Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1u87.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 amber.topology_file_name=4amber_1u87.prmtop amber.coordinate_file_name=4amber_1u87.rst7 amber.order_file_name=4amber_1u87.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_1u87.rst7 4amber_1u87.prmtop 4amber_1u87.order Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_1u87.pdb" } default_model = "4phenix_1u87.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } amber { use_amber = True topology_file_name = 4amber_1u87.prmtop coordinate_file_name = 4amber_1u87.rst7 order_file_name = 4amber_1u87.order } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 3505 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3470 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.48, per 1000 atoms: 0.14 Number of scatterers: 3505 At special positions: 0 Unit cell: (123.05, 123.05, 72.51, 90, 90, 120) Space group: P 63 2 2 (No. 182) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 316 8.00 N 282 7.00 C 1138 6.00 H 1755 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: 0.59 Conformation dependent library (CDL) restraints added in 119.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 1 sheets defined 56.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.093A pdb=" N ARG A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.265A pdb=" N HIS A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 110 removed outlier: 3.880A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 139 removed outlier: 4.783A pdb=" N VAL A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Proline residue: A 127 - end of helix removed outlier: 3.990A pdb=" N MET A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 4.289A pdb=" N TYR A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.716A pdb=" N LYS A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.849A pdb=" N TYR A 33 " --> pdb=" O PHE A 7 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.57 Time building geometry restraints manager: 0.67 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: 1750 1.15 - 1.33: 428 1.33 - 1.50: 640 1.50 - 1.68: 708 1.68 - 1.85: 23 Bond restraints: 3549 Sorted by residual: bond pdb=" N3 GSH A 500 " pdb=" HN3 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.00e-02 1.00e+04 2.57e+02 bond pdb=" N2 GSH A 500 " pdb=" HN2 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.10e-02 8.26e+03 2.12e+02 bond pdb=" CA2 GSH A 500 " pdb=" HA2 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CB2 GSH A 500 " pdb="HB23 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.44e+02 ... (remaining 3544 not shown) Histogram of bond angle deviations from ideal: 99.31 - 107.06: 254 107.06 - 114.81: 4243 114.81 - 122.56: 1410 122.56 - 130.32: 520 130.32 - 138.07: 15 Bond angle restraints: 6442 Sorted by residual: angle pdb=" N TYR A 164 " pdb=" CA TYR A 164 " pdb=" C TYR A 164 " ideal model delta sigma weight residual 114.31 102.34 11.97 1.29e+00 6.01e-01 8.61e+01 angle pdb="HN11 GSH A 500 " pdb=" N1 GSH A 500 " pdb="HN12 GSH A 500 " ideal model delta sigma weight residual 111.04 138.07 -27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" N ASP A 62 " pdb=" CA ASP A 62 " pdb=" C ASP A 62 " ideal model delta sigma weight residual 114.04 103.69 10.35 1.24e+00 6.50e-01 6.97e+01 angle pdb=" CA2 GSH A 500 " pdb=" C2 GSH A 500 " pdb=" O2 GSH A 500 " ideal model delta sigma weight residual 120.61 109.21 11.40 1.39e+00 5.18e-01 6.72e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 115.47 104.89 10.58 1.31e+00 5.83e-01 6.53e+01 ... (remaining 6437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.48: 1422 13.48 - 26.97: 124 26.97 - 40.45: 72 40.45 - 53.94: 29 53.94 - 67.42: 24 Dihedral angle restraints: 1671 sinusoidal: 918 harmonic: 753 Sorted by residual: dihedral pdb=" CA ASP A 190 " pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " pdb=" OD1 ASP A 190 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CA HIS A 150 " pdb=" CB HIS A 150 " ideal model delta harmonic sigma weight residual 122.80 130.92 -8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB MET A 132 " pdb=" CG MET A 132 " pdb=" SD MET A 132 " pdb=" CE MET A 132 " ideal model delta sinusoidal sigma weight residual 180.00 120.60 59.40 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1668 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 1.084: 254 1.084 - 2.167: 0 2.167 - 3.250: 0 3.250 - 4.334: 0 4.334 - 5.417: 1 Chirality restraints: 255 Sorted by residual: chirality pdb=" CA1 GSH A 500 " pdb=" CB1 GSH A 500 " pdb=" C1 GSH A 500 " pdb=" N1 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.66 2.76 -5.42 2.00e-01 2.50e+01 7.34e+02 chirality pdb=" CA HIS A 150 " pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CB HIS A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 252 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH A 500 " 0.313 2.00e-02 2.50e+03 2.24e-01 7.49e+02 pdb=" CA2 GSH A 500 " 0.101 2.00e-02 2.50e+03 pdb=" CA3 GSH A 500 " 0.137 2.00e-02 2.50e+03 pdb=" N3 GSH A 500 " 0.034 2.00e-02 2.50e+03 pdb=" O2 GSH A 500 " -0.303 2.00e-02 2.50e+03 pdb=" HN3 GSH A 500 " -0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 156 " -0.131 2.00e-02 2.50e+03 5.15e-02 7.95e+01 pdb=" CG TYR A 156 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 156 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 156 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 156 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 156 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 156 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 156 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 TYR A 156 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR A 156 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 156 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 156 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 201 " 0.100 2.00e-02 2.50e+03 3.02e-02 3.64e+01 pdb=" CG TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 201 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 201 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 201 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 201 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP A 201 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 201 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 201 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 201 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 201 " -0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 201 " 0.021 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 0.74 - 1.51: 19 1.51 - 2.29: 733 2.29 - 3.06: 10908 3.06 - 3.83: 14661 3.83 - 4.60: 24219 Warning: very small nonbonded interaction distances. Nonbonded interactions: 50540 Sorted by model distance: nonbonded pdb=" HG SER A 112 " pdb=" H LYS A 113 " model vdw 0.743 2.100 nonbonded pdb="HD12 LEU A 13 " pdb=" HG SER A 68 " model vdw 0.797 2.270 nonbonded pdb=" HG1 THR A 149 " pdb=" HD2 PRO A 151 " model vdw 0.808 2.270 nonbonded pdb="HG13 ILE A 109 " pdb=" H ALA A 110 " model vdw 1.183 2.270 nonbonded pdb="HH12 ARG A 103 " pdb="HE21 GLN A 204 " model vdw 1.249 2.100 ... (remaining 50535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1u87.prmtop atom order : 4amber_1u87.order coordinates : 4amber_1u87.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 14 15.91 1 O 316 7.97 1 N 282 6.97 1 C 1138 5.97 1 H 1755 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: 1755 of 3505 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3505 n_use_u_iso = 3505 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 = 3505 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3505 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3505 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 15 through 24 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 38 through 47 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 68 through 79 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 86 through 110 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 115 through 139 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 