Starting phenix.real_space_refine on Sat Sep 12 02:51:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5l08_8300/09_2026/5l08_8300.cif Found real_map, /net/cci-nas-00/data/ceres_data/5l08_8300/09_2026/5l08_8300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5l08_8300/09_2026/5l08_8300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5l08_8300/09_2026/5l08_8300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5l08_8300/09_2026/5l08_8300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5l08_8300/09_2026/5l08_8300.map" } resolution = 4.6 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 ------------------------------------------------------------------------------- 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= -31.220 sd= 18.086 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8658 2.51 5 N 2286 2.21 5 O 2601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13617 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "C" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "D" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "E" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "F" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "G" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "H" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "I" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Time building chain proxies: 3.39, per 1000 atoms: 0.25 Number of scatterers: 13617 At special positions: 0 Unit cell: (102.92, 103.54, 125.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2601 8.00 N 2286 7.00 C 8658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 603.0 milliseconds 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 8 through 13 removed outlier: 3.655A pdb=" N GLY A 11 " --> pdb=" O TYR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 82 through 91 removed outlier: 3.619A pdb=" N ARG A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.603A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 168 removed outlier: 4.294A pdb=" N VAL A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.990A pdb=" N LYS A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'B' and resid 2 through 2 No H-bonds generated for 'chain 'B' and resid 2 through 2' Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.807A pdb=" N ASP B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.535A pdb=" N ILE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 113 through 128 removed outlier: 4.761A pdb=" N GLU B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.874A pdb=" N GLY C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 12 " --> pdb=" O TYR C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 12' Processing helix chain 'C' and resid 15 through 27 Processing helix chain 'C' and resid 40 through 51 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 83 through 91 removed outlier: 4.117A pdb=" N GLU C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.972A pdb=" N SER C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 156 through 165 removed outlier: 3.685A pdb=" N LYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.576A pdb=" N GLY D 11 " --> pdb=" O TYR D 8 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 12 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 27 through 29 No H-bonds generated for 'chain 'D' and resid 27 through 29' Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 71 through 78 removed outlier: 3.520A pdb=" N LEU D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 156 through 166 removed outlier: 3.525A pdb=" N LEU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.719A pdb=" N LEU D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'E' and resid 2 through 2 No H-bonds generated for 'chain 'E' and resid 2 through 2' Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.844A pdb=" N ASP E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 40 through 51 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 71 through 78 Processing helix chain 'E' and resid 83 through 90 Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 113 through 128 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 156 through 166 removed outlier: 3.605A pdb=" N LEU E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.796A pdb=" N LEU E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 2 through 2 No H-bonds generated for 'chain 'F' and resid 2 through 2' Processing helix chain 'F' and resid 3 through 12 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 40 through 51 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 71 through 76 Processing helix chain 'F' and resid 82 through 88 removed outlier: 3.576A pdb=" N MET F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 92 removed outlier: 3.655A pdb=" N THR F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 156 through 166 removed outlier: 4.166A