Starting phenix.real_space_refine on Wed Aug 5 10:37:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30og_57891/08_2026/30og_57891.cif Found real_map, /net/cci-nas-00/data/ceres_data/30og_57891/08_2026/30og_57891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30og_57891/08_2026/30og_57891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30og_57891/08_2026/30og_57891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30og_57891/08_2026/30og_57891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30og_57891/08_2026/30og_57891.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.033 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 70 5.16 5 C 5832 2.51 5 N 1567 2.21 5 O 1749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9218 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1542 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 184} Chain breaks: 3 Chain: "E" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1531 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 183} Chain breaks: 2 Chain: "e" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1482 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain breaks: 3 Chain: "X" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1562 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 187} Chain breaks: 2 Chain: "Z" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1539 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 184} Chain breaks: 3 Chain: "a" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1562 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 187} Chain breaks: 2 Time building chain proxies: 2.25, per 1000 atoms: 0.24 Number of scatterers: 9218 At special positions: 0 Unit cell: (130.9, 129.8, 80.3, 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 70 16.00 O 1749 8.00 N 1567 7.00 C 5832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 300.3 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 4 sheets defined 75.1% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.661A pdb=" N LEU D 21 " --> pdb=" O SER D 17 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU D 29 " --> pdb=" O VAL D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 43 removed outlier: 3.841A pdb=" N MET D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.640A pdb=" N THR D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 84 removed outlier: 4.006A pdb=" N MET D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 126 through 144 removed outlier: 4.345A pdb=" N ARG D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.776A pdb=" N ILE D 154 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 175 removed outlier: 4.036A pdb=" N TYR D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL D 166 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 removed outlier: 4.394A pdb=" N LEU D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.795A pdb=" N ILE D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.838A pdb=" N LEU E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 removed outlier: 4.151A pdb=" N MET E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 63 through 82 removed outlier: 3.590A pdb=" N ASN E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 126 through 147 removed outlier: 4.002A pdb=" N LYS E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE E 142 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'E' and resid 161 through 174 Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 207 removed outlier: 3.934A pdb=" N ILE E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY E 207 " --> pdb=" O LEU E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'e' and resid 17 through 31 removed outlier: 4.971A pdb=" N ALA e 23 " --> pdb=" O ARG e 19 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP e 24 " --> pdb=" O THR e 20 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU e 29 " --> pdb=" O VAL e 25 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS e 31 " --> pdb=" O VAL e 27 " (cutoff:3.500A) Processing helix chain 'e' and resid 36 through 44 removed outlier: 4.362A pdb=" N MET e 40 " --> pdb=" O GLU e 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE e 41 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER e 42 " --> pdb=" O ILE e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 60 removed outlier: 3.693A pdb=" N VAL e 60 " --> pdb=" O MET e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 84 removed outlier: 3.960A pdb=" N GLN e 68 " --> pdb=" O GLN e 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET e 69 " --> pdb=" O ALA e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 107 Processing helix chain 'e' and resid 111 through 119 Processing helix chain 'e' and resid 126 through 144 removed outlier: 3.890A pdb=" N ARG e 144 " --> pdb=" O ASN e 140 " (cutoff:3.500A) Processing helix chain 'e' and resid 145 through 147 No H-bonds generated for 'chain 'e' and resid 145 through 147' Processing helix chain 'e' and resid 150 through 154 Processing helix chain 