Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_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 amber.topology_file_name=4amber_2pej.prmtop amber.coordinate_file_name=4amber_2pej.rst7 amber.order_file_name=4amber_2pej.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_2pej.order 4amber_2pej.prmtop 4amber_2pej.rst7 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 = "4phenix_2pej.pdb" } default_model = "4phenix_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 { 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_2pej.prmtop coordinate_file_name = 4amber_2pej.rst7 order_file_name = 4amber_2pej.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: 10708 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: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1807 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: 1.18, per 1000 atoms: 0.11 Number of scatterers: 10708 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 5474 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: 1.80 Conformation dependent library (CDL) restraints added in 263.8 milliseconds 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: 0.62 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: 1.76 Time building geometry restraints manager: 2.08 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: 5474 1.15 - 1.32: 909 1.32 - 1.49: 1985 1.49 - 1.66: 2363 1.66 - 1.83: 36 Bond restraints: 10767 Sorted by residual: 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 TRP C 40 " pdb=" H TRP C 40 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG E 75 " pdb="HH11 ARG E 75 " 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 84 " pdb=" H GLU D 84 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG B 108 " pdb="HH12 ARG B 108 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 10762 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: 4053 126.66 - 134.17: 45 Bond angle restraints: 19586 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 19581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4347 17.94 - 35.88: 335 35.88 - 53.82: 177 53.82 - 71.76: 56 71.76 - 89.70: 14 Dihedral angle restraints: 4929 sinusoidal: 2840 harmonic: 2089 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 4926 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: 28 1.27 - 2.10: 941 2.10 - 2.93: 28255 2.93 - 3.77: 48488 3.77 - 4.60: 77646 Warning: very small nonbonded interaction distances. Nonbonded interactions: 155358 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 155353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_2pej.prmtop atom order : 4amber_2pej.order coordinates : 4amber_2pej.rst7 ===================================== ... ===================================== ============================== 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 5474 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: 5474 of 10708 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 10708 n_use_u_iso = 10708 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 = 10708 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (10708 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 10708 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 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 } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_2pej.prmtop" coordinate_file_name = "4amber_2pej.rst7" order_file_name = "4amber_2pej.order" } } output { prefix = "4phenix_2pej_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: 3.40 - 19.99 A, n_refl.