Starting phenix.refine on Mon May 20 17:15:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 10709 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1791 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1774 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1789 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1760 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1808 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1787 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 1.95, per 1000 atoms: 0.18 Number of scatterers: 10709 At special positions: 0 Unit cell: (93.4462, 93.4462, 411.544, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 986 8.00 N 925 7.00 C 3305 6.00 H 5475 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 437.3 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 5 through 32 removed outlier: 3.565A pdb=" N GLU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 53 through 62 removed outlier: 4.092A pdb=" N LEU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 85 removed outlier: 4.792A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 110 removed outlier: 4.577A pdb=" N SER A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 Processing helix chain 'B' and resid 35 through 47 removed outlier: 4.012A pdb=" N ARG B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 3.777A pdb=" N GLU B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 85 removed outlier: 4.725A pdb=" N GLU B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 109 Processing helix chain 'C' and resid 3 through 33 removed outlier: 3.767A pdb=" N GLU C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 33 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 47 removed outlier: 3.632A pdb=" N SER C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.758A pdb=" N LEU C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 109 removed outlier: 5.207A pdb=" N GLU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Proline residue: C 87 - end of helix removed outlier: 3.508A pdb=" N SER C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 106 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 31 removed outlier: 3.529A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 65 through 108 removed outlier: 4.567A pdb=" N GLU D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Proline residue: D 87 - end of helix Processing helix chain 'E' and resid 4 through 30 removed outlier: 3.560A pdb=" N GLU E 9 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 40 No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 42 through 45 No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 53 through 62 removed outlier: 3.561A pdb=" N ALA E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 85 removed outlier: 3.669A pdb=" N LEU E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 108 removed outlier: 3.535A pdb=" N GLY E 99 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 33 removed outlier: 3.800A pdb=" N LEU F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU F 32 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 47 Processing helix chain 'F' and resid 53 through 63 removed outlier: 3.770A pdb=" N GLU F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 84 removed outlier: 3.730A pdb=" N GLU F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 108 removed outlier: 3.596A pdb=" N LEU F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN F 93 " --> pdb=" O MET F 89 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1203 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: 2.48 Time building geometry restraints manager: 3.14 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: 5475 1.15 - 1.32: 909 1.32 - 1.49: 1985 1.49 - 1.66: 2363 1.66 - 1.83: 36 Bond restraints: 10768 Sorted by residual: bond pdb=" N LEU D 57 " pdb=" H LEU D 57 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N TYR D 56 " pdb=" H TYR D 56 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA D 79 " pdb=" H ALA D 79 " 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 C 37 " pdb="HE21 GLN C 37 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU D 66 " pdb=" H GLU D 66 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 10763 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.11: 95 104.11 - 111.63: 12425 111.63 - 119.14: 2968 119.14 - 126.66: 4055 126.66 - 134.17: 45 Bond angle restraints: 19588 Sorted by residual: angle pdb=" N PHE C 3 " pdb=" CA PHE C 3 " pdb=" C PHE C 3 " ideal model delta sigma weight residual 111.69 119.66 -7.97 1.23e+00 6.61e-01 4.20e+01 angle pdb=" C HIS A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.84 126.47 -6.63 1.25e+00 6.40e-01 2.81e+01 angle pdb=" N GLN E 111 " pdb=" CA GLN E 