150 through 165 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 174 through 185 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 187 through 193 } sheet { first_strand = chain 'A' and resid 29 through 33 sheet_id = " A" strand { selection = chain 'A' and resid 4 through 8 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 5 and name N bond_start_previous = chain 'A' and resid 29 and name O } strand { selection = chain 'A' and resid 57 through 59 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 59 and name N bond_start_previous = chain 'A' and resid 4 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_1u87.prmtop" coordinate_file_name = "4amber_1u87.rst7" order_file_name = "4amber_1u87.order" } } output { prefix = "4phenix_1u87_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4185 (all), 10.01 % free)-------------| | | | r_work= 0.3291 r_free= 0.3496 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 4.034731 | | target function (ml) not normalized (work): 15194.798702 | | target function (ml) not normalized (free): 1682.746904 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.97 - 5.04 0.97 1353 151 0.3690 0.3748 4.5711 4.5069| | 2: 5.04 - 4.01 0.96 1235 137 0.2801 0.3145 3.9195 3.907| | 3: 4.00 - 3.50 0.92 1178 131 0.3179 0.3492 3.5395 3.5644| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.97 - 5.04 1353 151 0.58 43.55 0.90 0.05 1453.82| | 2: 5.04 - 4.01 1235 137 0.71 33.61 1.20 0.06 634.27| | 3: 4.00 - 3.50 1178 131 0.85 21.67 1.27 0.07 173.40| |alpha: min = 0.05 max = 0.07 mean = 0.06| |beta: min = 173.40 max = 1453.82 mean = 784.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.94 mean = 33.45| |phase err.(test): min = 0.00 max = 89.48 mean = 34.29| |-----------------------------------------------------------------------------| ----------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 : 0.011 0.121 1794 Z= 0.655 Angle : 1.713 19.034 2419 Z= 1.088 Chirality : 0.354 5.417 255 Planarity : 0.012 0.154 305 Dihedral : 17.263 67.421 697 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 38.80 Ramachandran Plot: Outliers : 8.70 % Allowed : 20.29 % Favored : 71.01 % Rotamer: Outliers : 9.57 % Allowed : 6.91 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -6.40 (0.37), residues: 207 helix: -4.33 (0.27), residues: 104 sheet: None (None), residues: 0 loop : -4.22 (0.45), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 103 TYR 0.107 0.013 TYR A 156 PHE 0.039 0.010 PHE A 179 TRP 0.068 0.013 TRP A 201 HIS 0.001 0.001 HIS A 139 Individual atomic B min max mean iso aniso Overall: 15.03 98.11 43.96 1.66 1750 0 Protein: 15.03 98.11 43.87 1.66 1730 0 Other: 41.47 63.03 52.15 N/A 20 0 Chain A: 15.03 98.11 43.96 N/A 1750 0 Histogram: Values Number of atoms 15.03 - 23.34 283 23.34 - 31.65 247 31.65 - 39.95 311 39.95 - 48.26 195 48.26 - 56.57 287 56.57 - 64.88 141 64.88 - 73.19 115 73.19 - 81.49 109 81.49 - 89.80 54 89.80 - 98.11 8 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4185 (all), 10.01 % free)-------------| | | | r_work= 0.3291 r_free= 0.3496 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 4.034731 | | target function (ml) not normalized (work): 15194.798702 | | target function (ml) not normalized (free): 1682.746904 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3310 0.3291 0.3496 n_refl.: 4185 re-set all scales: r(all,work,free)=0.3310 0.3291 0.3496 n_refl.: 4185 remove outliers: r(all,work,free)=0.3321 0.3303 0.3496 n_refl.: 4182 overall B=14.00 to atoms: r(all,work,free)=0.3720 0.3691 0.3987 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.2219 0.2215 0.2257 n_refl.: 4182 remove outliers: r(all,work,free)=0.2219 0.2215 0.2257 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2921 1104.326 1001.496 1.274 0.998 0.352 12.881-10.207 97.06 88 11 0.2182 1533.491 1475.510 1.352 0.999 0.334 10.181-8.045 98.52 181 19 0.1848 1232.108 1219.146 1.250 0.998 0.325 8.023-6.324 96.77 350 40 0.2505 756.950 729.118 1.028 0.996 0.298 6.311-4.969 96.87 696 77 0.2091 689.967 669.424 0.951 0.991 0.241 4.967-3.908 95.56 1374 153 0.2084 652.034 626.808 