=25915 (all), 5.09 % free)------------| | | | r_work= 0.4268 r_free= 0.4615 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 5.896862 | | target function (ml) not normalized (work): 145039.216811 | | target function (ml) not normalized (free): 7904.681144 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.4362 0.4721 7.3825 7.4804| | 2: 6.98 - 5.58 1.00 2800 148 0.4207 0.5143 6.6903 6.7702| | 3: 5.58 - 4.89 0.99 2720 172 0.3235 0.3533 6.1104 6.1219| | 4: 4.89 - 4.45 0.99 2703 139 0.3760 0.4030 5.9989 6.0922| | 5: 4.45 - 4.13 0.99 2734 139 0.4454 0.4594 5.779 5.9358| | 6: 4.13 - 3.89 0.99 2654 143 0.4793 0.5060 5.5651 5.7615| | 7: 3.89 - 3.70 0.99 2711 136 0.4985 0.5162 5.3575 5.4652| | 8: 3.70 - 3.54 0.99 2685 135 0.4835 0.5329 5.1066 5.1906| | 9: 3.54 - 3.40 1.00 2668 154 0.4774 0.4947 4.9107 4.9704| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 51.11 0.92 0.50 544630.84| | 2: 6.98 - 5.58 2800 148 0.30 66.75 0.95 0.53 215272.43| | 3: 5.58 - 4.89 2720 172 0.69 35.98 1.11 0.64 42554.48| | 4: 4.89 - 4.45 2703 139 0.79 27.27 1.44 0.80 27239.83| | 5: 4.45 - 4.13 2734 139 0.79 26.84 1.66 0.95 19901.86| | 6: 4.13 - 3.89 2654 143 0.78 28.35 1.78 1.04 14023.45| | 7: 3.89 - 3.70 2711 136 0.78 28.57 1.82 1.08 9277.16| | 8: 3.70 - 3.54 2685 135 0.77 29.61 1.76 1.05 6095.03| | 9: 3.54 - 3.40 2668 154 0.80 27.33 1.72 0.95 3687.97| |alpha: min = 0.50 max = 1.08 mean = 0.83| |beta: min = 3687.97 max = 544630.84 mean = 102699.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.98 mean = 36.03| |phase err.(test): min = 0.00 max = 89.91 mean = 35.99| |-----------------------------------------------------------------------------| ----------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= 0.4268 r_free= 0.4615 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 5.896862 | | target function (ml) not normalized (work): 145039.216811 | | target function (ml) not normalized (free): 7904.681144 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4286 0.4268 0.4615 n_refl.: 25915 re-set all scales: r(all,work,free)=0.4286 0.4268 0.4615 n_refl.: 25915 remove outliers: r(all,work,free)=0.4264 0.4244 0.4615 n_refl.: 25903 overall B=-18.18 to atoms: r(all,work,free)=0.3778 0.3756 0.4184 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2654 0.2629 0.3110 n_refl.: 25903 remove outliers: r(all,work,free)=0.2654 0.2629 0.3110 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 0.4983 1063.857 866.828 1.024 0.889 0.304 16.855-15.102 97.06 96 3 0.3858 1221.198 1156.374 1.091 0.885 0.300 15.055-13.543 96.90 117 8 0.3123 1276.922 1205.857 1.091 0.888 0.297 13.531-12.124 98.40 177 8 0.2353 1771.272 1686.815 1.281 0.887 0.298 12.122-10.863 98.00 231 14 0.2475 1912.286 1881.791 1.278 0.888 0.254 10.859-9.734 96.81 316 18 0.2179 1836.115 1791.027 1.338 0.889 0.251 9.728-8.719 98.71 440 18 0.2372 1557.726 1516.916 1.340 0.889 0.237 8.719-7.816 98.08 582 32 0.2646 1151.248 1093.924 1.326 0.889 0.235 7.812-7.000 98.44 835 46 0.3185 832.080 766.839 1.219 0.889 0.228 6.996-6.272 99.42 1131 61 0.3629 543.247 499.239 1.104 0.889 0.211 6.270-5.619 99.76 1581 82 