'e' and resid 161 through 175 removed outlier: 4.068A pdb=" N ASP e 167 " --> pdb=" O ARG e 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG e 168 " --> pdb=" O ASP e 164 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE e 169 " --> pdb=" O TYR e 165 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA e 175 " --> pdb=" O LYS e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 179 through 194 removed outlier: 4.645A pdb=" N LEU e 191 " --> pdb=" O THR e 187 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL e 192 " --> pdb=" O GLU e 188 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN e 193 " --> pdb=" O THR e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 196 through 207 removed outlier: 4.029A pdb=" N ILE e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 211 through 219 removed outlier: 3.523A pdb=" N MET e 215 " --> pdb=" O THR e 211 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 31 removed outlier: 3.683A pdb=" N LEU X 21 " --> pdb=" O SER X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 45 removed outlier: 3.613A pdb=" N MET X 40 " --> pdb=" O GLU X 36 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU X 44 " --> pdb=" O MET X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 59 removed outlier: 3.638A pdb=" N THR X 59 " --> pdb=" O THR X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 84 removed outlier: 3.553A pdb=" N MET X 67 " --> pdb=" O HIS X 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN X 75 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU X 76 " --> pdb=" O GLU X 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU X 77 " --> pdb=" O THR X 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP X 82 " --> pdb=" O ALA X 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 121 Processing helix chain 'X' and resid 126 through 146 removed outlier: 3.592A pdb=" N ARG X 144 " --> pdb=" O ASN X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 154 Processing helix chain 'X' and resid 161 through 176 removed outlier: 3.606A pdb=" N ASP X 167 " --> pdb=" O ARG X 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG X 168 " --> pdb=" O ASP X 164 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS X 171 " --> pdb=" O ASP X 167 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA X 175 " --> pdb=" O LYS X 171 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU X 176 " --> pdb=" O THR X 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 179 through 194 removed outlier: 4.838A pdb=" N LEU X 191 " --> pdb=" O THR X 187 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN X 193 " --> pdb=" O THR X 189 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN X 194 " --> pdb=" O LEU X 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 207 removed outlier: 3.835A pdb=" N ILE X 202 " --> pdb=" O ASP X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 211 through 219 Processing helix chain 'Z' and resid 17 through 31 removed outlier: 3.745A pdb=" N LEU Z 21 " --> pdb=" O SER Z 17 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU Z 29 " --> pdb=" O VAL Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 44 removed outlier: 3.730A pdb=" N MET Z 40 " --> pdb=" O GLU Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 59 removed outlier: 3.726A pdb=" N THR Z 59 " --> pdb=" O THR Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 84 removed outlier: 3.887A pdb=" N MET Z 67 " --> pdb=" O HIS Z 63 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN Z 68 " --> pdb=" O GLN Z 64 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET Z 69 " --> pdb=" O ALA Z 65 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Z 70 " --> pdb=" O ALA Z 66 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS Z 71 " --> pdb=" O MET Z 67 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU Z 76 " --> pdb=" O GLU Z 72 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA Z 78 " --> pdb=" O ILE Z 74 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 107 removed outlier: 3.620A pdb=" N GLY Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 103 through 107' Processing helix chain 'Z' and resid 111 through 121 Processing helix chain 'Z' and resid 126 through 143 Processing helix chain 'Z' and resid 144 through 147 Processing helix chain 'Z' and resid 150 through 154 Processing helix chain 'Z' and resid 162 through 174 removed outlier: 3.782A pdb=" N VAL Z 166 " --> pdb=" O PHE Z 162 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP Z 167 " --> pdb=" O ARG Z 163 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG Z 168 " --> pdb=" O ASP Z 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 179 through 194 removed outlier: 4.134A pdb=" N LEU Z 191 " --> pdb=" O THR Z 187 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN Z 194 " --> pdb=" O LEU Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 206 removed outlier: 4.393A pdb=" N ILE Z 202 " --> pdb=" O ASP Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 213 through 219 Processing