Starting phenix.real_space_refine on Fri Sep 11 21:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zhx_11220/09_2026/6zhx_11220.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zhx_11220/09_2026/6zhx_11220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zhx_11220/09_2026/6zhx_11220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zhx_11220/09_2026/6zhx_11220.map" model { file = "/net/cci-nas-00/data/ceres_data/6zhx_11220/09_2026/6zhx_11220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zhx_11220/09_2026/6zhx_11220.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6740 2.51 5 N 2299 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12313 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 2.51, per 1000 atoms: 0.20 Number of scatterers: 12313 At special positions: 0 Unit cell: (117.066, 103.986, 115.758, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2976 8.00 N 2299 7.00 C 6740 6.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 328.0 milliseconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.3% alpha, 2.6% beta 145 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.950A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.344A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.957A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.375A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.714A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.894A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.641A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.652A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.845A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 426 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2483 1.33 - 1.45: 4038 1.45 - 1.57: 5850 1.57 - 1.69: 577 1.69 - 1.80: 20 Bond restraints: 12968 Sorted by residual: bond pdb=" C3' DT J 54 " pdb=" C2' DT J 54 " ideal model delta sigma weight residual 1.516 1.560 -0.044 8.00e-03 1.56e+04 3.05e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.560 -0.044 8.00e-03 1.56e+04 3.01e+01 bond pdb=" C3' DC I 6 " pdb=" C2' DC I 6 " ideal model delta sigma weight residual 1.516 1.559 -0.043 8.00e-03 1.56e+04 2.88e+01 bond pdb=" C3' DT J 69 " pdb=" C2' DT J 69 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.75e+01 bond pdb=" C3' DG I 54 " pdb=" C2' DG I 54 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.59e+01 ... (remaining 12963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 16548 1.46 - 2.91: 1717 2.91 - 4.37: 369 4.37 - 5.82: 100 5.82 - 7.28: 11 Bond angle restraints: 18745 Sorted by residual: angle pdb=" O4' DG J -66 " pdb=" C1' DG J -66 " pdb=" N9 DG J -66 " ideal model delta sigma weight residual 108.00 113.70 -5.70 7.00e-01 2.04e+00 6.62e+01 angle pdb=" O5' DT I 30 " pdb=" C5' DT I 30 " pdb=" C4' DT I 30 " ideal model delta sigma weight residual 109.40 115.55 -6.15 8.00e-01 1.56e+00 5.91e+01 angle pdb=" O4' DG I -19 " pdb=" C1' DG I -19 " pdb=" N9 DG I -19 " ideal model delta sigma weight residual 108.00 113.16 -5.16 7.00e-01 2.04e+00 5.43e+01 angle pdb=" O4' DG I 26 " pdb=" C1' DG I 26 " pdb=" N9 DG I 26 " ideal model delta sigma weight residual 108.00 103.24 4.76 7.00e-01 2.04e+00 4.63e+01 angle pdb=" O4' DC I -2 " pdb=" C1' DC I -2 " pdb=" N1 DC I -2 " ideal model delta sigma weight residual 108.00 112.50 -4.50 7.00e-01 2.04e+00 4.13e+01 ... (remaining 18740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 5872 35.43 - 70.85: 1186 70.85 - 106.28: 17 106.28 - 141.71: 0 141.71 - 177.14: 3 Dihedral angle restraints: 7078 sinusoidal: 4806 harmonic: 2272 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ARG A 40 " pdb=" C ARG A 40 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA THR D 85 " pdb=" C THR D 85 " pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1596 0.070 - 0.141: 440 0.141 - 0.211: 71 0.211 - 0.281: 19 0.281 - 0.352: 8 Chirality restraints: 2134 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C1' DT I 31 " pdb=" O4' DT I 31 " pdb=" C2' DT I 31 " pdb=" N1 DT I 31 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2131 not shown) Planarity restraints: 1366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 6 " -0.058 2.00e-02 2.50e+03 3.17e-02 2.26e+01 pdb=" N1 DC I 6 " 0.068 2.00e-02 2.50e+03 pdb=" C2 DC I 6 " -0.012 2.00e-02 2.50e+03 pdb=" O2 DC I 6 " 0.016 2.00e-02 2.50e+03 pdb=" N3 DC I 6 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC I 6 " -0.006 2.00e-02 2.50e+03 pdb=" N4 DC I 6 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DC I 6 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC I 6 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 4 " -0.050 2.00e-02 2.50e+03 2.79e-02 1.76e+01 pdb=" N1 DC I 4 " 0.064 2.00e-02 2.50e+03 pdb=" C2 DC I 4 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 4 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 4 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC I 4 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 4 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DC I 4 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 4 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 60 " 0.037 2.00e-02 2.50e+03 2.72e-02 1.66e+01 pdb=" N1 DC J 60 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DC J 60 " 0.025 2.00e-02 2.50e+03 pdb=" O2 DC J 60 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC J 60 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC J 60 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC J 60 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC J 60 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 60 " 0.003 2.00e-02 2.50e+03 ... (remaining 1363 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1046 2.74 - 3.28: 10966 3.28 - 3.82: 24662 3.82 - 4.36: 30772 4.36 - 4.90: 42868 Nonbonded interactions: 110314 Sorted by model distance: nonbonded pdb=" OXT GLY F 102 " pdb=" O HOH F1001 " model vdw 2.203 3.040 nonbonded pdb=" O LEU G 23 " pdb=" O HOH G 201 " model vdw 2.257 3.040 nonbonded pdb=" O ALA A 135 " pdb=" O HOH A 201 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU B 53 " pdb=" O HOH B1001 " model vdw 2.277 3.040 nonbonded pdb=" O HOH B1015 " pdb=" O HOH I 102 " model vdw 2.284 