111 " pdb=" C GLN E 111 " ideal model delta sigma weight residual 108.48 116.85 -8.37 1.65e+00 3.67e-01 2.58e+01 angle pdb=" N LYS D 4 " pdb=" CA LYS D 4 " pdb=" C LYS D 4 " ideal model delta sigma weight residual 112.38 118.50 -6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" N ASN F 64 " pdb=" CA ASN F 64 " pdb=" C ASN F 64 " ideal model delta sigma weight residual 107.23 115.01 -7.78 1.67e+00 3.59e-01 2.17e+01 ... (remaining 19583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4334 17.94 - 35.88: 348 35.88 - 53.82: 177 53.82 - 71.76: 57 71.76 - 89.70: 14 Dihedral angle restraints: 4930 sinusoidal: 2840 harmonic: 2090 Sorted by residual: dihedral pdb=" CA GLU D 32 " pdb=" C GLU D 32 " pdb=" N THR D 33 " pdb=" CA THR D 33 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLU C 2 " pdb=" C GLU C 2 " pdb=" N PHE C 3 " pdb=" CA PHE C 3 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C GLN D 28 " pdb=" N GLN D 28 " pdb=" CA GLN D 28 " pdb=" CB GLN D 28 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 4927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 653 0.090 - 0.181: 165 0.181 - 0.271: 24 0.271 - 0.361: 7 0.361 - 0.452: 2 Chirality restraints: 851 Sorted by residual: chirality pdb=" CA GLN D 28 " pdb=" N GLN D 28 " pdb=" C GLN D 28 " pdb=" CB GLN D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA PHE C 3 " pdb=" N PHE C 3 " pdb=" C PHE C 3 " pdb=" CB PHE C 3 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA LEU C 83 " pdb=" N LEU C 83 " pdb=" C LEU C 83 " pdb=" CB LEU C 83 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 848 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 40 " -0.031 2.00e-02 2.50e+03 1.17e-02 5.43e+00 pdb=" CG TRP D 40 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP D 40 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP D 40 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP D 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 40 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 40 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 40 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 40 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 40 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TRP D 40 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP D 40 " -0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP D 40 " 0.014 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 40 " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 40 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP D 40 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 40 " 0.029 2.00e-02 2.50e+03 1.03e-02 4.23e+00 pdb=" CG TRP A 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 40 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 40 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 40 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 40 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 40 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 40 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 40 " -0.015 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 40 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 56 " 0.007 2.00e-02 2.50e+03 8.98e-03 2.42e+00 pdb=" CG TYR A 56 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 56 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 56 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 56 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 56 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 56 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 56 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 56 " -0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 56 " -0.012 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.27: 26 1.27 - 2.10: 952 2.10 - 2.93: 28374 2.93 - 3.77: 48439 3.77 - 4.60: 77822 Warning: very small nonbonded interaction distances. Nonbonded interactions: 155613 Sorted by model distance: nonbonded pdb=" HE2 LYS E 4 " pdb=" HE2 PHE F 85 " model vdw 0.437 2.270 nonbonded pdb=" HE2 PHE B 3 " pdb=" CE LYS B 4 " model vdw 0.479 2.750 nonbonded pdb=" O LEU A 109 " pdb=" HE3 LYS C 46 " model vdw sym.op. 0.570 2.620 x,y+1,z nonbonded pdb="HD22 LEU E 20 " pdb="HD12 ILE E 50 " model vdw 0.593 2.440 nonbonded pdb="HD23 LEU E 91 " pdb=" HE3 LYS E 95 " model vdw 0.689 2.440 ... (remaining 155608 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 18 15.91 1 O 986 7.97 1 N 925 6.97 1 C 3305 5.97 1 H 5475 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: 5475 of 10709 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 10709 n_use_u_iso = 10709 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 = 10709 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (10709 