1.012 0.981 0.158 3.907-3.500 91.76 983 109 0.2467 480.152 456.777 1.051 0.973 0.077 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.6409 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.736726 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.257537 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 0.1764 0.2525 0.0761 0.020 2.7 4.9 1.4 6.9 2 1.868 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.64 25.25 7.61 1.179 57.569 0.258 0.037 17.67 25.49 7.82 2.688 57.755 0.008 0.037 17.40 25.41 8.01 2.748 57.790 0.032 0.036 16.61 25.29 8.67 4.133 58.001 0.129 0.033 16.19 25.21 9.02 4.898 58.122 0.258 0.032 15.97 25.17 9.20 5.581 58.273 0.386 0.031 15.78 25.06 9.28 6.420 58.508 0.515 0.030 15.70 25.02 9.32 6.864 58.622 0.644 0.030 15.64 25.01 9.37 7.245 58.724 0.773 0.030 15.60 24.99 9.39 7.533 58.798 0.901 0.030 15.56 24.96 9.40 7.805 58.871 1.030 0.030 15.51 24.95 9.43 8.227 58.996 1.159 0.029 15.50 24.94 9.44 8.387 59.036 1.288 0.029 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.008 Accepted refinement result: 17.67 25.49 7.82 2.688 57.755 0.008 0.037 Individual atomic B min max mean iso aniso Overall: 30.74 110.88 58.34 1.76 1750 0 Protein: 30.74 110.88 58.29 1.76 1730 0 Other: 50.47 75.17 62.47 N/A 20 0 Chain A: 30.74 110.88 58.34 N/A 1750 0 Histogram: Values Number of atoms 30.74 - 38.76 242 38.76 - 46.77 284 46.77 - 54.79 340 54.79 - 62.80 241 62.80 - 70.81 238 70.81 - 78.83 132 78.83 - 86.84 124 86.84 - 94.86 90 94.86 - 102.87 53 102.87 - 110.88 6 =========================== Idealize ADP of riding H ========================== r_work=0.1767 r_free=0.2549 r_work=0.1769 r_free=0.2533 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1769 r_free= 0.2533 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ls_wunit_k1) (work): 0.037376 | | target function (ls_wunit_k1) not normalized (work): 140.645889 | | target function (ls_wunit_k1) not normalized (free): 31.606816 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1846 0.1769 0.2533 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3621 0.3557 0.4138 n_refl.: 4182 remove outliers: r(all,work,free)=0.3621 0.3557 0.4138 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3621 0.3557 0.4138 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1836 0.1759 0.2513 n_refl.: 4182 remove outliers: r(all,work,free)=0.1836 0.1759 0.2513 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2314 666.279 632.476 1.187 0.988 0.346 12.881-10.207 97.06 88 11 0.1431 925.209 896.766 1.318 0.990 0.330 10.181-8.045 98.52 181 19 0.1426 743.374 740.227 1.249 0.990 0.320 8.023-6.324 96.77 350 40 0.1984 456.695 448.697 1.054 0.989 0.310 6.311-4.969 96.87 696 77 0.1731 416.281 407.069 0.957 0.984 0.240 4.967-3.908 95.56 1374 153 0.1621 393.395 387.436 0.997 0.976 0.150 3.907-3.500 91.76 983 109 0.2060 289.693 280.263 1.029 0.969 0.079 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.7959 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.848004 wxc_scale = 0.218 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.055476 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 0.2281 0.2567 0.0286 0.015 1.9 0.9 1.0 3.7 0 0.018 0.2069 0.2530 0.0461 0.014 2.0 1.7 0.5 2.7 0 0.055 0.1930 0.2537 0.0607 0.015 2.2 2.9 0.5 3.2 0 0.111 0.1859 0.2546 0.0686 0.016 2.4 3.1 1.0 4.8 2 0.166 0.1813 0.2535 0.0723 0.017 2.6 4.3 1.0 8.0 2 0.221 0.1788 0.2606 0.0818 0.019 2.7 4.6 0.5 10.1 3 0.277 0.1755 0.2509 0.0754 0.020 2.7 5.1 1.4 6.9 2 0.332 0.1753 0.2508 0.0755 0.020 2.7 5.1 1.4 6.9 2 0.388 0.1845 0.2543 0.0698 0.017 2.4 3.4 1.0 6.4 2 0.185 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2069 0.2530 0.0461 0.014 2.0 1.7 0.5 2.7 0 0.055 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.69 25.30 4.61 8.576 63.769 0.055 6.051 21.14 25.91 4.77 9.375 64.656 0.002 6.075 20.19 25.44 5.25 9.300 64.083 0.007 6.040 18.93 24.82 5.89 9.634 64.122 0.028 5.993 18.55 24.70 6.15 10.140 64.413 0.055 5.980 18.33 24.67 6.35 10.658 64.702 0.083 5.974 18.21 24.66 6.45 11.025 64.887 0.111 5.971 18.11 24.66 6.54 11.437 65.084 0.139 5.967 18.05 24.64 6.59 11.759 65.230 