Starting phenix.real_space_refine on Wed Aug 5 18:42:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4c_45181/08_2026/9c4c_45181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4c_45181/08_2026/9c4c_45181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4c_45181/08_2026/9c4c_45181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4c_45181/08_2026/9c4c_45181.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4c_45181/08_2026/9c4c_45181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4c_45181/08_2026/9c4c_45181.cif" } resolution = 3.09 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= 0.023 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: 7 Type Number sf(0) Gaussians Mn 8 7.51 5 P 77 5.49 5 S 12 5.16 5 C 3622 2.51 5 N 1028 2.21 5 O 1329 1.98 5 H 5414 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11490 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1241 Classifications: {'DNA': 39} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 38} Chain: "B" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1215 Classifications: {'DNA': 38} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 37} Chain: "E" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2264 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain: "F" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2249 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "G" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2249 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "H" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2264 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.17, per 1000 atoms: 0.19 Number of scatterers: 11490 At special positions: 0 Unit cell: (78.8768, 78.8768, 146.771, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 8 24.99 S 12 16.00 P 77 15.00 O 1329 8.00 N 1028 7.00 C 3622 6.00 H 5414 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 - 3.00 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: 1.24 Conformation dependent library (CDL) restraints added in 188.4 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 4 sheets defined 81.2% alpha, 4.2% beta 33 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'E' and resid 3 through 21 removed outlier: 4.556A pdb=" N TYR E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE E 10 " --> pdb=" O MET E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.525A pdb=" N ILE E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 48 removed outlier: 3.596A pdb=" N VAL E 39 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS E 48 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 87 removed outlier: 3.854A pdb=" N LYS E 68 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 93 through 102 Processing helix chain 'E' and resid 106 through 122 Processing helix chain 'E' and resid 123 through 137 removed outlier: 4.214A pdb=" N LYS E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 21 removed outlier: 3.527A pdb=" N ASP F 8 " --> pdb=" O PRO F 4 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 10 " --> pdb=" O MET F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 35 through 47 removed outlier: 3.533A pdb=" N VAL F 39 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 88 removed outlier: 3.529A pdb=" N LYS F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 102 Processing helix chain 'F' and resid 106 through 122 Processing helix chain 'F' and resid 124 through 135 removed outlier: 3.561A pdb=" N LYS F 128 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 21 removed outlier: 4.082A pdb=" N TYR G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.816A pdb=" N GLU G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 47 removed outlier: 3.683A pdb=" N VAL G 39 " --> pdb=" O HIS G 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 88 removed outlier: 3.595A pdb=" N LYS G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 92 No H-bonds generated for 'chain 'G' and resid 90 through 92' Processing helix chain 'G' and resid 93 through 102 removed outlier: 3.565A pdb=" N GLU G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 100 " --> pdb=" O ASN G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 106 through 122 removed outlier: 3.733A pdb=" N GLN G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 136 removed outlier: 4.047A pdb=" N LYS G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS G 131 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 5 No H-bonds generated for 'chain 'H' and resid 3 through 5' Processing helix chain 'H' and resid 6 through 21 removed outlier: 4.518A pdb=" N ILE H 10 " --> pdb=" O MET H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 31 removed outlier: 3.919A pdb=" N GLU H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA H 31 " --> pdb=" O ASP H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 26 through 31' Processing helix chain 'H' and resid 35 through 48 removed outlier: 3.888A pdb=" N VAL H 39 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS H 48 " --> pdb=" O GLN H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 88 removed outlier: 3.955A pdb=" N LYS H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.778A pdb=" N ILE H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 120 removed outlier: 3.514A pdb=" N GLY H 114 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU H 116 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 137 removed outlier: 3.889A pdb=" N LYS H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 55 Processing sheet with id=AA3, first strand: chain 'G' and resid 52 through 55 Processing sheet with id=AA4, first strand: chain 'H' and resid 52 through 55 removed outlier: 6.470A pdb=" N ILE H 53 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU H 60 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU H 55 " --> pdb=" O ARG H 58 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5414 1.03 - 1.22: 32 1.22 - 1.42: 2651 1.42 - 1.61: 3621 1.61 - 1.81: 26 Bond restraints: 11744 Sorted by residual: bond pdb=" C3' DT A 25 " pdb=" C2' DT A 25 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.83e+01 bond pdb=" C1' DT B -51 " pdb=" N1 DT B -51 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 1.00e+01 bond pdb=" C1' DT B -53 " pdb=" N1 DT B -53 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.64e+00 bond pdb=" C1' DT A 32 " pdb=" N1 DT A 32 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.53e+00 bond pdb=" C3' DT B -34 " pdb=" C2' DT B -34 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.32e+00 ... (remaining 11739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 20485 1.74 - 3.47: 801 3.47 - 5.21: 32 5.21 - 6.94: 2 6.94 - 8.68: 1 Bond angle restraints: 21321 Sorted by residual: angle pdb=" N3 DT A 32 " pdb=" C4 DT A 32 " pdb=" O4 DT A 32 " ideal model delta sigma weight residual 119.90 123.34 -3.44 6.00e-01 2.78e+00 3.29e+01 angle pdb=" O4' DA A 50 " pdb=" C1' DA A 50 " pdb=" N9 DA A 50 " ideal model delta sigma weight residual 108.00 111.97 -3.97 7.00e-01 2.04e+00 3.21e+01 angle pdb=" O4 DT A 32 " pdb=" C4 DT A 32 " pdb=" C5 DT A 32 " ideal model delta sigma weight residual 124.90 121.45 3.45 7.00e-01 2.04e+00 2.42e+01 angle pdb=" N3 DT A 37 " pdb=" C4 DT A 37 " pdb=" O4 DT A 37 " ideal model delta sigma weight residual 119.90 122.84 -2.94 6.00e-01 2.78e+00 2.41e+01 angle pdb=" N3 DT B -34 " pdb=" C4 DT B -34 " pdb=" O4 DT B -34 " ideal model delta sigma weight residual 119.90 122.80 -2.90 6.00e-01 2.78e+00 2.34e+01 ... (remaining 21316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 4686 34.82 - 69.65: 492 69.65 - 104.47: 11 104.47 - 139.29: 0 139.29 - 174.11: 4 Dihedral angle restraints: 5193 sinusoidal: 3335 harmonic: 1858 Sorted by residual: dihedral pdb=" CA LYS H 93 " pdb=" C LYS H 93 " pdb=" N ILE H 94 " pdb=" CA ILE H 94 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C4' DT B -43 " pdb=" C3' DT B -43 " pdb=" O3' DT B -43 " pdb=" P DA B -42 " ideal model delta sinusoidal sigma weight residual 220.00 45.89 174.11 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA B -44 " pdb=" C3' DA B -44 " pdb=" O3' DA B -44 " pdb=" P DT B -43 " ideal model delta sinusoidal sigma weight residual 220.00 56.76 163.24 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 5190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 621 0.039 - 0.077: 208 0.077 - 0.115: 83 0.115 - 0.154: 53 0.154 - 0.192: 13 Chirality restraints: 978 Sorted by residual: chirality pdb=" C3' DA B -48 " pdb=" C4' DA B -48 " pdb=" O3' DA B -48 " pdb=" C2' DA B -48 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" C3' DC B -47 " pdb=" C4' DC B -47 " pdb=" O3' DC B -47 " pdb=" C2' DC B -47 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" C3' DG B -36 " pdb=" C4' DG B -36 " pdb=" O3' DG B -36 " pdb=" C2' DG B -36 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 975 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC A 59 " 0.025 2.00e-02 2.50e+03 2.61e-02 1.87e+01 pdb=" N1 DC A 59 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DC A 59 " 0.057 2.00e-02 2.50e+03 pdb=" O2 DC A 59 " -0.055 2.00e-02 2.50e+03 pdb=" N3 DC A 59 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC A 59 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC A 59 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC A 59 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC A 59 " -0.008 2.00e-02 2.50e+03 pdb=" H5 DC A 59 " -0.008 2.00e-02 2.50e+03 pdb=" H6 DC A 59 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT A 32 " 0.026 2.00e-02 2.50e+03 1.12e-02 3.77e+00 pdb=" N1 DT A 32 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT A 32 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT A 32 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT A 32 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT A 32 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT A 32 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT A 32 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT A 32 