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 10709 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 { 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 5 through 32 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 35 through 47 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 53 through 62 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 65 through 85 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 87 through 110 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 5 through 31 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 35 through 47 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 53 through 62 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 65 through 85 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 87 through 109 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'C' and resid 3 through 33 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'C' and resid 35 through 47 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'C' and resid 53 through 63 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'C' and resid 65 through 109 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'D' and resid 4 through 31 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'D' and resid 35 through 47 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'D' and resid 53 through 63 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'D' and resid 65 through 108 } helix { serial_number = "19" helix_identifier = "19" selection = chain 'E' and resid 4 through 30 } helix { serial_number = "20" helix_identifier = "20" selection = chain 'E' and resid 37 through 40 } helix { serial_number = "21" helix_identifier = "21" selection = chain 'E' and resid 42 through 45 } helix { serial_number = "22" helix_identifier = "22" selection = chain 'E' and resid 53 through 62 } helix { serial_number = "23" helix_identifier = "23" selection = chain 'E' and resid 65 through 85 } helix { serial_number = "24" helix_identifier = "24" selection = chain 'E' and resid 87 through 108 } helix { serial_number = "25" helix_identifier = "25" selection = chain 'F' and resid 5 through 33 } helix { serial_number = "26" helix_identifier = "26" selection = chain 'F' and resid 35 through 47 } helix { serial_number = "27" helix_identifier = "27" selection = chain 'F' and resid 53 through 63 } helix { serial_number = "28" helix_identifier = "28" selection = chain 'F' and resid 65 through 84 } helix { serial_number = "29" helix_identifier = "29" selection = chain 'F' and resid 86 through 108 } } enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2pej_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 5475 occupancy sum: 5475.00 (% of total atoms 53.37) Rotatable: count: 1628 occupancy sum: 1628.00 (% of total atoms 15.87) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.40 - 19.99 A, n_refl.=25915 (all), 5.09 % free)------------| | | | r_work= 0.4270 r_free= 0.4614 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 5.895891 | | target function (ml) not normalized (work): 145015.334724 | | target function (ml) not normalized (free): 7902.559553 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.99 - 6.98 0.98 2921 153 0.4360 0.4718 7.382 7.48| | 2: 6.98 - 5.58 1.00 2800 148 0.4215 0.5156 6.69 6.77| | 3: 5.58 - 4.89 0.99 2720 172 0.3241 0.3521 6.1102 6.1196| | 4: 4.89 - 4.45 0.99 2703 139 0.3764 0.4024 5.9987 6.0922| | 5: 4.45 - 4.13 0.99 2734 139 0.4458 0.4594 5.7787 5.9358| | 6: 4.13 - 3.89 0.99 2654 143 0.4796 0.5068 5.5643 5.7591| | 7: 3.89 - 3.70 0.99 2711 136 0.4992 0.5177 5.3566 5.4641| | 8: 3.70 - 3.54 0.99 2685 135 0.4835 0.5326 5.105 5.1893| | 9: 3.54 - 3.40 1.00 2668 154 0.4775 0.4950 4.9066 4.9642| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.99 - 6.98 2921 153 0.49 51.09 0.92 0.50 544086.03| | 2: 6.98 - 5.58 2800 148 0.30 66.73 0.95 0.53 214995.99| | 3: 5.58 - 4.89 2720 172 0.69 35.94 1.11 0.64 42450.73| | 4: 4.89 - 4.45 2703 139 0.79 27.26 1.44 0.80 27205.46| | 5: 4.45 - 4.13 2734 139 0.79 26.83 1.66 0.95 19864.90| | 6: 4.13 - 3.89 2654 143 0.78 28.28 1.78 1.04 13980.59| | 7: 3.89 - 3.70 2711 136 0.78 28.46 1.82 1.08 9226.84| | 8: 3.70 - 3.54 2685 135 0.77 29.33 1.76 1.05 6022.37| | 9: 3.54 - 3.40 2668 154 0.81 26.83 1.72 0.96 3599.32| |alpha: min = 0.50 max = 1.08 mean = 0.83| |beta: min = 3599.32 max = 544086.03 mean = 102556.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.69| |phase err.(work): min = 0.00 max = 89.99 mean = 35.92| |phase err.