Starting phenix.real_space_refine on Fri Jul 3 00:51:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4c_45181/07_2026/9c4c_45181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4c_45181/07_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_45181/07_2026/9c4c_45181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4c_45181/07_2026/9c4c_45181.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4c_45181/07_2026/9c4c_45181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4c_45181/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 2.20, 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: 0.81 Conformation dependent library (CDL) restraints added in 118.1 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: 1.68 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: 1.93 Time building geometry restraints manager: 1.11 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: 20489 1.74 - 3.47: 798 3.47 - 5.21: 31 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: 1.220 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: 0.070 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.590 Find NCS groups from input model: 0.160 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.600 ------------------------------------------------------------------------------- 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 : 0.809 8.675 8844 Z= 0.647 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 0.80874 / 0.65 ( 8844) hydrogen bonds : bond 0.13436 / 14.48 ( 350) hydrogen bonds : angle 6.20372 / 7.84 ( 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 : 0.245 Fit side-chains revert: symmetry clash REVERT: H 95 TYR cc_start: 0.7437 (t80) cc_final: 0.7225 (t80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1917 time to fit residues: 17.3528 Evaluate side-chains 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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: 0.9980 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: 1.5986 ------------------------------------------------------------------------------- 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 = 0.214745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.203077 restraints weight = 13363.165| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 0.57 r_work: 0.4041 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6330 Z= 0.211 Angle : 0.707 6.538 8844 Z= 0.429 Chirality : 0.046 0.298 978 Planarity : 0.004 0.023 849 Dihedral : 25.724 177.734 1478 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.61 % Allowed : 8.91 % Favored : 90.49 % 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: -0.41 (0.36), residues: 534 helix: -0.18 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.00 (0.61), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 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 E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 ( 6330) covalent geometry : angle 0.70702 / 0.43 ( 8844) hydrogen bonds : bond 0.07583 / 8.00 ( 350) hydrogen bonds : angle 5.27131 / 6.82 ( 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 57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.1397 time to fit residues: 10.5388 Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 124 ASP 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: 1.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.214515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.204543 restraints weight = 13328.858| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 0.48 r_work: 0.4053 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6330 Z= 0.178 Angle : 0.635 5.875 8844 Z= 0.390 Chirality : 0.043 0.272 978 Planarity : 0.004 0.025 849 Dihedral : 25.809 177.113 1478 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.81 % Allowed : 10.32 % Favored : 88.87 % 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: 0.22 (0.37), residues: 534 helix: 0.39 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.25 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 126 TYR 0.009 0.001 TYR F 57 PHE 0.007 0.001 PHE H 83 TRP 0.009 0.002 TRP F 107 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 ( 6330) covalent geometry : angle 0.63517 / 0.39 ( 8844) hydrogen bonds : bond 0.06402 / 6.75 ( 350) hydrogen bonds : angle 4.75896 / 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 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 ASN cc_start: 0.8091 (t0) cc_final: 0.7879 (t0) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.1697 time to fit residues: 11.9870 Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4450 r_free = 0.4450 target = 0.215694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.204856 restraints weight = 13236.784| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 0.49 r_work: 0.4073 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6330 Z= 0.144 Angle : 0.589 5.474 8844 Z= 0.364 Chirality : 0.042 0.278 978 Planarity : 0.003 0.023 849 Dihedral : 25.855 178.082 1478 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.01 % Allowed : 10.93 % Favored : 88.06 % 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: 0.90 (0.38), residues: 534 helix: 0.91 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -0.18 (0.60), residues: 122 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 0.005 0.001 PHE H 83 TRP 0.007 0.001 TRP F 107 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 ( 6330) covalent geometry : angle 0.58888 / 0.36 ( 8844) hydrogen bonds : bond 0.05177 / 5.55 ( 350) hydrogen bonds : angle 4.44030 / 5.86 ( 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 56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.204 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.1527 time to fit residues: 11.3074 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 : 0.278 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.214914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.201432 restraints weight = 13277.194| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 0.48 r_work: 0.4049 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3948 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2057 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= 0.150 Angle : 0.590 5.840 8844 Z= 0.362 Chirality : 0.042 0.273 978 Planarity : 0.003 0.023 849 Dihedral : 25.866 177.961 1478 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.01 % Allowed : 10.93 % Favored : 88.06 % 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: 1.21 (0.38), residues: 534 helix: 1.12 (0.27), residues: 410 sheet: None (None), residues: 0 loop : 0.00 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 24 TYR 0.012 0.001 TYR H 14 PHE 0.006 0.001 PHE E 120 TRP 0.007 0.002 TRP H 107 HIS 0.002 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 ( 6330) covalent geometry : angle 0.59006 / 0.36 ( 8844) hydrogen bonds : bond 0.05252 / 5.54 ( 350) hydrogen bonds : angle 4.34883 / 5.77 ( 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 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.276 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.1439 time to fit residues: 10.5621 Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 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 = 0.4431 r_free = 0.4431 target = 0.214155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.203021 restraints weight = 13273.462| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 0.56 