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT A 32 " -0.010 2.00e-02 2.50e+03 pdb=" H3 DT A 32 " 0.002 2.00e-02 2.50e+03 pdb=" H6 DT A 32 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT A 25 " 0.021 2.00e-02 2.50e+03 9.34e-03 2.62e+00 pdb=" N1 DT A 25 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DT A 25 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT A 25 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT A 25 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT A 25 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT A 25 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT A 25 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT A 25 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT A 25 " -0.002 2.00e-02 2.50e+03 pdb=" H3 DT A 25 " 0.002 2.00e-02 2.50e+03 pdb=" H6 DT A 25 " -0.002 2.00e-02 2.50e+03 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 161 2.09 - 2.72: 17757 2.72 - 3.35: 31233 3.35 - 3.97: 40782 3.97 - 4.60: 63110 Nonbonded interactions: 153043 Sorted by model distance: nonbonded pdb=" OP2 DT A 44 " pdb=" HG SER G 26 " model vdw 1.467 2.450 nonbonded pdb=" O ASP G 129 " pdb=" HG SER G 132 " model vdw 1.490 2.450 nonbonded pdb=" OE1 GLU H 30 " pdb=" H GLU H 30 " model vdw 1.688 2.450 nonbonded pdb=" OE1 GLU F 55 " pdb=" HH TYR G 22 " model vdw 1.689 2.450 nonbonded pdb=" OD2 ASP G 97 " pdb=" HG SER H 109 " model vdw 1.700 2.450 ... (remaining 153038 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 'E' and (resid 3 through 137 or resid 201 through 202)) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and (resid 3 through 137 or resid 201 through 202)) } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.180 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.005 0.044 6330 Z= 0.438 Angle : 0.813 8.675 8844 Z= 0.651 Chirality : 0.054 0.192 978 Planarity : 0.004 0.028 849 Dihedral : 22.353 174.115 2660 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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: -1.20 (0.35), residues: 534 helix: -0.80 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -0.09 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 112 TYR 0.017 0.002 TYR F 57 PHE 0.008 0.001 PHE H 83 TRP 0.002 0.001 TRP F 107 HIS 0.003 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.44 ( 6330) covalent geometry : angle 0.81250 / 0.65 ( 8844) hydrogen bonds : bond 0.13436 / 14.56 ( 350) hydrogen bonds : angle 6.20372 / 7.85 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7437 (t80) cc_final: 0.7216 (t80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2085 time to fit residues: 18.8252 Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.214706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.204220 restraints weight = 13294.064| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 0.45 r_work: 0.4057 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6330 Z= 0.222 Angle : 0.724 7.120 8844 Z= 0.436 Chirality : 0.049 0.335 978 Planarity : 0.004 0.025 849 Dihedral : 25.704 176.707 1478 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.01 % Allowed : 8.91 % Favored : 90.08 % 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: -0.44 (0.36), residues: 534 helix: -0.20 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.03 (0.61), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 24 TYR 0.013 0.001 TYR F 57 PHE 0.006 0.002 PHE H 83 TRP 0.008 0.002 TRP F 107 HIS 0.004 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 ( 6330) covalent geometry : angle 0.72449 / 0.44 ( 8844) hydrogen bonds : bond 0.07698 / 8.14 ( 350) hydrogen bonds : angle 5.28510 / 6.84 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 58 average time/residue: 0.1358 time to fit residues: 10.6490 Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.213975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.202591 restraints weight = 13134.428| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 0.45 r_work: 0.4058 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6330 Z= 0.189 Angle : 0.656 6.492 8844 Z= 0.398 Chirality : 0.045 0.297 978 Planarity : 0.004 0.026 849 Dihedral : 25.843 176.248 1478 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.01 % Allowed : 11.13 % Favored : 87.85 % 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: 0.11 (0.37), residues: 534 helix: 0.31 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.30 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 126 TYR 0.009 0.001 TYR E 119 PHE 0.007 0.001 PHE H 83 TRP 0.008 0.002 TRP F 107 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 ( 6330) covalent geometry : angle 0.65610 / 0.40 ( 8844) hydrogen bonds : bond 0.06685 / 7.04 ( 350) hydrogen bonds : angle 4.76816 / 6.22 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: H 18 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6837 (mm-30) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.1338 time to fit residues: 10.1353 Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 18 