(test): min = 0.00 max = 89.77 mean = 35.86| |-----------------------------------------------------------------------------| ----------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 0.057 5293 Z= 0.680 Angle : 1.400 9.726 7134 Z= 0.922 Chirality : 0.084 0.452 851 Planarity : 0.004 0.013 913 Dihedral : 18.241 89.696 2067 Min Nonbonded Distance : 0.751 Molprobity Statistics. All-atom Clashscore : 33.12 Ramachandran Plot: Outliers : 2.19 % Allowed : 15.16 % Favored : 82.66 % Rotamer: Outliers : 11.77 % Allowed : 11.09 % Favored : 77.13 % Cbeta Deviations : 0.16 % 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: -6.00 (0.23), residues: 640 helix: -3.54 (0.15), residues: 557 sheet: None (None), residues: 0 loop : -4.73 (0.48), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 103 TYR 0.018 0.004 TYR B 56 PHE 0.016 0.002 PHE C 44 TRP 0.026 0.005 TRP D 40 HIS 0.005 0.002 HIS A 101 Individual atomic B min max mean iso aniso Overall: 78.72 190.99 119.02 0.81 5234 0 Protein: 78.72 190.99 119.02 0.81 5234 0 Chain A: 78.72 132.62 102.27 N/A 876 0 Chain B: 94.80 147.44 118.99 N/A 867 0 Chain C: 85.82 131.82 108.29 N/A 876 0 Chain D: 84.11 124.52 104.22 N/A 860 0 Chain E: 118.58 190.99 151.35 N/A 883 0 Chain F: 108.44 147.31 128.51 N/A 872 0 Histogram: Values Number of atoms 78.72 - 89.95 313 89.95 - 101.17 702 101.17 - 112.40 1380 112.40 - 123.63 856 123.63 - 134.86 864 134.86 - 146.08 713 146.08 - 157.31 118 157.31 - 168.54 78 168.54 - 179.76 76 179.76 - 190.99 134 |-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: 3.40 - 19.99 A, n_refl.=25915 (all), 5.09 % free)------------| | | | r_work= 0.4270 r_free= 0.4614 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 5.895891 | | target function (ml) not normalized (work): 145015.334724 | | target function (ml) not normalized (free): 7902.559553 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4288 0.4270 0.4614 n_refl.: 25915 re-set all scales: r(all,work,free)=0.4288 0.4270 0.4614 n_refl.: 25915 remove outliers: r(all,work,free)=0.4266 0.4247 0.4614 n_refl.: 25903 overall B=-17.33 to atoms: r(all,work,free)=0.3800 0.3778 0.4198 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2653 0.2628 0.3103 n_refl.: 25903 remove outliers: r(all,work,free)=0.2653 0.2628 0.3103 n_refl.: 25903 ======================== 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 19.988-16.886 98.02 93 6 0.4981 1064.578 868.154 1.015 0.889 0.304 16.855-15.102 97.06 96 3 0.3850 1222.025 1136.069 1.082 0.884 0.305 15.055-13.543 96.90 117 8 0.3123 1277.787 1208.209 1.082 0.887 0.296 13.531-12.124 98.40 177 8 0.2353 1772.472 1690.272 1.270 0.886 0.298 12.122-10.863 98.00 231 14 0.2470 1913.581 1885.994 1.269 0.887 0.253 10.859-9.734 96.81 316 18 0.2173 1837.359 1794.637 1.328 0.888 0.250 9.728-8.719 98.71 440 18 0.2370 1558.782 1516.125 1.331 0.888 0.242 8.719-7.816 98.08 582 32 0.2649 1152.027 1095.392 1.318 0.888 0.235 7.812-7.000 98.44 835 46 0.3179 832.644 767.986 1.214 0.888 0.227 6.996-6.272 99.42 1131 61 0.3629 543.615 499.913 1.102 0.888 0.210 6.270-5.619 99.76 1581 82 0.3397 434.382 397.799 0.922 0.888 0.170 5.619-5.035 99.26 2133 136 0.2723 456.309 441.157 0.978 0.887 0.145 5.034-4.511 99.59 2966 163 0.2174 514.948 493.021 1.118 0.887 0.133 4.511-4.041 99.19 4079 206 0.2150 428.987 409.503 1.196 0.886 0.102 4.041-3.621 99.33 5632 291 0.2586 273.439 257.563 1.179 0.885 0.034 3.621-3.400 99.53 4175 227 0.2771 176.375 161.769 1.056 0.884 0.036 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9964 b_overall=0.3094 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2628 r_free=0.3103 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 37 GLN D 64 ASN Total number of N/Q/H flips: 3 r_work=0.2628 r_free=0.3104 ========================= Local real-space refinement ========================= Before: r_work=0.2628 r_free=0.3104 412 residues out of total 586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 344 time to evaluate : 1.216 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 39 residues processed: 68 average time/residue: 0.8415 time to fit residues: 80.9820 After: r_work=0.2662 r_free=0.3139 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.259620 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.197521 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 0.2825 0.3263 0.0438 0.004 0.7 7.6 0.2 7.0 0 0.125 0.2799 0.3238 0.0439 0.004 0.7 7.7 0.2 7.2 0 0.250 0.2761 0.3220 0.0458 0.004 0.7 8.2 0.2 7.3 0 0.500 0.2728 0.3214 0.0485 0.005 0.8 8.8 0.2 7.5 0 1.000 0.2685 0.3188 0.0503 0.006 0.9 10.7 0.2 7.3 0 2.000 0.2654 0.3157 0.0503 0.008 1.0 13.1 0.2 7.8 0 3.000 0.2640 0.3161 0.0522 0.009 1.1 15.4 0.2 8.9 0 4.000 0.2616 0.3146 0.0530 0.011 1.1 17.1 0.2 9.4 0 5.000 0.2600 0.3135 0.0535 0.012 1.2 19.5 0.2 9.7 0 6.000 0.2585 0.3128 0.0544 0.013 1.3 20.5 0.2 10.2 0 7.000 0.2570 0.3113 0.0543 0.014 1.4 22.0 0.2 10.9 0 8.000 0.2556 0.3110 0.0554 0.015 1.4 24.5 0.3 11.6 0 9.000 0.2547 0.3105 0.0559 0.016 1.5 25.2 0.3 13.1 0 10.000 