pdb=" N LEU F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 170 removed outlier: 6.968A pdb=" N SER F 170 " --> pdb=" O ILE F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 171 through 176 Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'G' and resid 2 through 2 No H-bonds generated for 'chain 'G' and resid 2 through 2' Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 27 through 29 No H-bonds generated for 'chain 'G' and resid 27 through 29' Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 40 through 51 removed outlier: 4.120A pdb=" N LYS G 51 " --> pdb=" O ARG G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 71 through 78 removed outlier: 3.579A pdb=" N LEU G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 removed outlier: 4.338A pdb=" N MET G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 113 through 128 removed outlier: 3.518A pdb=" N SER G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 148 Processing helix chain 'G' and resid 153 through 157 Processing helix chain 'G' and resid 158 through 159 No H-bonds generated for 'chain 'G' and resid 158 through 159' Processing helix chain 'G' and resid 160 through 165 Processing helix chain 'G' and resid 168 through 176 removed outlier: 3.677A pdb=" N LEU G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 182 removed outlier: 4.692A pdb=" N GLU G 180 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 14 removed outlier: 3.861A pdb=" N TYR H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP H 9 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 26 removed outlier: 4.064A pdb=" N ALA H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 29 No H-bonds generated for 'chain 'H' and resid 27 through 29' Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 40 through 51 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 71 through 78 removed outlier: 3.544A pdb=" N LEU H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.675A pdb=" N GLU H 89 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 112 Processing helix chain 'H' and resid 113 through 128 Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 156 through 159 Processing helix chain 'H' and resid 160 through 165 Processing helix chain 'H' and resid 168 through 176 removed outlier: 3.609A pdb=" N LEU H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 182 Processing helix chain 'I' and resid 2 through 8 removed outlier: 3.537A pdb=" N TYR I 8 " --> pdb=" O ARG I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 14 removed outlier: 4.169A pdb=" N GLN I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 26 Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'I' and resid 31 through 36 Processing helix chain 'I' and resid 40 through 51 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.975A pdb=" N ILE I 76 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 99 through 112 Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 138 through 149 Processing helix chain 'I' and resid 156 through 159 Processing helix chain 'I' and resid 160 through 165 Processing helix chain 'I' and resid 168 through 176 removed outlier: 3.613A pdb=" N LEU I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 182 668 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 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: 1.19 - 1.31: 2473 1.31 - 1.44: 3098 1.44 - 1.56: 8073 1.56 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 13770 Sorted by residual: bond pdb=" C TYR E 8 " pdb=" O TYR E 8 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.15e-02 7.56e+03 1.67e+01 bond pdb=" C TYR B 8 " pdb=" O TYR B 8 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.15e-02 7.56e+03 1.67e+01 bond pdb=" C TYR H 8 " pdb=" O TYR H 8 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" C TYR F 8 " pdb=" O TYR F 8 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.61e+01 bond pdb=" C TYR C 8 " pdb=" O TYR C 8 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.58e+01 ... (remaining 13765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 17746 2.32 - 4.63: 597 4.63 - 6.95: 63 6.95 - 9.26: 4 9.26 - 11.58: 4 Bond angle restraints: 18414 Sorted by residual: angle pdb=" C GLU F 36 " pdb=" N PRO F 37 " pdb=" CA PRO F 37 " ideal model delta sigma weight residual 120.83 114.92 5.91 1.02e+00 9.61e-01 3.35e+01 angle pdb=" O LEU H 7 " pdb=" C LEU H 7 " pdb=" N TYR H 8 " ideal model delta sigma weight residual 122.12 127.51 -5.39 1.06e+00 8.90e-01 2.59e+01 angle pdb=" O LEU E 7 " pdb=" C LEU E 7 " pdb=" N TYR E 8 " ideal model delta sigma weight residual 122.12 127.46 -5.34 1.06e+00 8.90e-01 2.54e+01 angle pdb=" O LEU F 7 " pdb=" C LEU F 7 " pdb=" N TYR F 8 " ideal model delta sigma weight residual 122.12 127.45 -5.33 1.06e+00 8.90e-01 2.53e+01 angle pdb=" O LEU B 7 " pdb=" C LEU B 7 " pdb=" N TYR B 8 " ideal model delta sigma weight residual 