0.3398 434.088 397.245 0.922 0.889 0.171 5.619-5.035 99.26 2133 136 0.2725 456.000 440.667 0.976 0.889 0.146 5.034-4.511 99.59 2966 163 0.2176 514.599 492.563 1.115 0.889 0.135 4.511-4.041 99.19 4079 206 0.2146 428.697 409.393 1.191 0.888 0.103 4.041-3.621 99.33 5632 291 0.2586 273.254 257.506 1.170 0.888 0.034 3.621-3.400 99.53 4175 227 0.2773 176.256 161.789 1.047 0.886 0.036 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=1.0493 ============================ 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 = 4.131017 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.201616 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 0.2928 0.3288 0.0359 0.013 2.1 0.3 0.8 4.9 0 0.125 0.2848 0.3263 0.0416 0.013 2.2 0.8 0.9 6.1 0 0.250 0.2724 0.3187 0.0463 0.014 2.2 2.0 0.8 6.1 0 0.500 0.2635 0.3141 0.0506 0.016 2.4 2.8 0.9 6.5 2 1.000 0.2545 0.3094 0.0549 0.021 2.9 5.5 1.9 9.0 6 2.000 0.2488 0.3067 0.0579 0.026 3.4 7.7 2.7 10.9 12 3.000 0.2449 0.3034 0.0585 0.030 3.7 10.7 2.8 12.1 17 4.000 0.2427 0.3022 0.0595 0.034 4.1 13.8 3.8 13.0 23 5.000 0.2402 0.3006 0.0605 0.038 4.4 15.7 4.5 13.8 25 6.000 0.2401 0.3026 0.0625 0.042 4.9 19.0 7.0 16.0 33 7.000 0.2387 0.3012 0.0625 0.045 5.1 22.0 6.6 16.2 35 8.000 0.2313 0.2987 0.0674 0.047 5.2 25.4 4.8 11.6 33 9.000 0.2300 0.2975 0.0675 0.049 5.3 26.9 5.0 11.9 34 10.000 0.2545 0.3096 0.0552 0.022 3.0 5.9 1.9 9.2 7 2.066 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2300 0.2975 0.0675 0.049 5.3 26.9 5.0 11.9 34 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.00 29.75 6.75 0.568 100.542 0.202 0.056 23.18 29.89 6.71 2.388 100.633 0.006 0.057 22.91 29.70 6.80 2.332 100.544 0.025 0.056 22.52 29.46 6.93 2.204 100.383 0.101 0.054 22.07 29.11 7.04 4.748 100.480 0.202 0.052 21.97 29.07 7.10 5.520 100.612 0.302 0.052 21.89 29.03 7.15 6.230 100.763 0.403 0.052 21.83 29.00 7.18 6.825 100.895 0.504 0.051 21.82 29.01 7.20 7.005 100.939 0.605 0.051 21.72 28.95 7.22 8.197 101.217 0.706 0.051 21.70 28.94 7.24 8.546 101.301 0.806 0.051 21.68 28.94 7.25 8.840 101.370 0.907 0.051 21.67 28.92 7.25 9.092 101.431 1.008 0.051 max suggested for this run: 20.11 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.101 Accepted refinement result: 22.52 29.46 6.93 2.204 100.383 0.101 0.054 Individual atomic B min max mean iso aniso Overall: 58.52 175.66 100.51 1.93 5234 0 Protein: 58.52 175.66 100.51 1.93 5234 0 Chain A: 58.52 117.86 83.76 N/A 876 0 Chain B: 74.10 131.59 100.28 N/A 867 0 Chain C: 67.04 118.16 89.94 N/A 876 0 Chain D: 63.88 115.59 85.72 N/A 860 0 Chain E: 97.35 175.66 132.83 N/A 883 0 Chain F: 89.44 135.07 110.03 N/A 872 0 Histogram: Values Number of atoms 58.52 - 70.23 264 70.23 - 81.95 714 81.95 - 93.66 1349 93.66 - 105.37 967 105.37 - 117.09 878 117.09 - 128.80 672 128.80 - 140.51 114 140.51 - 152.23 82 152.23 - 163.94 86 163.94 - 175.66 108 =========================== Idealize ADP of riding H ========================== r_work=0.2252 r_free=0.2946 r_work=0.2264 r_free=0.2941 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2264 r_free= 0.2941 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ls_wunit_k1) (work): 0.054792 | | target function (ls_wunit_k1) not normalized (work): 1347.002979 | | target function (ls_wunit_k1) not normalized (free): 134.788301 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2299 