11.0 3.1 18.5 0 0.496 0.2218 0.3052 0.0834 0.005 0.7 11.0 3.1 18.7 0 0.579 0.2290 0.3083 0.0793 0.004 0.7 9.1 2.9 16.1 0 0.276 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2218 0.3052 0.0834 0.005 0.7 11.0 3.1 18.7 0 0.579 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.18 30.52 8.34 45.486 111.225 0.039 5.640 28.28 31.70 3.42 33.272 126.715 0.001 5.691 26.95 30.85 3.90 32.988 125.567 0.005 5.681 24.22 29.21 4.98 33.939 122.398 0.019 5.655 22.33 28.54 6.21 36.318 119.813 0.039 5.611 21.26 28.53 7.27 38.509 117.747 0.058 5.584 20.78 28.58 7.81 40.026 116.465 0.078 5.574 20.51 28.70 8.19 40.951 115.174 0.097 5.571 20.38 28.73 8.35 41.674 114.679 0.116 5.568 20.30 28.79 8.49 42.212 114.341 0.136 5.567 20.25 28.83 8.58 42.624 114.126 0.155 5.566 20.22 28.88 8.67 42.950 113.987 0.175 5.566 20.18 28.93 8.75 43.205 113.928 0.194 5.566 max suggested for this run: 22.25 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.019 Accepted refinement result: 24.22 29.21 4.98 33.939 122.398 0.019 5.655 Individual atomic B min max mean iso aniso Overall: 34.97 476.56 121.74 37.65 3444 0 Protein: 34.97 476.56 121.74 37.65 3444 0 Chain A: 72.80 476.56 151.34 N/A 807 0 Chain B: 54.91 435.44 126.71 N/A 813 0 Chain C: 40.13 471.71 137.41 N/A 215 0 Chain D: 55.92 476.56 151.00 N/A 215 0 Chain E: 34.97 454.84 89.51 N/A 697 0 Chain F: 39.00 379.81 100.05 N/A 697 0 Histogram: Values Number of atoms 34.97 - 79.13 614 79.13 - 123.29 1398 123.29 - 167.45 979 167.45 - 211.61 290 211.61 - 255.76 81 255.76 - 299.92 35 299.92 - 344.08 24 344.08 - 388.24 14 388.24 - 432.40 3 432.40 - 476.56 6 =========================== Idealize ADP of riding H ========================== r_work=0.2422 r_free=0.2921 r_work=0.2463 r_free=0.2926 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2463 r_free= 0.2926 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ml) (work): 5.664961 | | target function (ml) not normalized (work): 44577.579010 | | target function (ml) not normalized (free): 5021.809809 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2508 0.2463 0.2926 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4664 0.4699 0.4385 n_refl.: 8738 remove outliers: r(all,work,free)=0.4664 0.4699 0.4385 n_refl.: 8738 overall B=-12.19 to atoms: r(all,work,free)=0.4217 0.4245 0.4011 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2430 0.2374 0.2952 n_refl.: 8738 remove outliers: r(all,work,free)=0.2430 0.2374 0.2952 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3219 655.850 611.990 1.244 0.965 0.327 15.490-12.512 99.01 89 11 0.1752 581.757 565.523 1.123 0.967 0.284 12.419-9.967 99.48 175 15 0.1483 657.482 643.414 1.196 0.972 0.277 9.933-7.985 99.73 337 34 0.1642 493.645 481.168 1.232 0.973 0.260 7.976-6.403 100.00 631 64 0.2604 271.632 254.586 1.136 0.977 0.223 6.399-5.132 99.93 1234 135 0.2443 257.492 243.205 0.991 0.981 0.165 5.129-4.115 99.81 2357 259 0.2062 249.231 241.731 0.970 0.987 0.093 4.114-3.501 98.83 2959 341 0.3109 150.545 141.450 0.979 0.994 0.037 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=5.2642 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2374 r_free=0.2952 After: r_work=0.2374 r_free=0.2952 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.204765 wxc_scale = 0.052 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.034213 