3.040 ... (remaining 110309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 38 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 26 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 12968 Z= 0.661 Angle : 1.017 7.276 18745 Z= 0.868 Chirality : 0.070 0.352 2134 Planarity : 0.013 0.140 1366 Dihedral : 26.790 177.136 5610 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.46 % Allowed : 0.77 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 764 helix: 0.55 (0.19), residues: 550 sheet: None (None), residues: 0 loop : 0.44 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.004 ARG G 88 TYR 0.024 0.005 TYR C 57 PHE 0.013 0.002 PHE F 100 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.66 (12968) covalent geometry : angle 1.01714 / 0.87 (18745) hydrogen bonds : bond 0.13232 / 8.87 ( 796) hydrogen bonds : angle 4.52145 / 3.27 ( 1988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.372 Fit side-chains REVERT: D 105 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8085 (mttt) outliers start: 3 outliers final: 2 residues processed: 179 average time/residue: 0.9212 time to fit residues: 173.3249 Evaluate side-chains 150 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain L residue 9 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS F 27 GLN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.096512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.068670 restraints weight = 18989.885| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.31 r_work: 0.2702 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12968 Z= 0.206 Angle : 0.825 10.459 18745 Z= 0.459 Chirality : 0.059 0.323 2134 Planarity : 0.005 0.029 1366 Dihedral : 31.671 165.033 4054 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.69 % Allowed : 11.08 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.29), residues: 764 helix: 2.05 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.29 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.018 0.002 TYR C 57 PHE 0.015 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.21 (12968) covalent geometry : angle 0.82512 / 0.46 (18745) hydrogen bonds : bond 0.05659 / 3.81 ( 796) hydrogen bonds : angle 3.20582 / 2.30 ( 1988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.223 Fit side-chains REVERT: A 133 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: C 64 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8510 (tp30) REVERT: D 105 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8618 (mttp) outliers start: 11 outliers final: 4 residues processed: 152 average time/residue: 0.9112 time to fit residues: 145.6846 Evaluate side-chains 147 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 19 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 31 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN C 104 GLN D 46 HIS E 108 ASN F 27 GLN F 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.096202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068214 restraints weight = 19024.621| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.31 r_work: 0.2721 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12968 Z= 0.186 Angle : 0.717 9.146 18745 Z= 0.411 Chirality : 0.052 0.331 2134 Planarity : 0.005 0.031 1366 Dihedral : 31.660 166.774 4048 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.15 % Allowed : 12.31 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.29), residues: 764 helix: 2.41 (0.22), residues: 558 sheet: None (None), residues: 0 loop : 0.17 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 9 TYR 0.020 0.001 TYR C 57 PHE 0.013 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (12968) covalent geometry : angle 0.71747 / 0.41 (18745) hydrogen bonds : bond 0.05518 / 3.71 ( 796) hydrogen bonds : angle 3.06244 / 2.19 ( 1988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.367 Fit side-chains REVERT: A 59 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8077 (pm20) REVERT: A 133 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: C 64 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: C 74 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8691 (mtmm) REVERT: D 105 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8541 (mttp) REVERT: G 64 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: G 92 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: H 30 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7790 (ttm170) REVERT: H 68 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8294 (mp0) outliers start: 14 outliers final: 3 residues processed: 144 average time/residue: 0.9342 time to fit residues: 141.2993 Evaluate side-chains 149 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.095300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.067151 restraints weight = 18877.951| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.31 r_work: 0.2701 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9220 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12968 Z= 0.208 Angle : 0.729 9.240 18745 Z= 0.404 Chirality : 0.053 0.353 2134 Planarity : 0.004 0.034 1366 Dihedral : 31.773 169.695 4048 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.92 % Allowed : 12.92 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.29), residues: 764 helix: 2.43 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.00 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.014 0.002 TYR G 57 PHE 0.013 0.002 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (12968) covalent geometry : angle 0.72909 / 0.40 (18745) hydrogen bonds : bond 0.05445 / 3.67 ( 796) hydrogen bonds : angle 3.07587 / 2.20 ( 1988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.340 Fit side-chains REVERT: A 59 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: A 133 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: C 64 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8494 (tp30) REVERT: C 74 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8686 (mtmm) REVERT: D 102 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8559 (mm-30) REVERT: D 105 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8574 (mttp) REVERT: G 64 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: G 92 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: H 30 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7816 (ttm170) REVERT: H 68 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8192 (mp0) outliers start: 19 outliers final: 6 residues processed: 146 average time/residue: 0.9371 time to fit residues: 143.7806 Evaluate side-chains 155 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 27 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.067362 restraints weight = 18817.113| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.35 r_work: 0.2687 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12968 Z= 0.176 Angle : 0.705 9.884 18745 Z= 0.393 Chirality : 0.051 0.345 2134 Planarity : 0.004 0.053 1366 Dihedral : 31.731 170.699 4048 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.77 % Allowed : 13.23 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.29), residues: 764 helix: 2.48 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.01 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (12968) covalent geometry : angle 0.70473 / 0.39 (18745) hydrogen bonds : bond 0.05081 / 3.41 ( 796) hydrogen bonds : angle 3.02507 / 2.17 ( 1988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.302 Fit side-chains REVERT: A 59 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: A 76 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8640 (pt0) REVERT: A 133 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: C 64 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: C 74 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8650 (mtmm) REVERT: G 13 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8338 (tttm) REVERT: G 64 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: G 92 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: H 30 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7791 (ttm170) REVERT: H 68 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8203 (mp0) outliers start: 18 outliers final: 5 residues processed: 147 average time/residue: 0.9102 time to fit residues: 140.6553 Evaluate side-chains 155 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 28 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 40.0000 chunk 82 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 27 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.068280 restraints weight = 18960.760| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.32 r_work: 0.2723 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12968 Z= 0.139 Angle : 0.692 9.849 18745 Z= 0.388 Chirality : 0.050 0.346 2134 Planarity : 0.004 0.043 1366 Dihedral : 31.721 170.439 4048 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.46 % Allowed : 13.85 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.29), residues: 764 helix: 2.55 (0.22), residues: 558 sheet: None (None), residues: 0 loop : 0.02 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (12968) covalent geometry : angle 0.69160 / 0.39 (18745) hydrogen bonds : bond 0.04843 / 3.25 ( 796) hydrogen bonds : angle 3.01315 / 2.16 ( 1988) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.356 Fit side-chains REVERT: A 59 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: A 76 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8620 (pt0) REVERT: A 120 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: A 133 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: C 57 TYR cc_start: 0.9400 (t80) cc_final: 0.9174 (t80) REVERT: C 64 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8458 (tp30) REVERT: C 74 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8687 (mtmm) REVERT: D 105 LYS cc_start: 0.8904 (mtpm) cc_final: 0.8547 (mttp) REVERT: G 64 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: G 92 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: H 68 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8187 (mp0) outliers start: 16 outliers final: 6 residues processed: 144 average time/residue: 0.9743 time to fit residues: 147.3580 Evaluate side-chains 156 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.066422 restraints weight = 18592.902| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.33 r_work: 0.2674 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9220 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12968 Z= 0.212 Angle : 0.709 10.262 18745 Z= 0.393 Chirality : 0.051 0.364 2134 Planarity : 0.005 0.043 1366 Dihedral : 31.697 171.188 4048 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.54 % Allowed : 12.62 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.29), residues: 764 helix: 2.46 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -0.12 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 30 TYR 0.013 0.002 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (12968) covalent geometry : angle 0.70920 / 0.39 (18745) hydrogen bonds : bond 0.05642 / 3.82 ( 796) hydrogen bonds : angle 3.07935 / 2.20 ( 1988) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.377 Fit side-chains REVERT: A 59 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8220 (pm20) REVERT: A 76 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8655 (pt0) REVERT: A 133 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: C 64 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: C 74 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8655 (mtmm) REVERT: D 105 LYS cc_start: 0.8910 (mtpm) cc_final: 0.8599 (mttt) REVERT: F 77 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8929 (mttp) REVERT: G 13 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8294 (tttm) REVERT: G 64 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8046 (tp30) REVERT: G 92 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: H 68 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8188 (mp0) outliers start: 23 outliers final: 6 residues processed: 146 average time/residue: 1.0152 time to fit residues: 155.5575 Evaluate side-chains 156 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.067011 restraints weight = 18583.683| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.34 r_work: 0.2683 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9213 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12968 