0.2264 0.2941 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3446 0.3411 0.4053 n_refl.: 25903 remove outliers: r(all,work,free)=0.3446 0.3411 0.4053 n_refl.: 25903 overall B=0.21 to atoms: r(all,work,free)=0.3451 0.3417 0.4057 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2267 0.2229 0.2968 n_refl.: 25903 remove outliers: r(all,work,free)=0.2267 0.2229 0.2968 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 0.4099 826.763 743.164 1.000 0.914 0.290 16.855-15.102 97.06 96 3 0.3190 949.038 897.853 1.003 0.910 0.277 15.055-13.543 96.90 117 8 0.2662 992.343 961.944 0.973 0.912 0.257 13.531-12.124 98.40 177 8 0.1951 1376.520 1314.236 1.081 0.912 0.238 12.122-10.863 98.00 231 14 0.1735 1486.108 1479.660 1.217 0.912 0.230 10.859-9.734 96.81 316 18 0.1472 1426.912 1415.009 1.291 0.914 0.230 9.728-8.719 98.71 440 18 0.1634 1210.566 1207.264 1.295 0.914 0.210 8.719-7.816 98.08 582 32 0.1891 894.677 884.919 1.291 0.915 0.210 7.812-7.000 98.44 835 46 0.2268 646.640 621.960 1.193 0.915 0.199 6.996-6.272 99.42 1131 61 0.2720 422.177 406.004 1.074 0.915 0.170 6.270-5.619 99.76 1581 82 0.2812 337.346 319.973 0.909 0.916 0.150 5.619-5.035 99.26 2133 136 0.2313 354.374 345.384 0.959 0.916 0.120 5.034-4.511 99.59 2966 163 0.1891 399.914 390.166 1.115 0.917 0.110 4.511-4.041 99.19 4079 206 0.1973 333.156 323.743 1.180 0.917 0.070 4.041-3.621 99.33 5632 291 0.2597 212.356 201.516 1.150 0.918 0.022 3.621-3.400 99.53 4175 227 0.3047 136.975 123.749 1.017 0.918 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0825 ============================ 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 = 1.756060 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.045875 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 0.2737 0.3170 0.0433 0.013 2.1 1.0 0.6 6.1 0 0.088 0.2570 0.3052 0.0482 0.015 2.4 3.0 0.8 8.5 1 0.263 0.2459 0.3011 0.0551 0.020 3.0 5.6 2.3 11.6 3 0.527 0.2410 0.2985 0.0575 0.025 3.4 8.5 3.6 11.9 7 0.790 0.2367 0.2970 0.0603 0.029 3.9 11.6 4.7 13.7 13 1.054 0.2323 0.2938 0.0615 0.034 4.4 14.6 5.9 15.4 20 1.317 0.2299 0.2948 0.0648 0.038 4.7 18.7 7.2 17.1 24 1.580 0.2275 0.2919 0.0643 0.042 4.9 20.7 8.1 17.2 26 1.844 0.2394 0.2982 0.0588 0.026 3.6 10.1 3.4 12.5 9 0.878 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2275 0.2919 0.0643 0.042 4.9 20.7 8.1 17.2 26 1.844 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.75 29.19 6.43 14.656 110.729 0.046 5.846 23.43 29.76 6.32 14.880 110.913 0.001 5.869 22.79 29.20 6.41 14.824 110.696 0.006 5.844 22.56 29.05 6.49 14.863 110.666 0.023 5.835 21.83 28.31 6.48 15.915 111.291 0.046 5.798 21.78 28.27 6.49 16.159 111.509 0.069 5.796 21.74 28.33 6.59 16.116 111.451 0.092 5.795 21.71 28.30 6.59 16.289 111.603 0.115 5.794 21.69 28.28 6.59 16.447 111.726 0.138 5.793 21.67 28.27 6.60 16.589 111.829 0.161 5.792 21.66 28.26 6.60 16.717 111.915 0.184 5.792 21.65 28.26 6.61 16.826 111.986 0.206 5.791 21.65 28.26 6.61 16.930 112.050 0.229 5.791 max suggested for this run: 22.15 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 22.79 29.20 6.41 14.824 110.696 0.006 5.844 Individual atomic B min max mean iso aniso Overall: 60.10 174.32 100.66 1.96 5234 0 Protein: 60.10 174.32 100.66 1.96 5234 0 Chain A: 60.10 118.15 84.02 N/A 876 0 Chain B: 73.20 131.17 100.37 N/A 867 0 Chain C: 68.04 