0.2566 0.3111 0.0544 0.014 1.4 22.0 0.2 10.6 0 8.130 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2799 0.3238 0.0439 0.004 0.7 7.7 0.2 7.2 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2799 r_free=0.3238 402 residues out of total 586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 360 time to evaluate : 2.190 revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 2 residues processed: 42 average time/residue: 0.7196 time to fit residues: 48.3319 After: r_work=0.2848 r_free=0.3293 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 28.48 32.93 4.45 0.568 101.402 0.198 0.093 28.53 32.96 4.43 1.760 101.455 0.006 0.093 28.18 32.73 4.55 1.898 101.443 0.025 0.091 27.56 32.32 4.75 3.062 101.456 0.099 0.088 26.65 31.47 4.83 8.141 102.470 0.198 0.082 26.44 31.29 4.85 9.791 102.908 0.296 0.080 26.32 31.25 4.93 9.894 103.115 0.395 0.080 26.02 30.96 4.94 13.744 104.043 0.494 0.077 25.95 30.92 4.96 14.527 104.252 0.593 0.077 25.91 30.91 5.00 15.136 104.413 0.691 0.076 25.80 30.82 5.02 16.427 104.804 0.790 0.076 25.76 30.77 5.01 16.907 104.934 0.889 0.075 25.70 30.72 5.02 17.825 105.204 0.988 0.075 max suggested for this run: 20.28 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.988 Accepted refinement result: 25.70 30.72 5.02 17.825 105.204 0.988 0.075 Individual atomic B min max mean iso aniso Overall: 58.91 225.72 109.47 13.94 5234 0 Protein: 58.91 225.72 109.47 13.94 5234 0 Chain A: 58.91 184.71 92.43 N/A 876 0 Chain B: 73.63 183.83 109.72 N/A 867 0 Chain C: 64.28 199.04 99.75 N/A 876 0 Chain D: 63.09 220.75 94.99 N/A 860 0 Chain E: 96.25 225.72 142.12 N/A 883 0 Chain F: 87.44 184.02 117.31 N/A 872 0 Histogram: Values Number of atoms 58.91 - 75.59 487 75.59 - 92.28 1224 92.28 - 108.96 1158 108.96 - 125.64 1074 125.64 - 142.32 565 142.32 - 159.00 380 159.00 - 175.68 233 175.68 - 192.36 72 192.36 - 209.04 33 209.04 - 225.72 8 =========================== Idealize ADP of riding H ========================== r_work=0.2570 r_free=0.3072 r_work=0.2552 r_free=0.3036 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2552 r_free= 0.3036 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ls_wunit_k1) (work): 0.072805 | | target function (ls_wunit_k1) not normalized (work): 1789.834867 | | target function (ls_wunit_k1) not normalized (free): 139.207186 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2577 0.2552 0.3036 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3731 0.3705 0.4183 n_refl.: 25903 remove outliers: r(all,work,free)=0.3731 0.3705 0.4183 n_refl.: 25903 overall B=-0.30 to atoms: r(all,work,free)=0.3723 0.3697 0.4176 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2539 0.2511 0.3065 n_refl.: 25903 remove outliers: r(all,work,free)=0.2539 0.2511 0.3065 n_refl.: 25903 ======================== 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 19.988-16.886 98.02 93 6 0.4839 798.364 673.130 0.810 0.978 0.280 16.855-15.102 97.06 96 3 0.3815 916.439 840.044 0.823 0.973 0.276 15.055-13.543 96.90 117 8 0.3192 958.257 909.702 0.835 0.976 0.254 13.531-12.124 98.40 177 8 0.2217 1329.238 1268.897 0.952 0.976 0.243 12.122-10.863 98.00 231 14 0.2115 1435.061 1422.130 1.062 0.978 0.237 10.859-9.734 96.81 316 18 0.1888 1377.899 1362.245 1.125 0.980 0.234 9.728-8.719 98.71 440 18 0.1965 1168.985 1150.010 1.122 0.981 0.226 8.719-7.816 98.08 582 32 0.2217 863.946 839.085 1.120 0.983 0.224 7.812-7.000 98.44 835 46 0.2625 624.429 594.522 1.025 0.984 0.200 6.996-6.272 99.42 1131 61 0.3103 407.676 384.296 0.948 0.986 0.170 6.270-5.619 99.76 1581 82 0.3120 325.758 305.033 0.836 0.989 0.150 5.619-5.035 99.26 2133 136 0.2573 342.202 329.325 0.884 0.992 0.120 5.034-4.511 99.59 2966 163 0.2199 386.178 372.551 1.004 0.995 0.110 4.511-4.041 99.19 4079 206 0.2164 321.712 310.333 1.051 0.999 0.070 4.041-3.621 99.33 5632 291 0.2781 205.062 192.693 1.018 1.005 0.025 3.621-3.400 99.53 4175 227 0.3136 132.270 118.581 0.895 1.009 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0509 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2511 r_free=0.3065 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN C 21 GLN C 28 GLN C 34 ASN C 37 GLN D 37 GLN D 64 ASN E 21 GLN E 100 ASN Total number of N/Q/H flips: 9 r_work=0.2515 r_free=0.3064 ========================= Local real-space refinement ========================= Before: r_work=0.2515 r_free=0.3064 379 residues out of total 586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 376 time to evaluate : 1.039 revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.3291 time to fit residues: 3.1271 After: r_work=0.2515 r_free=0.3063 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.439526 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.042118 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 