Z= 0.151 Angle : 0.697 10.318 18745 Z= 0.389 Chirality : 0.050 0.353 2134 Planarity : 0.004 0.038 1366 Dihedral : 31.695 171.630 4048 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.92 % Allowed : 13.08 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.29), residues: 764 helix: 2.48 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (12968) covalent geometry : angle 0.69683 / 0.39 (18745) hydrogen bonds : bond 0.05356 / 3.63 ( 796) hydrogen bonds : angle 3.07354 / 2.20 ( 1988) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.339 Fit side-chains REVERT: A 59 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: A 76 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8646 (pt0) REVERT: A 133 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: C 64 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: C 74 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8663 (mtmm) REVERT: D 105 LYS cc_start: 0.8895 (mtpm) cc_final: 0.8577 (mttt) REVERT: F 77 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8926 (mttp) REVERT: G 13 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8294 (tttm) REVERT: G 64 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: G 92 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: H 68 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8208 (mp0) outliers start: 19 outliers final: 5 residues processed: 144 average time/residue: 0.9604 time to fit residues: 145.2129 Evaluate side-chains 154 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.066772 restraints weight = 18688.448| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.34 r_work: 0.2677 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9215 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12968 Z= 0.198 Angle : 0.700 10.390 18745 Z= 0.388 Chirality : 0.050 0.361 2134 Planarity : 0.004 0.038 1366 Dihedral : 31.679 172.230 4048 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.62 % Allowed : 13.38 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.29), residues: 764 helix: 2.46 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.13 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (12968) covalent geometry : angle 0.69985 / 0.39 (18745) hydrogen bonds : bond 0.05291 / 3.57 ( 796) hydrogen bonds : angle 3.04955 / 2.18 ( 1988) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.318 Fit side-chains REVERT: A 59 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: A 76 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8648 (pt0) REVERT: A 133 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: C 64 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: C 74 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8659 (mtmm) REVERT: D 105 LYS cc_start: 0.8899 (mtpm) cc_final: 0.8578 (mttt) REVERT: F 77 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8929 (mttp) REVERT: G 13 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8302 (tttm) REVERT: G 64 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: G 92 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: H 68 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8203 (mp0) outliers start: 17 outliers final: 5 residues processed: 144 average time/residue: 1.0105 time to fit residues: 152.6425 Evaluate side-chains 154 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.066885 restraints weight = 18730.615| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.34 r_work: 0.2678 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9214 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12968 Z= 0.183 Angle : 0.697 10.442 18745 Z= 0.387 Chirality : 0.050 0.360 2134 Planarity : 0.004 0.038 1366 Dihedral : 31.677 172.181 4048 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.62 % Allowed : 13.85 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.29), residues: 764 helix: 2.49 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.12 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (12968) covalent geometry : angle 0.69715 / 0.39 (18745) hydrogen bonds : bond 0.05247 / 3.54 ( 796) hydrogen bonds : angle 3.04861 / 2.18 ( 1988) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.422 Fit side-chains REVERT: A 59 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: A 76 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8645 (pt0) REVERT: A 133 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: B 93 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8070 (mm110) REVERT: C 64 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8461 (tp30) REVERT: C 74 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8660 (mtmm) REVERT: D 105 LYS cc_start: 0.8899 (mtpm) cc_final: 0.8579 (mttt) REVERT: F 77 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8926 (mttp) REVERT: G 13 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8304 (tttm) REVERT: G 64 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: G 92 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: H 68 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8213 (mp0) outliers start: 17 outliers final: 5 residues processed: 143 average time/residue: 1.0163 time to fit residues: 152.6277 Evaluate side-chains 154 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 74 optimal weight: 40.0000 chunk 90 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.067026 restraints weight = 18580.914| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.33 r_work: 0.2682 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9212 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12968 Z= 0.167 Angle : 0.695 10.439 18745 Z= 0.386 Chirality : 0.049 0.359 2134 Planarity : 0.004 0.038 1366 Dihedral : 31.676 172.185 4048 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.62 % Allowed : 13.85 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.29), residues: 764 helix: 2.49 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (12968) covalent geometry : angle 0.69498 / 0.39 (18745) hydrogen bonds : bond 0.05188 / 3.50 ( 796) hydrogen bonds : angle 3.04636 / 2.18 ( 1988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4581.69 seconds wall clock time: 78 minutes 25.48 seconds (4705.48 seconds total)