0.166 5.965 17.96 24.63 6.66 12.345 65.469 0.194 5.962 17.92 24.63 6.71 12.652 65.588 0.222 5.961 17.89 24.62 6.73 12.905 65.683 0.250 5.960 17.86 24.62 6.76 13.145 65.774 0.277 5.960 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.028 Accepted refinement result: 18.93 24.82 5.89 9.634 64.122 0.028 5.993 Individual atomic B min max mean iso aniso Overall: 27.06 129.30 59.05 5.28 1750 0 Protein: 27.06 129.30 59.04 5.29 1730 0 Other: 45.92 71.91 59.74 N/A 20 0 Chain A: 27.06 129.30 59.05 N/A 1750 0 Histogram: Values Number of atoms 27.06 - 37.28 177 37.28 - 47.51 396 47.51 - 57.73 374 57.73 - 67.95 281 67.95 - 78.18 196 78.18 - 88.40 169 88.40 - 98.63 107 98.63 - 108.85 34 108.85 - 119.08 15 119.08 - 129.30 1 =========================== Idealize ADP of riding H ========================== r_work=0.1893 r_free=0.2482 r_work=0.1880 r_free=0.2479 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1880 r_free= 0.2479 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ml) (work): 5.989475 | | target function (ml) not normalized (work): 22538.396140 | | target function (ml) not normalized (free): 2582.514470 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1940 0.1880 0.2479 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3687 0.3626 0.4187 n_refl.: 4182 remove outliers: r(all,work,free)=0.3687 0.3626 0.4187 n_refl.: 4182 overall B=10.84 to atoms: r(all,work,free)=0.4071 0.4008 0.4578 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1914 0.1856 0.2426 n_refl.: 4182 remove outliers: r(all,work,free)=0.1914 0.1856 0.2426 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2470 666.279 635.518 1.055 0.995 0.340 12.881-10.207 97.06 88 11 0.1451 925.209 910.581 1.205 0.996 0.323 10.181-8.045 98.52 181 19 0.1481 743.374 741.488 1.169 0.994 0.319 8.023-6.324 96.77 350 40 0.1991 456.695 449.435 1.048 0.991 0.303 6.311-4.969 96.87 696 77 0.1974 416.281 402.006 0.958 0.984 0.238 4.967-3.908 95.56 1374 153 0.1684 393.395 381.096 0.994 0.971 0.147 3.907-3.500 91.76 983 109 0.2148 289.693 272.151 1.067 0.961 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9964 b_overall=0.2007 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.812552 wxc_scale = 0.390 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044369 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 0.1966 0.2416 0.0449 0.015 1.9 0.6 1.0 3.2 0 0.032 0.1856 0.2426 0.0569 0.014 2.0 1.7 0.5 2.7 0 0.095 0.1856 0.2426 0.0569 0.014 2.0 1.7 0.5 2.7 0 0.190 0.1856 0.2426 0.0569 0.014 2.0 1.7 0.5 2.7 0 0.285 0.1856 0.2426 0.0569 0.014 2.0 1.7 0.5 2.7 0 0.380 0.1856 0.2426 0.0569 0.014 2.0 1.7 0.5 2.7 0 0.475 0.1856 0.2426 0.0569 0.014 2.0 1.7 0.5 2.7 0 0.570 0.1853 0.2426 0.0573 0.014 2.0 1.7 0.5 2.7 0 0.665 0.1856 0.2426 0.0569 0.014 2.0 1.7 0.5 2.7 0 0.317 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1966 0.2416 0.0449 0.015 1.9 0.6 1.0 3.2 0 0.032 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.66 24.16 4.49 9.437 75.513 0.044 6.011 21.76 25.47 3.71 9.137 78.156 0.001 6.081 20.79 24.90 4.11 9.580 76.693 0.006 6.052 19.56 24.10 4.55 9.510 75.468 0.022 6.007 19.12 23.96 4.83 9.966 75.364 0.044 5.992 18.25 23.85 5.60 11.152 75.847 0.067 5.966 18.09 23.83 5.75 11.576 76.086 0.089 5.962 17.99 23.84 5.85 11.924 76.266 0.111 5.959 17.91 23.86 5.95 12.245 76.423 0.133 5.958 17.83 23.89 6.06 12.622 76.603 0.155 5.956 17.79 23.91 6.12 12.850 76.700 0.177 5.955 17.75 23.92 6.17 13.082 76.799 0.200 5.954 17.73 23.93 6.20 13.197 76.848 0.222 5.953 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.089 Accepted refinement result: 18.09 23.83 5.75 11.576 76.086 0.089 5.962 Individual atomic B min max mean iso aniso Overall: 32.89 165.08 71.03 10.83 1750 0 Protein: 32.89 165.08 71.03 10.82 1730 0 Other: 53.24 84.02 71.15 N/A 20 0 Chain A: 32.89 165.08 71.03 N/A 1750 0 Histogram: Values Number of atoms 32.89 - 46.11 188 46.11 - 59.33 429 59.33 - 72.55 423 72.55 - 85.77 288 85.77 - 98.99 198 98.99 - 112.21 140 112.21 - 125.42 53 125.42 - 138.64 27 138.64 - 151.86 3 151.86 - 165.08 1 =========================== Idealize ADP of riding H ========================== r_work=0.1809 r_free=0.2383 r_work=0.1795 r_free=0.2386 ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1795 r_free= 0.2386 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ml) (work): 5.958205 | | target function (ml) not normalized (work): 22420.724608 | | target function (ml) not normalized (free): 2575.973894 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.97 - 5.04 0.97 1352 151 0.1818 0.2215 6.1667 6.3148| | 2: 5.04 - 4.01 0.96 1235 137 0.1613 0.2365 5.9094 6.1122| | 3: 4.00 - 3.50 0.92 1176 131 0.2012 0.2746 5.7698 5.9929| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.97 - 5.04 1352 151 0.85 19.44 1.00 1.11 34264.40| | 2: 5.04 - 4.01 1235 137 0.85 20.87 1.00 1.10 28551.53| | 3: 4.00 - 3.50 1176 131 0.80 26.15 0.99 1.05 22860.25| |alpha: min = 1.05 max = 1.11 mean = 1.09| |beta: min = 22860.25 max = 34264.40 mean = 28825.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.73 mean = 22.00| |phase err.(test): min = 0.00 max = 87.62 mean = 21.11| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1855 0.1795 0.2386 n_refl.: 4182 re-set all scales: r(all,work,free)=0.4074 0.4009 0.4585 n_refl.: 4182 remove outliers: r(all,work,free)=0.4074 0.4009 0.4585 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.4074 0.4009 0.4585 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1839 0.1781 0.2359 n_refl.: 4182 remove outliers: r(all,work,free)=0.1839 0.1781 0.2359 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2429 575.749 551.401 0.992 1.047 0.338 12.881-10.207 97.06 88 11 0.1459 799.498 783.996 1.161 1.040 0.320 10.181-8.045 98.52 181 19 0.1484 642.370 635.727 1.144 1.030 0.310 8.023-6.324 96.77 350 40 0.1912 394.642 387.378 1.065 1.015 0.310 6.311-4.969 96.87 696 77 0.1856 359.720 349.156 0.975 0.985 0.240 4.967-3.908 95.56 1374 153 0.1602 339.944 329.727 1.040 0.938 0.160 3.907-3.500 91.76 983 109 0.2064 250.331 235.461 1.158 0.893 0.079 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.6067 ================= 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 : 0.3291 0.3496 0.011 1.713 15.0 98.1 44.0 0 0.000 1_bss: 0.2215 0.2257 0.011 1.713 29.0 112.1 58.0 0 0.000 1_settarget: 0.2215 0.2257 0.011 1.713 29.0 112.1 58.0 0 0.000 1_weight: 0.2215 0.2257 0.011 1.713 29.0 112.1 58.0 0 0.000 1_xyzrec: 0.1764 0.2525 0.020 2.741 29.0 112.1 58.0 0 0.422 1_adp: 0.1767 0.2549 0.020 2.741 30.7 110.9 58.3 0 0.422 1_regHadp: 0.1769 0.2533 0.020 2.741 30.7 110.9 58.3 0 0.422 2_bss: 0.1759 0.2513 0.020 2.741 30.7 110.9 58.3 0 0.422 2_settarget: 0.1759 0.2513 0.020 2.741 30.7 110.9 58.3 0 0.422 2_updatecdl: 0.1759 0.2513 0.020 2.736 30.7 110.9 58.3 0 0.422 2_weight: 0.1759 0.2513 0.020 2.736 30.7 110.9 58.3 0 0.422 2_xyzrec: 0.2069 0.2530 0.014 1.995 30.7 110.9 58.3 0 0.488 2_adp: 0.1893 0.2482 0.014 1.995 27.1 129.3 59.0 0 0.488 2_regHadp: 0.1880 0.2479 0.014 1.995 27.1 129.3 59.0 0 0.488 3_bss: 0.1856 0.2426 0.014 1.995 37.9 140.1 69.9 0 0.488 3_settarget: 0.1856 0.2426 0.014 1.995 37.9 140.1 69.9 0 0.488 3_updatecdl: 0.1856 0.2426 0.014 1.986 37.9 140.1 69.9 0 0.488 3_setrh: 0.1856 0.2426 0.014 1.986 37.9 140.1 69.9 0 0.488 3_weight: 0.1856 0.2426 0.014 1.986 37.9 140.1 69.9 0 0.488 3_xyzrec: 0.1966 0.2416 0.015 1.921 37.9 140.1 69.9 0 0.551 3_adp: 0.1809 0.2383 0.015 1.921 32.9 165.1 71.0 0 0.551 3_regHadp: 0.1795 0.2386 0.015 1.921 32.9 165.1 71.0 0 0.551 end: 0.1781 0.2359 0.015 1.921 32.9 165.1 71.0 0 0.551 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1u87_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1u87_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 1.9900 Refinement macro-cycles (run) : 247.7300 Write final files (write_after_run_outputs) : 7.0800 Total : 256.8000 Total CPU time: 4.77 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:38:52 PDT -0700 (1723221532.27 s) Start R-work = 0.2215, R-free = 0.2257 Final R-work = 0.1781, R-free = 0.2359 =============================================================================== Job complete usr+sys time: 291.95 seconds wall clock time: 7 minutes 20.95 seconds (440.95 seconds total)