117.52 90.10 N/A 876 0 Chain D: 63.95 115.78 85.93 N/A 860 0 Chain E: 94.97 174.32 132.84 N/A 883 0 Chain F: 89.93 135.42 110.19 N/A 872 0 Histogram: Values Number of atoms 60.10 - 71.52 295 71.52 - 82.94 745 82.94 - 94.36 1383 94.36 - 105.79 889 105.79 - 117.21 870 117.21 - 128.63 653 128.63 - 140.05 123 140.05 - 151.48 79 151.48 - 162.90 80 162.90 - 174.32 117 =========================== Idealize ADP of riding H ========================== r_work=0.2279 r_free=0.2920 r_work=0.2280 r_free=0.2920 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2280 r_free= 0.2920 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 5.843696 | | target function (ml) not normalized (work): 143661.419754 | | target function (ml) not normalized (free): 7918.627612 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2313 0.2280 0.2920 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3465 0.3433 0.4026 n_refl.: 25903 remove outliers: r(all,work,free)=0.3465 0.3433 0.4026 n_refl.: 25903 overall B=0.44 to atoms: r(all,work,free)=0.3477 0.3446 0.4036 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2310 0.2277 0.2924 n_refl.: 25903 remove outliers: r(all,work,free)=0.2310 0.2277 0.2924 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 0.4611 826.763 702.077 0.831 0.981 0.280 16.855-15.102 97.06 96 3 0.3661 949.038 874.177 0.901 0.977 0.280 15.055-13.543 96.90 117 8 0.3059 992.343 942.397 0.896 0.981 0.261 13.531-12.124 98.40 177 8 0.2229 1376.520 1309.284 1.020 0.980 0.250 12.122-10.863 98.00 231 14 0.2163 1486.108 1459.226 1.104 0.981 0.225 10.859-9.734 96.81 316 18 0.1836 1426.912 1402.704 1.169 0.984 0.220 9.728-8.719 98.71 440 18 0.2098 1210.566 1188.421 1.196 0.985 0.220 8.719-7.816 98.08 582 32 0.2415 894.677 861.761 1.198 0.986 0.220 7.812-7.000 98.44 835 46 0.2964 646.640 601.527 1.109 0.987 0.200 6.996-6.272 99.42 1131 61 0.3321 422.177 388.524 1.023 0.989 0.170 6.270-5.619 99.76 1581 82 0.3432 337.346 306.414 0.876 0.991 0.159 5.619-5.035 99.26 2133 136 0.2307 354.374 340.146 0.873 0.993 0.114 5.034-4.511 99.59 2966 163 0.1649 399.914 388.454 1.007 0.996 0.109 4.511-4.041 99.19 4079 206 0.1626 333.156 323.146 1.075 0.999 0.070 4.041-3.621 99.33 5632 291 0.2131 212.356 201.762 1.062 1.003 0.020 3.621-3.400 99.53 4175 227 0.2586 136.975 125.149 0.923 1.006 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.1698 ============================ 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 = 1.676163 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.042558 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 0.2724 0.3126 0.0403 0.013 2.1 2.3 0.6 6.7 0 0.084 0.2560 0.3059 0.0499 0.016 2.5 3.8 0.8 11.1 1 0.251 0.2454 0.3012 0.0558 0.021 3.1 6.6 2.8 12.8 5 0.503 0.2399 0.2990 0.0591 0.026 3.6 9.3 3.9 14.2 9 0.754 0.2359 0.2980 0.0621 0.031 4.1 12.5 5.9 14.5 15 1.006 0.2320 0.2953 0.0632 0.036 4.6 16.7 7.2 16.9 21 1.257 0.2289 0.2942 0.0652 0.040 5.0 20.3 8.6 18.3 26 1.509 0.2277 0.2924 0.0647 0.042 4.9 20.7 8.1 17.2 26 1.760 0.2382 0.2987 0.0605 0.028 3.8 10.6 4.2 13.8 12 0.838 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2277 0.2924 0.0647 0.042 4.9 20.7 8.1 17.2 26 1.