122.12 127.43 -5.31 1.06e+00 8.90e-01 2.51e+01 ... (remaining 18409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8342 17.69 - 35.37: 253 35.37 - 53.06: 95 53.06 - 70.75: 39 70.75 - 88.44: 10 Dihedral angle restraints: 8739 sinusoidal: 3879 harmonic: 4860 Sorted by residual: dihedral pdb=" CB GLU F 55 " pdb=" CG GLU F 55 " pdb=" CD GLU F 55 " pdb=" OE1 GLU F 55 " ideal model delta sinusoidal sigma weight residual 0.00 88.44 -88.44 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA ASP C 15 " pdb=" CB ASP C 15 " pdb=" CG ASP C 15 " pdb=" OD1 ASP C 15 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CB GLU A 89 " pdb=" CG GLU A 89 " pdb=" CD GLU A 89 " pdb=" OE1 GLU A 89 " ideal model delta sinusoidal sigma weight residual 0.00 86.06 -86.06 1 3.00e+01 1.11e-03 9.93e+00 ... (remaining 8736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1200 0.028 - 0.055: 343 0.055 - 0.083: 86 0.083 - 0.110: 352 0.110 - 0.138: 89 Chirality restraints: 2070 Sorted by residual: chirality pdb=" CA VAL C 150 " pdb=" N VAL C 150 " pdb=" C VAL C 150 " pdb=" CB VAL C 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL H 150 " pdb=" N VAL H 150 " pdb=" C VAL H 150 " pdb=" CB VAL H 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL E 150 " pdb=" N VAL E 150 " pdb=" C VAL E 150 " pdb=" CB VAL E 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2067 not shown) Planarity restraints: 2367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 32 " 0.014 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C GLN F 32 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN F 32 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG F 33 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 32 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C GLN A 32 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN A 32 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 33 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 32 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.91e+00 pdb=" C GLN B 32 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN B 32 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG B 33 " -0.018 2.00e-02 2.50e+03 ... (remaining 2364 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 102 2.61 - 3.18: 13739 3.18 - 3.76: 20829 3.76 - 4.33: 32333 4.33 - 4.90: 48222 Nonbonded interactions: 115225 Sorted by model distance: nonbonded pdb=" CE1 PHE A 122 " pdb=" O LEU B 42 " model vdw 2.041 3.340 nonbonded pdb=" O GLU F 127 " pdb=" CG1 ILE F 128 " model vdw 2.236 3.440 nonbonded pdb=" O ARG F 118 " pdb=" CD2 PHE F 122 " model vdw 2.239 3.340 nonbonded pdb=" O GLU C 127 " pdb=" CG1 ILE C 128 " model vdw 2.257 3.440 nonbonded pdb=" O GLU A 127 " pdb=" CG1 ILE A 128 " model vdw 2.259 3.440 ... (remaining 115220 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.480 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.800 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 : 0.011 0.053 13770 Z= 0.631 Angle : 1.031 11.579 18414 Z= 0.757 Chirality : 0.051 0.138 2070 Planarity : 0.003 0.030 2367 Dihedral : 11.660 88.436 5553 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.04 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -0.41 (0.22), residues: 1611 helix: -1.38 (0.15), residues: 952 sheet: None (None), residues: 0 loop : 1.97 (0.29), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.007 0.000 TYR D 29 PHE 0.002 0.000 PHE F 45 Details of bonding type rmsd/Z covalent geometry : bond 0.01100 / 0.63 (13770) covalent geometry : angle 1.03062 / 0.76 (18414) hydrogen bonds : bond 0.19228 / 12.51 ( 668) hydrogen bonds : angle 7.26414 / 5.03 ( 1806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.7136 (mt) cc_final: 0.6884 (mt) REVERT: A 40 ASP cc_start: 0.8831 (p0) cc_final: 0.8542 (p0) REVERT: A 51 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8632 (mmtm) REVERT: A 61 PHE cc_start: 0.8366 (t80) cc_final: 0.7560 (t80) REVERT: A 62 LEU cc_start: 0.9136 (tp) cc_final: 0.8874 (tp) REVERT: A 69 ILE cc_start: 0.9271 (pt) cc_final: 0.9019 (mp) REVERT: A 74 LEU cc_start: 0.9179 (mt) cc_final: 0.8973 (mt) REVERT: A 97 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7018 (mt0) REVERT: A 103 VAL cc_start: 0.8960 (p) cc_final: 0.8383 (m) REVERT: A 106 TYR cc_start: 0.8451 (t80) cc_final: 0.8054 (t80) REVERT: A 151 ILE cc_start: 0.8064 (pt) cc_final: 0.7769 (pt) REVERT: A 152 LEU cc_start: 0.7996 (tp) cc_final: 0.7624 (tp) REVERT: A 160 LEU cc_start: 0.8948 (mt) cc_final: 0.8563 (mt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0899 time to fit residues: 10.3908 Evaluate side-chains 68 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 9.9990 overall best weight: 1.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.124456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.109819 restraints weight = 4922.