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 0.2387 0.2954 0.0567 0.004 0.7 12.5 2.9 18.2 0 0.033 0.2383 0.2954 0.0571 0.004 0.7 12.2 2.9 18.5 0 0.098 0.2380 0.2953 0.0574 0.004 0.7 12.5 3.1 18.5 0 0.195 0.2376 0.2951 0.0575 0.004 0.7 11.9 3.1 18.5 0 0.293 0.2373 0.2952 0.0579 0.004 0.8 11.9 3.1 18.5 0 0.390 0.2370 0.2951 0.0581 0.004 0.8 11.9 3.1 18.5 0 0.488 0.2367 0.2951 0.0584 0.005 0.8 12.3 3.1 18.5 0 0.586 0.2363 0.2954 0.0591 0.005 0.8 12.5 3.1 18.7 0 0.683 0.2375 0.2951 0.0576 0.004 0.7 11.9 3.1 18.5 0 0.325 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2376 0.2951 0.0575 0.004 0.7 11.9 3.1 18.5 0 0.293 0.2375 0.2951 0.0576 0.004 0.7 11.9 3.1 18.5 0 0.325 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.76 29.51 5.75 32.669 121.771 0.034 5.666 29.10 31.84 2.73 27.733 130.583 0.001 5.724 28.47 31.45 2.98 27.118 130.908 0.004 5.707 25.18 29.68 4.50 29.340 127.162 0.017 5.649 22.85 28.81 5.96 31.645 123.357 0.034 5.619 22.48 28.85 6.36 32.221 122.515 0.051 5.617 22.32 28.91 6.59 32.496 122.361 0.068 5.614 22.36 28.92 6.56 32.605 122.022 0.086 5.618 22.32 28.93 6.61 32.713 121.971 0.103 5.618 22.29 28.95 6.66 32.795 121.949 0.120 5.617 22.27 28.96 6.69 32.863 121.942 0.137 5.617 22.26 28.98 6.72 32.919 121.943 0.154 5.617 22.24 28.99 6.74 32.965 121.949 0.171 5.616 max suggested for this run: 24.35 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.017 Accepted refinement result: 25.18 29.68 4.50 29.340 127.162 0.017 5.649 Individual atomic B min max mean iso aniso Overall: 50.29 459.37 120.25 33.46 3444 0 Protein: 50.29 459.37 120.25 33.46 3444 0 Chain A: 84.05 459.37 148.62 N/A 807 0 Chain B: 59.30 418.25 124.53 N/A 813 0 Chain C: 58.46 454.52 133.88 N/A 215 0 Chain D: 67.49 459.37 148.79 N/A 215 0 Chain E: 50.29 437.65 91.23 N/A 697 0 Chain F: 53.83 362.62 98.44 N/A 697 0 Histogram: Values Number of atoms 50.29 - 91.20 1060 91.20 - 132.11 1276 132.11 - 173.01 764 173.01 - 213.92 214 213.92 - 254.83 62 254.83 - 295.74 29 295.74 - 336.64 18 336.64 - 377.55 13 377.55 - 418.46 4 418.46 - 459.37 4 =========================== Idealize ADP of riding H ========================== r_work=0.2518 r_free=0.2968 r_work=0.2527 r_free=0.2979 ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2527 r_free= 0.2979 coordinate error (max.-lik. estimate): 0.15 A | | | | normalized target function (ml) (work): 5.653309 | | target function (ml) not normalized (work): 44485.889627 | | target function (ml) not normalized (free): 5017.478151 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1354 141 0.2223 0.2762 6.1898 6.4342| | 2: 6.35 - 5.05 1.00 1326 136 0.2349 0.2877 5.8123 5.9609| | 3: 5.04 - 4.41 1.00 1320 143 0.2136 0.2555 5.6186 5.6913| | 4: 4.41 - 4.01 0.99 1291 153 0.2665 0.3058 5.4991 5.6929| | 5: 4.01 - 3.72 0.99 1285 148 0.3170 0.3454 5.3654 5.4596| | 6: 3.72 - 3.50 0.99 1293 148 0.3671 0.3902 5.4041 5.4506| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1354 141 0.72 33.53 0.92 0.84 55636.21| | 2: 6.35 - 5.05 1326 136 0.70 35.59 1.02 0.89 29400.08| | 3: 5.04 - 4.41 1320 143 0.82 24.52 1.12 0.95 14374.00| | 4: 4.41 - 4.01 1291 153 0.77 29.74 1.14 0.97 11336.63| | 5: 4.01 - 3.72 1285 148 0.68 37.70 1.19 0.96 10026.70| | 6: 3.72 - 3.50 1293 148 0.68 38.35 1.25 0.94 9883.82| |alpha: min = 0.84 max = 0.97 mean = 0.92| |beta: min = 9883.82 max = 55636.21 mean = 22059.