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.77 29.24 6.47 14.659 111.049 0.043 5.846 23.30 29.68 6.37 14.793 111.079 0.001 5.867 22.77 29.25 6.47 14.660 111.048 0.005 5.846 22.75 29.23 6.48 14.679 111.041 0.021 5.845 21.84 28.49 6.65 15.619 111.348 0.043 5.801 21.76 28.48 6.72 15.874 111.548 0.064 5.799 21.72 28.45 6.74 15.994 111.680 0.085 5.797 21.68 28.43 6.75 16.131 111.816 0.106 5.796 21.66 28.40 6.75 16.274 111.941 0.128 5.795 21.64 28.39 6.76 16.410 112.049 0.149 5.794 21.62 28.39 6.77 16.533 112.139 0.170 5.793 21.61 28.38 6.77 16.638 112.211 0.192 5.793 21.61 28.38 6.77 16.727 112.271 0.213 5.793 max suggested for this run: 22.21 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 22.77 29.25 6.47 14.660 111.048 0.005 5.846 Individual atomic B min max mean iso aniso Overall: 60.54 174.75 101.09 1.96 5234 0 Protein: 60.54 174.75 101.09 1.96 5234 0 Chain A: 60.54 118.58 84.46 N/A 876 0 Chain B: 73.64 131.61 100.81 N/A 867 0 Chain C: 68.49 117.96 90.54 N/A 876 0 Chain D: 64.39 116.22 86.37 N/A 860 0 Chain E: 95.39 174.75 133.28 N/A 883 0 Chain F: 90.37 135.86 110.63 N/A 872 0 Histogram: Values Number of atoms 60.54 - 71.96 295 71.96 - 83.38 745 83.38 - 94.80 1384 94.80 - 106.22 888 106.22 - 117.65 870 117.65 - 129.07 653 129.07 - 140.49 123 140.49 - 151.91 79 151.91 - 163.33 80 163.33 - 174.75 117 =========================== Idealize ADP of riding H ========================== r_work=0.2277 r_free=0.2925 r_work=0.2277 r_free=0.2925 ----------X-ray data---------- |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2277 r_free= 0.2925 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 5.845783 | | target function (ml) not normalized (work): 143712.717958 | | target function (ml) not normalized (free): 7921.388150 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2445 0.3148 7.1615 7.3366| | 2: 6.98 - 5.58 1.00 2800 148 0.3376 0.4425 6.5553 6.6784| | 3: 5.58 - 4.89 0.99 2720 172 0.2161 0.2656 6.0511 6.152| | 4: 4.89 - 4.45 0.99 2703 139 0.1588 0.2082 5.8356 6.0007| | 5: 4.45 - 4.13 0.99 2734 139 0.1607 0.2059 5.6686 5.914| | 6: 4.13 - 3.89 0.99 2654 143 0.1924 0.2633 5.5432 5.7445| | 7: 3.89 - 3.70 0.99 2711 136 0.2106 0.2628 5.3851 5.5754| | 8: 3.70 - 3.54 0.99 2684 135 0.2522 0.3131 5.2226 5.3396| | 9: 3.54 - 3.40 1.00 2668 154 0.2541 0.3072 5.0447 5.1663| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.72 31.80 1.00 0.93 339672.19| | 2: 6.98 - 5.58 2800 148 0.50 51.16 1.00 0.91 146887.47| | 3: 5.58 - 4.89 2720 172 0.76 29.23 1.00 0.92 41269.08| | 4: 4.89 - 4.45 2703 139 0.86 20.50 1.00 0.95 24645.16| | 5: 4.45 - 4.13 2734 139 0.86 19.97 1.00 0.96 17751.24| | 6: 4.13 - 3.89 2654 143 0.84 22.56 1.02 0.95 13557.04| | 7: 3.89 - 3.70 2711 136 0.82 24.53 1.00 0.94 10527.85| | 8: 3.70 - 3.54 2684 135 0.78 28.23 0.98 0.90 7882.28| | 9: 3.54 - 3.40 2668 154 0.80 27.73 0.96 0.83 5532.46| |alpha: min = 0.83 max = 0.96 mean = 0.92| |beta: min = 5532.46 max = 339672.19 mean = 70272.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.97 mean = 28.53| |phase err.