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.112827 restraints weight = 3137.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.115032 restraints weight = 2220.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.116650 restraints weight = 1665.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.117889 restraints weight = 1303.079| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 1.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 13770 Z= 0.290 Angle : 1.250 17.178 18414 Z= 0.645 Chirality : 0.058 0.254 2070 Planarity : 0.015 0.199 2367 Dihedral : 7.271 24.220 1800 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.74 % Allowed : 5.23 % Favored : 93.02 % 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: -2.17 (0.19), residues: 1611 helix: -1.90 (0.13), residues: 1188 sheet: None (None), residues: 0 loop : 0.81 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 33 TYR 0.023 0.003 TYR F 78 PHE 0.011 0.002 PHE E 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.29 (13770) covalent geometry : angle 1.24981 / 0.64 (18414) hydrogen bonds : bond 0.13459 / 8.35 ( 668) hydrogen bonds : angle 8.76413 / 6.12 ( 1806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LEU cc_start: 0.8001 (mt) cc_final: 0.7778 (mt) REVERT: D 24 PHE cc_start: 0.8571 (t80) cc_final: 0.8068 (t80) REVERT: D 27 LEU cc_start: 0.9015 (mt) cc_final: 0.8529 (tp) REVERT: D 30 ILE cc_start: 0.9046 (tp) cc_final: 0.8747 (tt) REVERT: D 45 PHE cc_start: 0.8973 (m-10) cc_final: 0.8420 (m-80) REVERT: D 48 LEU cc_start: 0.9519 (mt) cc_final: 0.9182 (mt) REVERT: D 52 ARG cc_start: 0.6591 (mpt180) cc_final: 0.6377 (mmt180) REVERT: D 53 MET cc_start: 0.7997 (mmm) cc_final: 0.7628 (mmt) REVERT: D 62 LEU cc_start: 0.9034 (tp) cc_final: 0.8732 (tp) REVERT: D 64 GLU cc_start: 0.8134 (pt0) cc_final: 0.7913 (pt0) REVERT: D 65 LEU cc_start: 0.9173 (mm) cc_final: 0.8793 (pp) REVERT: D 67 PHE cc_start: 0.8503 (t80) cc_final: 0.7901 (t80) REVERT: D 79 LEU cc_start: 0.8654 (mt) cc_final: 0.8163 (mt) REVERT: D 85 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7522 (tp30) REVERT: D 97 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7449 (tp-100) REVERT: D 102 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7943 (tpp80) REVERT: D 142 ILE cc_start: 0.8548 (mm) cc_final: 0.8016 (mm) REVERT: D 152 LEU cc_start: 0.7614 (tp) cc_final: 0.6973 (tp) REVERT: D 168 ASN cc_start: 0.5545 (t0) cc_final: 0.4353 (t0) REVERT: D 172 LEU cc_start: 0.8879 (mm) cc_final: 0.8669 (mm) outliers start: 3 outliers final: 0 residues processed: 116 average time/residue: 0.0900 time to fit residues: 11.2381 Evaluate side-chains 81 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 44 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 chunk 129 optimal weight: 0.0770 chunk 161 optimal weight: 9.9990 chunk 139 optimal weight: 50.0000 chunk 154 optimal weight: 0.9980 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 80 ASN D 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.115484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100876 restraints weight = 5430.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103478 restraints weight = 3416.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.105270 restraints weight = 2434.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106705 restraints weight = 1839.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107899 restraints weight = 1462.737| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 1.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13770 Z= 0.239 Angle : 1.165 15.262 18414 Z= 0.595 Chirality : 0.056 0.222 2070 Planarity : 0.010 0.097 2367 Dihedral : 7.262 25.115 1800 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 40.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.20), residues: 1611 helix: -2.03 (0.13), residues: 1152 sheet: None (None), residues: 0 loop : 0.54 (0.34), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 71 TYR 0.016 0.002 TYR D 8 PHE 0.037 0.003 PHE G 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 (13770) covalent geometry : angle 1.16549 / 0.59 (18414) hydrogen bonds : bond 0.11261 / 7.12 ( 668) hydrogen bonds : angle 8.38163 / 5.84 ( 1806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 24 PHE cc_start: 0.8553 (t80) cc_final: 0.8346 (t80) REVERT: F 48 LEU cc_start: 0.9374 (mt) cc_final: 0.9153 (mt) REVERT: F 54 LEU cc_start: 0.8841 (tt) cc_final: 0.8174 (tt) REVERT: F 62 LEU cc_start: 0.9002 (tp) cc_final: 0.8556 (tp) REVERT: F 64 GLU cc_start: 0.8452 (pt0) cc_final: 0.8175 (pt0) REVERT: F 104 MET cc_start: 0.8545 (ptm) cc_final: 0.8039 (ppp) REVERT: F 105 LEU cc_start: 0.9474 (mt) cc_final: 0.8940 (mt) REVERT: F 106 TYR cc_start: 0.8717 (t80) cc_final: 0.6930 (t80) REVERT: F 111 GLU cc_start: 0.8182 (tp30) cc_final: 0.7755 (tp30) REVERT: F 139 LEU cc_start: 0.9079 (tp) cc_final: 0.8172 (tp) REVERT: F 141 ASP cc_start: 0.8272 (m-30) cc_final: 