0.2514 0.3016 0.0502 0.003 0.6 5.8 0.0 1.4 0 0.125 0.2472 0.2985 0.0513 0.003 0.6 6.5 0.0 1.4 0 0.250 0.2431 0.2956 0.0526 0.005 0.7 7.8 0.0 1.0 0 0.500 0.2390 0.2933 0.0543 0.007 0.9 9.5 0.0 1.5 0 1.000 0.2351 0.2906 0.0555 0.012 1.2 13.3 0.0 1.4 0 2.000 0.2324 0.2888 0.0565 0.016 1.4 14.9 0.2 2.2 0 3.000 0.2283 0.2854 0.0571 0.017 1.5 20.7 0.3 12.3 0 4.000 0.2295 0.2871 0.0577 0.024 1.7 18.7 0.3 2.2 0 5.000 0.2293 0.2867 0.0574 0.026 1.8 19.3 0.3 2.2 0 6.000 0.2243 0.2813 0.0569 0.025 2.1 28.8 1.7 15.9 0 7.000 0.2236 0.2815 0.0579 0.028 2.2 31.3 2.0 16.6 0 8.000 0.2230 0.2816 0.0586 0.030 2.4 33.0 2.2 17.1 0 9.000 0.2222 0.2812 0.0590 0.032 2.5 34.8 1.9 18.8 0 10.000 0.2321 0.2890 0.0569 0.017 1.4 15.2 0.2 2.2 0 3.220 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2431 0.2956 0.0526 0.005 0.7 7.8 0.0 1.0 0 0.500 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2431 r_free=0.2956 391 residues out of total 586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 385 time to evaluate : 0.615 outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1676 time to fit residues: 2.4852 After: r_work=0.2438 r_free=0.2964 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.38 29.64 5.26 18.991 121.260 0.042 5.913 30.86 34.78 3.91 16.851 132.398 0.001 5.995 26.99 31.35 4.36 15.454 127.345 0.005 5.939 25.14 29.86 4.72 17.818 124.885 0.021 5.891 24.37 29.52 5.15 19.042 123.218 0.042 5.872 24.15 29.41 5.26 19.555 122.803 0.063 5.867 24.07 29.40 5.33 19.967 122.832 0.084 5.865 24.03 29.40 5.37 20.301 122.905 0.105 5.863 23.86 29.35 5.48 20.188 122.612 0.126 5.861 23.84 29.34 5.50 20.368 122.674 0.147 5.860 23.83 29.35 5.52 20.534 122.741 0.168 5.859 23.82 29.34 5.52 20.679 122.802 0.190 5.859 23.79 29.34 5.55 20.579 122.663 0.211 5.859 max suggested for this run: 24.25 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.211 Accepted refinement result: 23.79 29.34 5.55 20.579 122.663 0.211 5.859 Individual atomic B min max mean iso aniso Overall: 53.66 229.74 112.04 17.52 5234 0 Protein: 53.66 229.74 112.04 17.52 5234 0 Chain A: 53.66 186.85 95.36 N/A 876 0 Chain B: 68.33 189.31 112.21 N/A 867 0 Chain C: 60.19 203.10 102.07 N/A 876 0 Chain D: 57.79 218.70 98.26 N/A 860 0 Chain E: 90.95 229.74 143.84 N/A 883 0 Chain F: 82.14 182.95 120.03 N/A 872 0 Histogram: Values Number of atoms 53.66 - 71.27 297 71.27 - 88.88 942 88.88 - 106.49 1203 106.49 - 124.09 1175 124.09 - 141.70 746 141.70 - 159.31 514 159.31 - 176.92 232 176.92 - 194.53 87 194.53 - 212.13 30 212.13 - 229.74 8 =========================== Idealize ADP of riding H ========================== r_work=0.2379 r_free=0.2934 r_work=0.2383 r_free=0.2934 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2383 r_free= 0.2934 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 5.858254 | | target function (ml) not normalized (work): 144019.323481 | | target function (ml) not normalized (free): 7899.328549 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2411 0.2383 0.2934 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3726 0.3701 0.4167 n_refl.: 25903 remove outliers: r(all,work,free)=0.3726 0.3701 0.4167 n_refl.: 25903 overall B=-0.84 to atoms: r(all,work,free)=0.3702 0.3676 0.4146 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2408 0.2380 0.2944 n_refl.: 25903 remove outliers: r(all,work,free)=0.2408 0.2380 0.2944 n_refl.: 25903 ======================== 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 19.988-16.886 98.02 93 6 0.4816 798.364 671.345 0.791 0.977 0.280 16.855-15.102 97.06 96 3 0.3803 916.439 838.432 0.834 0.972 0.279 15.055-13.543 96.90 117 8 0.3219 958.257 903.887 0.833 0.976 0.258 13.531-12.124 98.40 177 8 0.2243 1329.238 1265.479 0.953 0.975 0.247 12.122-10.863 98.00 231 14 0.2201 1435.061 1416.142 1.045 0.977 0.233 10.859-9.734 96.81 316 18 0.1987 1377.899 1357.438 1.106 0.980 0.229 9.728-8.719 98.71 440 18 0.2084 1168.985 1144.583 1.111 0.981 0.227 8.719-7.816 98.08 582 32 0.2361 863.946 830.710 1.114 0.983 0.225 7.812-7.000 98.44 835 46 0.2884 624.429 584.137 1.021 0.984 0.201 6.996-6.272 99.42 1131 61 0.3249 407.676 380.673 0.970 0.986 0.171 6.270-5.619 99.76 1581 82 0.3271 325.758 301.989 0.861 0.989 0.151 5.619-5.035 99.26 2133 136 0.2405 342.202 329.249 0.893 0.992 0.116 5.034-4.511 99.59 2966 163 0.1906 386.178 373.763 0.999 0.996 0.101 4.511-4.041 99.19 4079 206 0.1805 321.712 311.408 1.059 1.000 0.071 4.041-3.621 99.33 5632 291 0.2356 205.062 194.378 1.043 1.006 0.020 3.621-3.400 99.53 4175 227 0.2756 132.270 120.496 0.902 1.011 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.9121 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2380 r_free=0.2944 After: r_work=0.2380 r_free=0.2944 ================================== NQH flips ================================== r_work=0.2380 r_free=0.2944 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN C 37 GLN F 34 ASN Total number of N/Q/H flips: 3 r_work=0.2380 r_free=0.2942 ========================= Local real-space refinement ========================= Before: r_work=0.2380 r_free=0.2942 385 residues out of total 586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 0.426 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5124 After: r_work=0.2380 r_free=0.2942 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.051936 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037798 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 0.2947 0.0560 0.004 0.7 9.5 0.0 0.0 0 0.125 0.2383 0.2941 0.0558 0.004 0.7 9.3 0.0 0.0 0 0.250 0.2377 0.2940 0.0563 0.004 0.8 9.4 0.0 0.0 0 0.500 0.2352 0.2921 0.0568 0.007 0.9 10.4 0.0 0.2 0 1.000 0.2284 0.2879 0.0594 0.012 1.4 13.8 0.0 1.5 0 2.000 0.2254 0.2860 0.0607 0.014 1.8 18.0 0.2 4.1 0 3.000 0.2240 0.2845 0.0605 0.015 1.9 22.6 0.2 5.6 0 4.000 0.2226 0.2838 0.0612 0.018 2.2 25.2 0.5 7.2 0 5.000 0.2215 0.2832 0.0617 0.020 2.3 30.2 0.9 9.0 0 6.000 0.2208 0.2825 0.0618 0.022 2.5 31.6 1.1 9.6 0 7.000 0.2198 0.2818 0.0620 0.024 2.7 34.1 1.7 10.6 0 8.000 0.2192 0.2817 0.0625 0.026 2.9 37.7 2.2 12.1 0 9.000 0.2186 0.2805 0.0620 0.028 3.0 38.4 2.0 13.3 0 10.000 0.2246 0.2849 0.0603 0.014 1.8 21.7 0.2 5.3 0 3.526 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2383 0.2941 0.0558 0.004 0.7 9.3 0.0 0.0 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2383 r_free=0.2941 388 residues out of total 586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 0.426 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3984 After: r_work=0.2383 r_free=0.2941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.83 29.41 5.58 20.599 123.022 0.038 5.862 30.19 33.92 3.73 17.392 132.698 0.001 5.985 28.76 32.74 3.98 17.564 132.128 0.005 5.974 25.77 30.47 4.70 17.923 127.143 0.019 5.910 24.78 29.87 5.08 18.772 125.001 0.038 5.881 24.34 29.58 5.24 19.324 124.193 0.057 5.867 24.06 29.40 5.33 19.766 123.751 0.076 5.859 23.94 29.32 5.38 20.073 123.686 0.094 5.854 23.86 29.26 5.40 20.317 123.757 0.113 5.852 23.72 29.19 5.47 20.547 123.598 0.132 5.848 23.68 29.18 5.50 20.730 123.656 0.151 5.846 23.63 29.17 5.53 20.877 123.591 0.170 5.846 23.60 29.17 5.57 20.978 123.464 0.189 5.845 max suggested for this run: 24.60 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.170 Accepted refinement result: 23.63 29.17 5.53 20.877 123.591 0.170 5.846 Individual atomic B min max mean iso aniso Overall: 47.82 233.71 112.36 18.41 5234 0 Protein: 47.82 233.71 112.36 18.41 5234 0 Chain A: 47.82 185.84 95.33 N/A 876 0 Chain B: 62.49 197.10 112.53 N/A 867 0 Chain C: 55.54 204.64 102.34 N/A 876 0 Chain D: 51.95 214.27 98.63 N/A 860 0 Chain E: 85.11 233.71 144.01 N/A 883 0 Chain F: 76.30 183.67 120.87 N/A 872 0 Histogram: Values Number of atoms 47.82 - 66.41 145 66.41 - 85.00 791 85.00 - 103.59 1305 103.59 - 122.18 1268 122.18 - 140.76 813 140.76 - 159.35 529 159.35 - 177.94 258 177.94 - 196.53 83 196.53 - 215.12 35 215.12 - 233.71 7 =========================== Idealize ADP of riding H ========================== r_work=0.2363 r_free=0.2917 r_work=0.2365 r_free=0.2919 ----------X-ray data---------- |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2365 r_free= 0.2919 coordinate error (max.-lik. estimate): 0.36 A | | | | normalized target function (ml) (work): 5.845564 | | target function (ml) not normalized (work): 143707.339605 | | target function (ml) not normalized (free): 7888.767037 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.99 - 6.98 0.98 2910 153 0.2502 0.3035 7.1232 7.2633| | 2: 6.98 - 5.58 1.00 2800 148 0.3293 0.4026 6.5003 6.6123| | 3: 5.58 - 4.89 0.99 2720 172 0.2302 0.2898 6.0514 6.1287| | 4: 4.89 - 4.45 0.99 2703 139 0.1796 0.2074 5.8708 5.9843| | 5: 4.45 - 4.13 0.99 2734 139 0.1714 0.2122 5.689 5.871| | 6: 4.13 - 3.89 0.99 2654 143 0.2041 0.2878 5.5643 5.7761| | 7: 3.89 - 3.70 0.99 2711 136 0.2266 0.2932 5.4142 5.6294| | 8: 3.70 - 3.54 0.99 2684 135 0.2635 0.3191 5.23 5.3176| | 9: 3.54 - 3.40 1.00 2668 154 0.2624 0.3082 5.0272 5.1129| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.99 - 6.98 2910 153 0.73 30.50 0.99 1.01 292485.49| | 2: 6.98 - 5.58 2800 148 0.52 49.44 1.00 0.98 128477.18| | 3: 5.58 - 4.89 2720 172 0.77 28.83 1.00 0.98 38241.84| | 4: 4.89 - 4.45 2703 139 0.85 20.74 1.01 1.02 23631.54| | 5: 4.45 - 4.13 2734 139 0.86 20.25 1.02 1.04 17677.00| | 6: 4.13 - 3.89 2654 143 0.83 23.44 1.04 1.04 14071.63| | 7: 3.89 - 3.70 2711 136 0.81 25.76 1.03 1.03 10899.94| | 8: 3.70 - 3.54 2684 135 0.78 28.81 1.00 0.99 7829.76| | 9: 3.54 - 3.40 2668 154 0.81 26.81 0.98 0.93 5058.38| |alpha: min = 0.93 max = 1.04 mean = 1.00| |beta: min = 5058.38 max = 292485.49 mean = 62174.