(test): min = 0.00 max = 89.40 mean = 28.75| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2310 0.2277 0.2925 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3477 0.3446 0.4036 n_refl.: 25903 remove outliers: r(all,work,free)=0.3477 0.3446 0.4036 n_refl.: 25903 overall B=0.17 to atoms: r(all,work,free)=0.3482 0.3450 0.4040 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2310 0.2277 0.2924 n_refl.: 25903 remove outliers: r(all,work,free)=0.2310 0.2277 0.2924 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 0.4611 826.763 702.065 0.831 0.982 0.280 16.855-15.102 97.06 96 3 0.3661 949.038 874.275 0.901 0.978 0.280 15.055-13.543 96.90 117 8 0.3065 992.343 941.987 0.902 0.981 0.263 13.531-12.124 98.40 177 8 0.2222 1376.520 1309.706 1.029 0.980 0.253 12.122-10.863 98.00 231 14 0.2163 1486.108 1459.264 1.104 0.981 0.225 10.859-9.734 96.81 316 18 0.1836 1426.912 1402.634 1.169 0.984 0.220 9.728-8.719 98.71 440 18 0.2098 1210.566 1188.510 1.196 0.985 0.220 8.719-7.816 98.08 582 32 0.2416 894.677 861.754 1.198 0.986 0.220 7.812-7.000 98.44 835 46 0.2965 646.640 601.530 1.109 0.987 0.200 6.996-6.272 99.42 1131 61 0.3322 422.177 388.526 1.024 0.989 0.170 6.270-5.619 99.76 1581 82 0.3433 337.346 306.402 0.877 0.991 0.160 5.619-5.035 99.26 2133 136 0.2306 354.374 340.135 0.874 0.993 0.115 5.034-4.511 99.59 2966 163 0.1649 399.914 388.459 1.009 0.996 0.110 4.511-4.041 99.19 4079 206 0.1626 333.156 323.109 1.074 0.999 0.060 4.041-3.621 99.33 5632 291 0.2132 212.356 201.773 1.064 1.003 0.020 3.621-3.400 99.53 4175 227 0.2586 136.975 125.147 0.926 1.006 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0644 ================= 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 : 0.4268 0.4615 0.010 1.400 78.7 191.0 119.0 0 0.000 1_bss: 0.2629 0.3110 0.010 1.400 60.5 172.8 100.8 0 0.000 1_settarget: 0.2629 0.3110 0.010 1.400 60.5 172.8 100.8 0 0.000 1_weight: 0.2629 0.3110 0.010 1.400 60.5 172.8 100.8 0 0.000 1_xyzrec: 0.2300 0.2975 0.049 5.282 60.5 172.8 100.8 0 0.305 1_adp: 0.2252 0.2946 0.049 5.282 58.5 175.7 100.5 0 0.305 1_regHadp: 0.2264 0.2941 0.049 5.282 58.5 175.7 100.5 0 0.305 2_bss: 0.2229 0.2968 0.049 5.282 58.7 175.9 100.7 0 0.305 2_settarget: 0.2229 0.2968 0.049 5.282 58.7 175.9 100.7 0 0.305 2_updatecdl: 0.2229 0.2968 0.049 5.283 58.7 175.9 100.7 0 0.305 2_weight: 0.2229 0.2968 0.049 5.283 58.7 175.9 100.7 0 0.305 2_xyzrec: 0.2275 0.2919 0.042 4.938 58.7 175.9 100.7 0 0.314 2_adp: 0.2279 0.2920 0.042 4.938 60.1 174.3 100.7 0 0.314 2_regHadp: 0.2280 0.2920 0.042 4.938 60.1 174.3 100.7 0 0.314 3_bss: 0.2277 0.2924 0.042 4.938 60.5 174.8 101.1 0 0.314 3_settarget: 0.2277 0.2924 0.042 4.938 60.5 174.8 101.1 0 0.314 3_updatecdl: 0.2277 0.2924 0.042 4.938 60.5 174.8 101.1 0 0.314 3_setrh: 0.2277 0.2924 0.042 4.938 60.5 174.8 101.1 0 0.314 3_weight: 0.2277 0.2924 0.042 4.938 60.5 174.8 101.1 0 0.314 3_xyzrec: 0.2277 0.2924 0.042 4.938 60.5 174.8 101.1 0 0.314 3_adp: 0.2277 0.2925 0.042 4.938 60.5 174.8 101.1 0 0.314 3_regHadp: 0.2277 0.2925 0.042 4.938 60.5 174.8 101.1 0 0.314 end: 0.2277 0.2924 0.042 4.938 60.7 174.9 101.3 0 0.314 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2pej_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2pej_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.4300 Refinement macro-cycles (run) : 425.9400 Write final files (write_after_run_outputs) : 20.0800 Total : 453.4500 Total CPU time: 8.50 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:52:33 PDT -0700 (1723222353.15 s) Start R-work = 0.2629, R-free = 0.3110 Final R-work = 0.2277, R-free = 0.2924 =============================================================================== Job complete usr+sys time: 535.54 seconds wall clock time: 21 minutes 21.78 seconds (1281.78 seconds total)