r_work: 0.4023 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2282 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= 0.191 Angle : 0.626 6.657 8844 Z= 0.379 Chirality : 0.043 0.296 978 Planarity : 0.003 0.025 849 Dihedral : 25.891 178.743 1478 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.21 % Allowed : 10.73 % Favored : 88.06 % 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: 1.02 (0.38), residues: 534 helix: 0.96 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.02 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 112 TYR 0.014 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 0.00394 / 0.19 ( 6330) covalent geometry : angle 0.62594 / 0.38 ( 8844) hydrogen bonds : bond 0.06026 / 6.21 ( 350) hydrogen bonds : angle 4.40321 / 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 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.289 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1280 time to fit residues: 9.2823 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 : 0.264 ------------------------------------------------------------------------------- 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: 0.9980 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.213897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.200351 restraints weight = 13065.823| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 0.49 r_work: 0.4021 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 0.026 6330 Z= 0.166 Angle : 0.594 6.033 8844 Z= 0.363 Chirality : 0.042 0.277 978 Planarity : 0.003 0.026 849 Dihedral : 25.922 178.714 1478 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 1.19 (0.38), residues: 534 helix: 1.10 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.03 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 126 TYR 0.022 0.001 TYR H 119 PHE 0.006 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 0.00325 / 0.17 ( 6330) covalent geometry : angle 0.59374 / 0.36 ( 8844) hydrogen bonds : bond 0.05315 / 5.55 ( 350) hydrogen bonds : angle 4.29216 / 5.73 ( 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 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 49 average time/residue: 0.1292 time to fit residues: 9.2267 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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: 7.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4442 r_free = 0.4442 target = 0.220134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.211108 restraints weight = 12923.344| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 0.41 r_work: 0.4104 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2586 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= 0.139 Angle : 0.566 5.415 8844 Z= 0.349 Chirality : 0.041 0.275 978 Planarity : 0.003 0.025 849 Dihedral : 25.907 178.600 1478 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.01 % Allowed : 12.15 % Favored : 86.84 % 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: 1.54 (0.39), residues: 534 helix: 1.38 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.04 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.024 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 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 ( 6330) covalent geometry : angle 0.56595 / 0.35 ( 8844) hydrogen bonds : bond 0.04622 / 4.89 ( 350) hydrogen bonds : angle 4.14788 / 5.58 ( 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 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.288 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.1459 time to fit residues: 11.0698 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 : 0.300 ------------------------------------------------------------------------------- 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 121 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.219303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.210213 restraints weight = 12865.347| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 0.41 r_work: 0.4090 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6330 Z= 0.151 Angle : 0.575 6.002 8844 Z= 0.351 Chirality : 0.041 0.280 978 Planarity : 0.003 0.025 849 Dihedral : 25.916 178.645 1478 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.01 % Allowed : 11.94 % Favored : 87.04 % 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: 1.54 (0.38), residues: 534 helix: 1.40 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.13 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.015 0.001 TYR H 14 PHE 0.008 0.001 PHE E 120 TRP 0.006 0.001 TRP F 107 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 ( 6330) covalent geometry : angle 0.57492 / 0.35 ( 8844) hydrogen bonds : bond 0.05015 / 5.23 ( 350) hydrogen bonds : angle 4.16232 / 5.60 ( 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 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.294 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 51 average time/residue: 0.1279 time to fit residues: 9.5220 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 : 0.290 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.219114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.209984 restraints weight = 12922.140| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 0.40 r_work: 0.4077 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.4016 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6330 Z= 0.159 Angle : 0.585 6.106 8844 Z= 0.356 Chirality : 0.042 0.284 978 Planarity : 0.003 0.028 849 Dihedral : 25.949 179.805 1478 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.01 % Allowed : 12.15 % Favored : 86.84 % 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: 1.50 (0.38), residues: 534 helix: 1.38 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.17 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 112 TYR 0.018 0.001 TYR H 14 PHE 0.006 0.001 PHE E 120 TRP 0.006 0.002 TRP E 107 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 ( 6330) covalent geometry : angle 0.58489 / 0.36 ( 8844) hydrogen bonds : bond 0.05096 / 5.31 ( 350) hydrogen bonds : angle 4.16409 / 5.61 ( 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: 5 poor density : 46 time to evaluate : 0.281 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 51 average time/residue: 0.1165 time to fit residues: 8.6107 Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.219904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.210788 restraints weight = 12849.447| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 0.40 r_work: 0.4088 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6330 Z= 0.135 Angle : 0.557 5.523 8844 Z= 0.343 Chirality : 0.040 0.268 978 Planarity : 0.003 0.026 849 Dihedral : 25.960 178.873 1478 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.01 % Allowed : 12.15 % Favored : 86.84 % 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: 1.73 (0.39), residues: 534 helix: 1.55 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -0.13 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.016 0.001 TYR H 14 PHE 0.005 0.001 PHE E 120 TRP 0.007 0.001 TRP F 107 HIS 0.003 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 ( 6330) covalent geometry : angle 0.55742 / 0.34 ( 8844) hydrogen bonds : bond 0.04546 / 4.80 ( 350) hydrogen bonds : angle 4.07960 / 5.50 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.18 seconds wall clock time: 47 minutes 11.61 seconds (2831.61 seconds total)