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.99 mean = 28.39| |phase err.(test): min = 0.00 max = 89.35 mean = 28.77| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2394 0.2365 0.2919 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3749 0.3724 0.4186 n_refl.: 25903 remove outliers: r(all,work,free)=0.3749 0.3724 0.4186 n_refl.: 25903 overall B=-0.90 to atoms: r(all,work,free)=0.3722 0.3697 0.4164 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2392 0.2364 0.2921 n_refl.: 25903 remove outliers: r(all,work,free)=0.2392 0.2364 0.2921 n_refl.: 25903 ======================== 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 19.988-16.886 98.02 93 6 0.4824 798.364 672.047 0.792 0.982 0.280 16.855-15.102 97.06 96 3 0.3844 916.439 834.291 0.828 0.977 0.279 15.055-13.543 96.90 117 8 0.3244 958.257 902.480 0.829 0.980 0.258 13.531-12.124 98.40 177 8 0.2280 1329.238 1263.792 0.951 0.980 0.247 12.122-10.863 98.00 231 14 0.2244 1435.061 1414.897 1.038 0.981 0.230 10.859-9.734 96.81 316 18 0.2004 1377.899 1355.980 1.105 0.984 0.230 9.728-8.719 98.71 440 18 0.2105 1168.985 1143.768 1.109 0.985 0.226 8.719-7.816 98.08 582 32 0.2395 863.946 829.146 1.112 0.986 0.221 7.812-7.000 98.44 835 46 0.2967 624.429 581.665 1.023 0.988 0.201 6.996-6.272 99.42 1131 61 0.3313 407.676 379.176 0.974 0.989 0.171 6.270-5.619 99.76 1581 82 0.3300 325.758 301.489 0.864 0.991 0.151 5.619-5.035 99.26 2133 136 0.2386 342.202 329.354 0.896 0.994 0.116 5.034-4.511 99.59 2966 163 0.1874 386.178 374.378 1.004 0.997 0.101 4.511-4.041 99.19 4079 206 0.1734 321.712 312.234 1.074 1.000 0.071 4.041-3.621 99.33 5632 291 0.2264 205.062 195.186 1.073 1.004 0.015 3.621-3.400 99.53 4175 227 0.2681 132.270 120.964 0.923 1.007 0.015 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.2209 ================= 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 : 0.4270 0.4614 0.010 1.400 78.7 191.0 119.0 0 0.000 1_bss: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_settarget: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_updatephipsi: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_nqh: 0.2628 0.3104 0.010 1.400 61.4 173.7 101.7 0 0.003 1_realsrl: 0.2662 0.3139 0.010 1.400 61.4 173.7 101.7 0 0.035 1_weight: 0.2662 0.3139 0.010 1.400 61.4 173.7 101.7 0 0.035 1_xyzrec: 0.2799 0.3238 0.004 0.733 61.4 173.7 101.7 0 0.242 1_realsrl2: 0.2848 0.3293 0.004 0.733 61.4 173.7 101.7 0 0.262 1_adp: 0.2570 0.3072 0.004 0.733 58.9 225.7 109.5 0 0.262 1_regHadp: 0.2552 0.3036 0.004 0.733 58.9 225.7 109.5 0 0.262 2_bss: 0.2511 0.3065 0.004 0.733 58.6 225.4 109.2 0 0.262 2_settarget: 0.2511 0.3065 0.004 0.733 58.6 225.4 109.2 0 0.262 2_updatephipsi: 0.2511 0.3065 0.004 0.733 58.6 225.4 109.2 0 0.262 2_updatecdl: 0.2511 0.3065 0.004 0.757 58.6 225.4 109.2 0 0.262 2_nqh: 0.2515 0.3064 0.004 0.757 58.6 225.4 109.2 0 0.265 2_realsrl: 0.2515 0.3063 0.004 0.757 58.6 225.4 109.2 0 0.265 2_weight: 0.2515 0.3063 0.004 0.757 58.6 225.4 109.2 0 0.265 2_xyzrec: 0.2431 0.2956 0.005 0.749 58.6 225.4 109.2 0 0.268 2_realsrl2: 0.2438 0.2964 0.005 0.749 58.6 225.4 109.2 0 0.270 2_adp: 0.2379 0.2934 0.005 0.749 53.7 229.7 112.0 0 0.270 2_regHadp: 0.2383 0.2934 0.005 0.749 53.7 229.7 112.0 0 0.270 3_bss: 0.2380 0.2944 0.005 0.749 52.8 228.9 111.2 0 0.270 3_settarget: 0.2380 0.2944 0.005 0.749 52.8 228.9 111.2 0 0.270 3_updatephipsi: 0.2380 0.2944 0.005 0.749 52.8 228.9 111.2 0 0.270 3_updatecdl: 0.2380 0.2944 0.005 0.758 52.8 228.9 111.2 0 0.270 3_setrh: 0.2380 0.2944 0.005 0.758 52.8 228.9 111.2 0 0.270 3_nqh: 0.2380 0.2942 0.005 0.758 52.8 228.9 111.2 0 0.269 3_realsrl: 0.2380 0.2942 0.005 0.758 52.8 228.9 111.2 0 0.269 3_weight: 0.2380 0.2942 0.005 0.758 52.8 228.9 111.2 0 0.269 3_xyzrec: 0.2383 0.2941 0.004 0.743 52.8 228.9 111.2 0 0.271 3_realsrl2: 0.2383 0.2941 0.004 0.743 52.8 228.9 111.2 0 0.271 3_adp: 0.2363 0.2917 0.004 0.743 47.8 233.7 112.4 0 0.271 3_regHadp: 0.2365 0.2919 0.004 0.743 47.8 233.7 112.4 0 0.271 end: 0.2364 0.2921 0.004 0.743 46.9 232.8 111.5 0 0.271 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2pej_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2pej_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 8.9500 Refinement macro-cycles (run) : 544.8900 Write final files (write_after_run_outputs) : 23.9300 Total : 577.7700 Total CPU time: 10.24 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:39:22 PDT -0700 (1716251962.64 s) Start R-work = 0.2628, R-free = 0.3103 Final R-work = 0.2364, R-free = 0.2921 =============================================================================== Job complete usr+sys time: 646.42 seconds wall clock time: 24 minutes 30.10 seconds (1470.10 seconds total)