0.7836 (m-30) REVERT: F 142 ILE cc_start: 0.8383 (mm) cc_final: 0.7869 (mm) REVERT: F 143 PHE cc_start: 0.9177 (m-10) cc_final: 0.8830 (m-10) REVERT: F 152 LEU cc_start: 0.7498 (tp) cc_final: 0.7155 (tp) REVERT: F 162 ARG cc_start: 0.7814 (tpt170) cc_final: 0.7550 (tpm170) REVERT: F 168 ASN cc_start: 0.6429 (t0) cc_final: 0.5332 (t0) REVERT: F 169 LYS cc_start: 0.7501 (pttp) cc_final: 0.7291 (pttp) REVERT: F 173 LYS cc_start: 0.8811 (ptmm) cc_final: 0.8408 (mptt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0767 time to fit residues: 8.9809 Evaluate side-chains 78 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 40 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 149 optimal weight: 40.0000 chunk 47 optimal weight: 0.0980 chunk 123 optimal weight: 0.0270 chunk 75 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 108 optimal weight: 40.0000 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 46 GLN F 49 GLN F 97 GLN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.118161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100079 restraints weight = 5536.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.102638 restraints weight = 3808.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.104598 restraints weight = 2864.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106065 restraints weight = 2277.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107281 restraints weight = 1874.281| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 1.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13770 Z= 0.249 Angle : 1.160 13.048 18414 Z= 0.602 Chirality : 0.058 0.218 2070 Planarity : 0.009 0.098 2367 Dihedral : 7.538 26.468 1800 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 38.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.16 % Allowed : 4.65 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.20), residues: 1611 helix: -2.02 (0.13), residues: 1143 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.012 0.003 TYR C 8 PHE 0.050 0.003 PHE D 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.25 (13770) covalent geometry : angle 1.16041 / 0.60 (18414) hydrogen bonds : bond 0.10380 / 6.88 ( 668) hydrogen bonds : angle 8.28928 / 5.72 ( 1806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.6920 (m-30) cc_final: 0.6279 (m-30) REVERT: F 30 ILE cc_start: 0.8905 (tp) cc_final: 0.8684 (tp) REVERT: F 33 ARG cc_start: 0.6744 (ptp-170) cc_final: 0.6409 (ptp-170) REVERT: F 49 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: F 53 MET cc_start: 0.8195 (mpp) cc_final: 0.7524 (mtm) REVERT: F 54 LEU cc_start: 0.8286 (tt) cc_final: 0.8054 (tt) REVERT: F 61 PHE cc_start: 0.8555 (t80) cc_final: 0.6826 (t80) REVERT: F 64 GLU cc_start: 0.8546 (pt0) cc_final: 0.8090 (pt0) REVERT: F 65 LEU cc_start: 0.9340 (pp) cc_final: 0.9109 (pp) REVERT: F 79 LEU cc_start: 0.7914 (mm) cc_final: 0.7357 (tt) REVERT: F 97 GLN cc_start: 0.8495 (tt0) cc_final: 0.8149 (tt0) REVERT: F 104 MET cc_start: 0.8612 (ptm) cc_final: 0.7906 (ppp) REVERT: F 105 LEU cc_start: 0.9393 (mt) cc_final: 0.9094 (mt) REVERT: F 139 LEU cc_start: 0.8729 (tp) cc_final: 0.8217 (tp) REVERT: F 152 LEU cc_start: 0.7572 (tp) cc_final: 0.7341 (tp) REVERT: F 168 ASN cc_start: 0.6215 (t0) cc_final: 0.4953 (t0) REVERT: F 173 LYS cc_start: 0.8859 (ptmm) cc_final: 0.8398 (mptt) REVERT: F 178 TYR cc_start: 0.8252 (t80) cc_final: 0.7959 (t80) outliers start: 2 outliers final: 0 residues processed: 100 average time/residue: 0.0822 time to fit residues: 8.9265 Evaluate side-chains 76 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 3.9990 chunk 126 optimal weight: 50.0000 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 108 optimal weight: 50.0000 chunk 160 optimal weight: 0.0570 chunk 49 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.117095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101377 restraints weight = 5130.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103801 restraints weight = 3238.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105799 restraints weight = 2308.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107324 restraints weight = 1756.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108343 restraints weight = 1394.351| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 1.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13770 Z= 0.222 Angle : 1.027 10.198 18414 Z= 0.551 Chirality : 0.056 0.164 2070 Planarity : 0.009 0.081 2367 Dihedral : 7.336 27.194 1800 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 33.