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.215420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.203037 restraints weight = 13075.273| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 0.46 r_work: 0.4061 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.3781 rms_B_bonded: 3.43 restraints_weight: 0.1250 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6330 Z= 0.143 Angle : 0.599 5.735 8844 Z= 0.367 Chirality : 0.043 0.302 978 Planarity : 0.003 0.024 849 Dihedral : 25.843 177.678 1478 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.01 % Allowed : 11.13 % Favored : 87.85 % 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: 0.82 (0.38), residues: 534 helix: 0.83 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -0.08 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 112 TYR 0.010 0.001 TYR H 14 PHE 0.004 0.001 PHE E 120 TRP 0.007 0.001 TRP F 107 HIS 0.002 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 ( 6330) covalent geometry : angle 0.59941 / 0.37 ( 8844) hydrogen bonds : bond 0.05234 / 5.61 ( 350) hydrogen bonds : angle 4.45754 / 5.87 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7669 (t80) cc_final: 0.7466 (t80) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.1273 time to fit residues: 9.3542 Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.214520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.203053 restraints weight = 13129.426| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 0.44 r_work: 0.4061 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work: 0.3804 rms_B_bonded: 4.71 restraints_weight: 0.1250 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6330 Z= 0.161 Angle : 0.615 6.514 8844 Z= 0.371 Chirality : 0.043 0.304 978 Planarity : 0.003 0.025 849 Dihedral : 25.854 177.058 1478 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.21 % Allowed : 11.34 % Favored : 87.45 % 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: 1.01 (0.38), residues: 534 helix: 0.98 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -0.10 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.012 0.001 TYR H 14 PHE 0.007 0.001 PHE E 120 TRP 0.006 0.002 TRP F 107 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 ( 6330) covalent geometry : angle 0.61467 / 0.37 ( 8844) hydrogen bonds : bond 0.05622 / 5.89 ( 350) hydrogen bonds : angle 4.40401 / 5.85 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7683 (t80) cc_final: 0.7424 (t80) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.1094 time to fit residues: 8.3610 Evaluate side-chains 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.214220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.205004 restraints weight = 13162.222| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 0.44 r_work: 0.4040 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6330 Z= 0.186 Angle : 0.627 6.875 8844 Z= 0.378 Chirality : 0.044 0.317 978 Planarity : 0.003 0.027 849 Dihedral : 25.888 178.377 1478 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.21 % Allowed : 12.35 % Favored : 86.44 % 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: 0.88 (0.38), residues: 534 helix: 0.88 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.15 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 112 TYR 0.012 0.001 TYR H 14 PHE 0.009 0.002 PHE E 120 TRP 0.006 0.002 TRP G 107 HIS 0.004 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 ( 6330) covalent geometry : angle 0.62715 / 0.38 ( 8844) hydrogen bonds : bond 0.05856 / 6.07 ( 350) hydrogen bonds : angle 4.41022 / 5.86 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.249 Fit side-chains REVERT: H 95 TYR cc_start: 0.7687 (t80) cc_final: 0.7414 (t80) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.1079 time to fit residues: 8.0275 Evaluate side-chains 46 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.214028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.201240 restraints weight = 13183.092| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 0.48 r_work: 0.3972 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work: 0.3729 rms_B_bonded: 4.96 restraints_weight: 0.1250 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6330 Z= 0.181 Angle : 0.623 6.732 8844 Z= 0.375 Chirality : 0.044 0.314 978 Planarity : 0.003 0.028 849 Dihedral : 25.900 177.719 1478 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.01 % Allowed : 12.96 % Favored : 86.03 % 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: 0.91 (0.38), residues: 534 helix: 0.91 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.17 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 126 TYR 0.018 0.001 TYR H 119 PHE 0.008 0.002 PHE E 120 TRP 0.006 0.002 TRP G 107 HIS 0.004 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 ( 6330) covalent geometry : angle 0.62266 / 0.37 ( 8844) hydrogen bonds : bond 0.05787 / 6.03 ( 350) hydrogen bonds : angle 4.38584 / 5.84 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.276 Fit side-chains REVERT: H 95 TYR cc_start: 0.7694 (t80) cc_final: 0.7404 (t80) outliers start: 5 outliers final: 5 residues processed: 48 average time/residue: 0.0974 time to fit residues: 6.9529 Evaluate side-chains 46 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.219117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.210115 restraints weight = 12911.001| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 0.41 r_work: 0.4105 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6330 Z= 0.140 Angle : 0.579 5.890 8844 Z= 0.354 Chirality : 0.042 0.294 978 Planarity : 0.003 0.027 849 Dihedral : 25.900 178.438 1478 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.42 % Allowed : 13.56 % Favored : 85.02 % 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: 1.24 (0.38), residues: 534 helix: 1.17 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.15 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 126 TYR 0.026 0.001 TYR H 119 PHE 0.004 0.001 PHE E 120 TRP 0.007 0.001 TRP F 107 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 ( 6330) covalent geometry : angle 0.57918 / 0.35 ( 8844) hydrogen bonds : bond 0.04853 / 5.16 ( 350) hydrogen bonds : angle 4.22486 / 5.64 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.273 Fit side-chains REVERT: H 95 TYR cc_start: 0.7498 (t80) cc_final: 0.7234 (t80) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.1061 time to fit residues: 8.0921 Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.219084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.210008 restraints weight = 12939.816| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 0.40 r_work: 0.4108 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6330 Z= 0.158 Angle : 0.597 6.470 8844 Z= 0.361 Chirality : 0.042 0.310 978 Planarity : 0.003 0.026 849 Dihedral : 25.904 177.723 1478 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.21 % Allowed : 13.36 % Favored : 85.43 % 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: 1.23 (0.38), residues: 534 helix: 1.18 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.26 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 112 TYR 0.031 0.001 TYR H 119 PHE 0.008 0.001 PHE E 120 TRP 0.006 0.001 TRP F 107 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 6330) covalent geometry : angle 0.59737 / 0.36 ( 8844) hydrogen bonds : bond 0.05251 / 5.50 ( 350) hydrogen bonds : angle 4.23894 / 5.68 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.191 Fit side-chains REVERT: H 95 TYR cc_start: 0.7518 (t80) cc_final: 0.7317 (t80) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1164 time to fit residues: 8.4592 Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.218766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.210140 restraints weight = 12987.128| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 0.40 r_work: 0.4105 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.4037 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6330 Z= 0.144 Angle : 0.575 6.185 8844 Z= 0.350 Chirality : 0.042 0.293 978 Planarity : 0.003 0.028 849 Dihedral : 25.932 179.081 1478 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.21 % Allowed : 13.56 % Favored : 85.22 % 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: 1.36 (0.39), residues: 534 helix: 1.29 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.25 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.019 0.001 TYR H 119 PHE 0.006 0.001 PHE E 120 TRP 0.007 0.001 TRP F 107 HIS 0.002 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 ( 6330) covalent geometry : angle 0.57472 / 0.35 ( 8844) hydrogen bonds : bond 0.04769 / 5.05 ( 350) hydrogen bonds : angle 4.15961 / 5.59 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.254 Fit side-chains REVERT: H 95 TYR cc_start: 0.7492 (t80) cc_final: 0.7290 (t80) outliers start: 6 outliers final: 6 residues processed: 51 average time/residue: 0.1065 time to fit residues: 8.0308 Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.218419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.209321 restraints weight = 12940.141| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 0.40 r_work: 0.4088 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6330 Z= 0.163 Angle : 0.597 6.580 8844 Z= 0.360 Chirality : 0.043 0.313 978 Planarity : 0.003 0.028 849 Dihedral : 25.940 178.088 1478 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.21 % Allowed : 13.97 % Favored : 84.82 % 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: 1.29 (0.38), residues: 534 helix: 1.25 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.34 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 112 TYR 0.023 0.001 TYR H 119 PHE 0.008 0.001 PHE E 120 TRP 0.005 0.001 TRP F 107 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 6330) covalent geometry : angle 0.59700 / 0.36 ( 8844) hydrogen bonds : bond 0.05250 / 5.49 ( 350) hydrogen bonds : angle 4.21420 / 5.67 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.98 seconds wall clock time: 42 minutes 50.17 seconds (2570.17 seconds total)