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.73| |phase err.(work): min = 0.00 max = 89.94 mean = 33.22| |phase err.(test): min = 0.00 max = 88.51 mean = 32.90| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2527 0.2979 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4850 0.4888 0.4547 n_refl.: 8738 remove outliers: r(all,work,free)=0.4850 0.4888 0.4547 n_refl.: 8738 overall B=-15.64 to atoms: r(all,work,free)=0.4281 0.4311 0.4069 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2407 0.2349 0.2938 n_refl.: 8738 remove outliers: r(all,work,free)=0.2407 0.2349 0.2938 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3223 655.850 610.879 1.219 0.962 0.328 15.490-12.512 99.01 89 11 0.1722 581.757 566.353 1.103 0.964 0.285 12.419-9.967 99.48 175 15 0.1516 657.482 642.699 1.173 0.968 0.279 9.933-7.985 99.73 337 34 0.1645 493.645 480.817 1.203 0.970 0.263 7.976-6.403 100.00 631 64 0.2532 271.632 254.628 1.118 0.974 0.238 6.399-5.132 99.93 1234 135 0.2416 257.492 243.384 0.983 0.979 0.181 5.129-4.115 99.81 2357 259 0.2046 249.231 243.155 0.988 0.987 0.097 4.114-3.501 98.83 2959 341 0.3062 150.545 142.213 1.006 0.995 0.053 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=1.6391 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3573 0.3825 0.003 0.846 2.0 500.0 94.7 0 0.000 1_bss: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_settarget: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_weight: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_xyzrec: 0.1881 0.3217 0.013 1.195 19.6 517.6 112.3 0 0.335 1_adp: 0.2482 0.3249 0.013 1.195 64.8 512.6 130.6 0 0.335 1_regHadp: 0.2574 0.3251 0.013 1.195 64.8 512.6 130.6 0 0.335 2_bss: 0.2216 0.3090 0.013 1.195 33.7 481.6 99.6 0 0.335 2_settarget: 0.2216 0.3090 0.013 1.195 33.7 481.6 99.6 0 0.335 2_updatecdl: 0.2216 0.3090 0.013 1.240 33.7 481.6 99.6 0 0.335 2_weight: 0.2216 0.3090 0.013 1.240 33.7 481.6 99.6 0 0.335 2_xyzrec: 0.2218 0.3052 0.005 0.741 33.7 481.6 99.6 0 0.317 2_adp: 0.2422 0.2921 0.005 0.741 35.0 476.6 121.7 0 0.317 2_regHadp: 0.2463 0.2926 0.005 0.741 35.0 476.6 121.7 0 0.317 3_bss: 0.2374 0.2952 0.005 0.741 22.8 464.4 109.6 0 0.317 3_settarget: 0.2374 0.2952 0.005 0.741 22.8 464.4 109.6 0 0.317 3_updatecdl: 0.2374 0.2952 0.005 0.797 22.8 464.4 109.6 0 0.317 3_setrh: 0.2374 0.2952 0.005 0.797 22.8 464.4 109.6 0 0.316 3_weight: 0.2374 0.2952 0.005 0.797 22.8 464.4 109.6 0 0.316 3_xyzrec: 0.2376 0.2951 0.004 0.747 22.8 464.4 109.6 0 0.316 3_adp: 0.2518 0.2968 0.004 0.747 50.3 459.4 120.3 0 0.316 3_regHadp: 0.2527 0.2979 0.004 0.747 50.3 459.4 120.3 0 0.316 end: 0.2349 0.2938 0.004 0.747 34.7 443.7 104.6 0 0.316 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/3fm7_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/3fm7_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 8.5500 Refinement macro-cycles (run) : 248.3100 Write final files (write_after_run_outputs) : 24.5400 Total : 281.4000 Total CPU time: 5.20 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:33:06 PDT -0700 (1716251586.16 s) Start R-work = 0.2135, R-free = 0.3139 Final R-work = 0.2349, R-free = 0.2938 =============================================================================== Job complete usr+sys time: 336.18 seconds wall clock time: 17 minutes 14.50 seconds (1034.50 seconds total)