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.19), residues: 1611 helix: -2.09 (0.13), residues: 1161 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG F 95 TYR 0.010 0.002 TYR B 101 PHE 0.015 0.002 PHE G 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (13770) covalent geometry : angle 1.02665 / 0.55 (18414) hydrogen bonds : bond 0.09592 / 6.44 ( 668) hydrogen bonds : angle 7.72633 / 5.32 ( 1806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 ARG cc_start: 0.8655 (tmm160) cc_final: 0.8070 (tpt170) REVERT: D 25 LEU cc_start: 0.8302 (mm) cc_final: 0.7416 (tp) REVERT: D 48 LEU cc_start: 0.9613 (mt) cc_final: 0.9150 (mt) REVERT: D 49 GLN cc_start: 0.8063 (pm20) cc_final: 0.7740 (mp10) REVERT: D 67 PHE cc_start: 0.7856 (t80) cc_final: 0.7528 (t80) REVERT: D 79 LEU cc_start: 0.8171 (mm) cc_final: 0.7736 (tt) REVERT: D 97 GLN cc_start: 0.8205 (tt0) cc_final: 0.7225 (tt0) REVERT: D 98 ILE cc_start: 0.7153 (pt) cc_final: 0.6204 (pt) REVERT: D 102 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7779 (tpp80) REVERT: D 104 MET cc_start: 0.8902 (ptm) cc_final: 0.8403 (ppp) REVERT: D 111 GLU cc_start: 0.8351 (tp30) cc_final: 0.7928 (tp30) REVERT: D 152 LEU cc_start: 0.7946 (tp) cc_final: 0.7547 (tp) REVERT: D 178 TYR cc_start: 0.8354 (t80) cc_final: 0.7375 (t80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0825 time to fit residues: 8.6440 Evaluate side-chains 68 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 139 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 7 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 overall best weight: 1.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.121768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.101648 restraints weight = 5081.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.104271 restraints weight = 3587.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.106295 restraints weight = 2759.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107890 restraints weight = 2230.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.109078 restraints weight = 1875.102| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 1.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13770 Z= 0.238 Angle : 1.105 13.406 18414 Z= 0.578 Chirality : 0.055 0.168 2070 Planarity : 0.008 0.071 2367 Dihedral : 7.249 26.855 1800 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 39.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.19), residues: 1611 helix: -1.87 (0.14), residues: 1125 sheet: None (None), residues: 0 loop : -0.39 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 33 TYR 0.017 0.002 TYR D 101 PHE 0.022 0.002 PHE B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 (13770) covalent geometry : angle 1.10507 / 0.58 (18414) hydrogen bonds : bond 0.09781 / 6.60 ( 668) hydrogen bonds : angle 7.93520 / 5.42 ( 1806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 LEU cc_start: 0.8585 (mm) cc_final: 0.8100 (pp) REVERT: E 46 GLN cc_start: 0.9182 (mm110) cc_final: 0.8934 (mm110) REVERT: E 48 LEU cc_start: 0.9494 (mt) cc_final: 0.9149 (mt) REVERT: E 50 GLU cc_start: 0.8972 (mm-30) cc_final: 0.7877 (tm-30) REVERT: E 54 LEU cc_start: 0.8314 (tt) cc_final: 0.8085 (tt) REVERT: E 56 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7164 (mt-10) REVERT: E 67 PHE cc_start: 0.8178 (t80) cc_final: 0.7792 (t80) REVERT: E 104 MET cc_start: 0.9140 (ptm) cc_final: 0.8421 (ppp) REVERT: E 142 ILE cc_start: 0.8598 (mm) cc_final: 0.8367 (mm) REVERT: E 159 ILE cc_start: 0.8262 (tp) cc_final: 0.7998 (tp) REVERT: E 160 LEU cc_start: 0.8828 (mt) cc_final: 0.8474 (mt) REVERT: E 172 LEU cc_start: 0.8973 (mm) cc_final: 0.8377 (mt) REVERT: E 173 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8697 (mttt) REVERT: E 178 TYR cc_start: 0.8581 (t80) cc_final: 0.7903 (t80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0806 time to fit residues: 7.9036 Evaluate side-chains 61 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 148 optimal weight: 10.0000 chunk 131 optimal weight: 0.0470 chunk 22 optimal weight: 9.9990 chunk 146 optimal weight: 0.2980 chunk 154 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 overall best weight: 3.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.125491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.106702 restraints weight = 4836.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109283 restraints weight = 3348.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111378 restraints weight = 2561.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.112817 restraints weight = 2071.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.113807 restraints weight = 1742.375| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 1.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13770 Z= 0.236 Angle : 1.168 12.658 18414 Z= 0.621 Chirality : 0.058 0.192 2070 Planarity : 0.010 0.071 2367 Dihedral : 7.763 28.264 1800 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 39.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.19), residues: 1611 helix: -1.97 (0.13), residues: 1107 sheet: None (None), residues: 0 loop : -0.51 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 71 TYR 0.022 0.002 TYR D 8 PHE 0.011 0.002 PHE H 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 (13770) covalent geometry : angle 1.16795 / 0.62 (18414) hydrogen bonds : bond 0.09797 / 6.59 ( 668) hydrogen bonds : angle 8.24513 / 5.66 ( 1806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8399 (ttmt) REVERT: E 25 LEU cc_start: 0.8587 (mm) cc_final: 0.8230 (pp) REVERT: E 48 LEU cc_start: 0.9382 (mt) cc_final: 0.9141 (mt) REVERT: E 110 GLU cc_start: 0.7209 (tp30) cc_final: 0.6872 (mm-30) REVERT: E 142 ILE cc_start: 0.8678 (mm) cc_final: 0.8343 (mm) REVERT: E 146 MET cc_start: 0.8922 (mtp) cc_final: 0.8648 (mtp) REVERT: E 162 ARG cc_start: 0.8372 (tpt90) cc_final: 0.8152 (tpt170) REVERT: E 169 LYS cc_start: 0.7108 (pttp) cc_final: 0.6853 (pttp) REVERT: E 172 LEU cc_start: 0.9235 (mm) cc_final: 0.8938 (mt) REVERT: E 178 TYR cc_start: 0.8558 (t80) cc_final: 0.8225 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0754 time to fit residues: 7.0283 Evaluate side-chains 65 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 11 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 49 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 153 optimal weight: 7.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.128525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.106708 restraints weight = 4978.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.109237 restraints weight = 3770.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111086 restraints weight = 3000.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.112501 restraints weight = 2499.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.113630 restraints weight = 2162.772| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 1.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13770 Z= 0.235 Angle : 1.123 11.795 18414 Z= 0.604 Chirality : 0.056 0.176 2070 Planarity : 0.008 0.070 2367 Dihedral : 7.545 29.038 1800 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 37.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.19), residues: 1611 helix: -2.07 (0.13), residues: 1098 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 118 TYR 0.016 0.002 TYR B 106 PHE 0.019 0.002 PHE F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.24 (13770) covalent geometry : angle 1.12258 / 0.60 (18414) hydrogen bonds : bond 0.09670 / 6.53 ( 668) hydrogen bonds : angle 8.19520 / 5.66 ( 1806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8462 (ttmt) REVERT: E 25 LEU cc_start: 0.8626 (mm) cc_final: 0.8357 (pp) REVERT: E 48 LEU cc_start: 0.9534 (mt) cc_final: 0.9214 (mt) REVERT: E 66 LEU cc_start: 0.8981 (mt) cc_final: 0.8762 (tt) REVERT: E 111 GLU cc_start: 0.8454 (tp30) cc_final: 0.8165 (tp30) REVERT: E 118 ARG cc_start: 0.8795 (mmm160) cc_final: 0.8279 (ttm110) REVERT: E 169 LYS cc_start: 0.7114 (pttp) cc_final: 0.6767 (pttp) REVERT: E 172 LEU cc_start: 0.9244 (mm) cc_final: 0.8974 (mt) REVERT: E 178 TYR cc_start: 0.8585 (t80) cc_final: 0.8315 (t80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0572 time to fit residues: 4.7354 Evaluate side-chains 59 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 57 optimal weight: 0.1980 chunk 77 optimal weight: 40.0000 chunk 15 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 153 optimal weight: 40.0000 chunk 90 optimal weight: 40.0000 chunk 85 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.127362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108884 restraints weight = 4844.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111305 restraints weight = 3520.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.113361 restraints weight = 2741.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.114535 restraints weight = 2207.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.115826 restraints weight = 1885.740| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 1.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13770 Z= 0.223 Angle : 1.054 10.768 18414 Z= 0.565 Chirality : 0.052 0.150 2070 Planarity : 0.009 0.076 2367 Dihedral : 7.519 28.394 1800 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 36.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -2.57 (0.19), residues: 1611 helix: -1.92 (0.13), residues: 1116 sheet: None (None), residues: 0 loop : -0.60 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 118 TYR 0.013 0.001 TYR F 8 PHE 0.023 0.002 PHE C 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (13770) covalent geometry : angle 1.05435 / 0.57 (18414) hydrogen bonds : bond 0.09320 / 6.29 ( 668) hydrogen bonds : angle 7.94884 / 5.51 ( 1806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 ILE cc_start: 0.8962 (mp) cc_final: 0.8268 (mt) REVERT: E 25 LEU cc_start: 0.8558 (mm) cc_final: 0.8313 (pp) REVERT: E 48 LEU cc_start: 0.9563 (mt) cc_final: 0.9313 (mt) REVERT: E 50 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8082 (tm-30) REVERT: E 51 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8670 (mmmt) REVERT: E 74 LEU cc_start: 0.8902 (mm) cc_final: 0.8649 (mt) REVERT: E 106 TYR cc_start: 0.9022 (t80) cc_final: 0.8300 (t80) REVERT: E 107 GLN cc_start: 0.9201 (mt0) cc_final: 0.8909 (mp10) REVERT: E 142 ILE cc_start: 0.8612 (mm) cc_final: 0.8323 (mt) REVERT: E 152 LEU cc_start: 0.8069 (tp) cc_final: 0.7802 (tp) REVERT: E 166 GLN cc_start: 0.8414 (mm110) cc_final: 0.8050 (mm-40) REVERT: E 178 TYR cc_start: 0.8525 (t80) cc_final: 0.8012 (t80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0707 time to fit residues: 6.1750 Evaluate side-chains 60 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 13 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 146 optimal weight: 0.0870 chunk 39 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.127222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109092 restraints weight = 4772.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111514 restraints weight = 3414.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.113327 restraints weight = 2637.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.114698 restraints weight = 2156.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.115660 restraints weight = 1802.938| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 1.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13770 Z= 0.220 Angle : 1.097 10.849 18414 Z= 0.590 Chirality : 0.055 0.165 2070 Planarity : 0.007 0.062 2367 Dihedral : 7.593 29.089 1800 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 39.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.19), residues: 1611 helix: -1.95 (0.13), residues: 1125 sheet: None (None), residues: 0 loop : -0.44 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 118 TYR 0.011 0.002 TYR A 8 PHE 0.028 0.003 PHE B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (13770) covalent geometry : angle 1.09680 / 0.59 (18414) hydrogen bonds : bond 0.09389 / 6.36 ( 668) hydrogen bonds : angle 7.89097 / 5.48 ( 1806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 ILE cc_start: 0.8935 (mp) cc_final: 0.8558 (mt) REVERT: E 24 PHE cc_start: 0.8635 (t80) cc_final: 0.8326 (t80) REVERT: E 25 LEU cc_start: 0.8517 (mm) cc_final: 0.8317 (pp) REVERT: E 43 MET cc_start: 0.8720 (ptp) cc_final: 0.8482 (ptp) REVERT: E 48 LEU cc_start: 0.9575 (mt) cc_final: 0.9325 (mt) REVERT: E 50 GLU cc_start: 0.8938 (mm-30) cc_final: 0.7946 (tm-30) REVERT: E 106 TYR cc_start: 0.8779 (t80) cc_final: 0.8116 (t80) REVERT: E 111 GLU cc_start: 0.8228 (tp30) cc_final: 0.7882 (tp30) REVERT: E 115 SER cc_start: 0.9455 (t) cc_final: 0.9095 (t) REVERT: E 139 LEU cc_start: 0.8727 (tp) cc_final: 0.8469 (tp) REVERT: E 142 ILE cc_start: 0.8591 (mm) cc_final: 0.8311 (mt) REVERT: E 152 LEU cc_start: 0.8082 (tp) cc_final: 0.7862 (tp) REVERT: E 166 GLN cc_start: 0.8362 (mm110) cc_final: 0.7987 (mm-40) REVERT: E 172 LEU cc_start: 0.9085 (mm) cc_final: 0.8654 (mt) REVERT: E 178 TYR cc_start: 0.8397 (t80) cc_final: 0.7967 (t80) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0455 time to fit residues: 3.9741 Evaluate side-chains 65 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 45 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 134 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 0.0970 chunk 46 optimal weight: 10.0000 chunk 20 optimal weight: 0.0030 chunk 159 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.1946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.129748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.110060 restraints weight = 4796.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.112658 restraints weight = 3498.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.114749 restraints weight = 2718.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.116373 restraints weight = 2204.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.117446 restraints weight = 1831.360| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 1.7531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13770 Z= 0.223 Angle : 1.104 11.473 18414 Z= 0.583 Chirality : 0.057 0.328 2070 Planarity : 0.007 0.061 2367 Dihedral : 7.537 28.727 1800 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 38.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.19), residues: 1611 helix: -1.70 (0.14), residues: 1107 sheet: None (None), residues: 0 loop : -0.65 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 118 TYR 0.019 0.002 TYR A 106 PHE 0.027 0.003 PHE B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (13770) covalent geometry : angle 1.10367 / 0.58 (18414) hydrogen bonds : bond 0.09464 / 6.40 ( 668) hydrogen bonds : angle 7.71443 / 5.38 ( 1806) =============================================================================== Job complete usr+sys time: 1453.61 seconds wall clock time: 26 minutes 18.51 seconds (1578.51 seconds total)