helix chain 'a' and resid 17 through 31 removed outlier: 3.789A pdb=" N LEU a 21 " --> pdb=" O SER a 17 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS a 31 " --> pdb=" O VAL a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 45 Processing helix chain 'a' and resid 49 through 58 Processing helix chain 'a' and resid 63 through 84 removed outlier: 3.757A pdb=" N MET a 67 " --> pdb=" O HIS a 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN a 75 " --> pdb=" O LYS a 71 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU a 76 " --> pdb=" O GLU a 72 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU a 77 " --> pdb=" O THR a 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 107 Processing helix chain 'a' and resid 111 through 121 removed outlier: 3.640A pdb=" N MET a 119 " --> pdb=" O GLN a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 147 removed outlier: 3.607A pdb=" N LYS a 141 " --> pdb=" O LEU a 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG a 144 " --> pdb=" O ASN a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 154 Processing helix chain 'a' and resid 161 through 174 Processing helix chain 'a' and resid 179 through 194 removed outlier: 4.332A pdb=" N LEU a 191 " --> pdb=" O THR a 187 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 196 through 206 removed outlier: 3.728A pdb=" N THR a 201 " --> pdb=" O PRO a 197 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE a 202 " --> pdb=" O ASP a 198 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU a 206 " --> pdb=" O ILE a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 211 through 216 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.629A pdb=" N VAL D 4 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 3 through 4 Processing sheet with id=AA3, first strand: chain 'Z' and resid 3 through 4 removed outlier: 3.631A pdb=" N VAL Z 4 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 3 through 4 493 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3030 1.34 - 1.46: 1918 1.46 - 1.58: 4319 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 9395 Sorted by residual: bond pdb=" CB GLN D 113 " pdb=" CG GLN D 113 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB GLU Z 181 " pdb=" CG GLU Z 181 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB ILE D 142 " pdb=" CG2 ILE D 142 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.69e-01 bond pdb=" CB ILE e 142 " pdb=" CG1 ILE e 142 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.91e-01 bond pdb=" CG1 ILE e 151 " pdb=" CD1 ILE e 151 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.30e-01 ... (remaining 9390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 12167 1.12 - 2.23: 435 2.23 - 3.35: 87 3.35 - 4.47: 40 4.47 - 5.59: 6 Bond angle restraints: 12735 Sorted by residual: angle pdb=" CB GLU Z 181 " pdb=" CG GLU Z 181 " pdb=" CD GLU Z 181 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.70e+00 3.46e-01 8.70e+00 angle pdb=" CA GLN D 113 " pdb=" CB GLN D 113 " pdb=" CG GLN D 113 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.80e+00 angle pdb=" C MET e 69 " pdb=" CA MET e 69 " pdb=" CB MET e 69 " ideal model delta sigma weight residual 109.99 115.50 -5.51 2.09e+00 2.29e-01 6.96e+00 angle pdb=" CB GLN D 113 " pdb=" CG GLN D 113 " pdb=" CD GLN D 113 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.70e+00 3.46e-01 5.96e+00 angle pdb=" C ILE X 38 " pdb=" CA ILE X 38 " pdb=" CB ILE X 38 " ideal model delta sigma weight residual 114.00 111.04 2.96 1.31e+00 5.83e-01 5.11e+00 ... (remaining 12730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5220 18.00 - 35.99: 401 35.99 - 53.99: 80 53.99 - 71.99: 24 71.99 - 89.99: 8 Dihedral angle restraints: 5733 sinusoidal: 2346 harmonic: 3387 Sorted by residual: dihedral pdb=" CA ASP X 167 " pdb=" C ASP X 167 " pdb=" N ARG X 168 " pdb=" CA ARG X 168 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA VAL Z 28 " pdb=" C VAL Z 28 " pdb=" N GLU Z 29 " pdb=" CA GLU Z 29 " ideal model delta harmonic sigma weight residual 180.00 162.58 17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN e 184 " pdb=" CB ASN e 184 " pdb=" CG ASN e 184 " pdb=" OD1 ASN e 184 " ideal model delta sinusoidal sigma weight residual 120.00 -169.11 -70.89 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 5730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 964 0.033 - 0.065: 342 0.065 - 0.098: 103 0.098 - 0.131: 37 0.131 - 0.163: 5 Chirality restraints: 1451 Sorted by residual: chirality pdb=" CA MET e 69 " pdb=" N MET e 69 " pdb=" C MET e 69 " pdb=" CB MET e 69 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ILE E 125 " pdb=" N ILE E 125 " pdb=" C ILE E 125 " pdb=" CB ILE E 125 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE Z 125 " pdb=" N ILE Z 125 " pdb=" C ILE Z 125 " pdb=" CB ILE Z 125 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1448 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET e 69 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C MET e 69 " -0.033 2.00e-02 2.50e+03 pdb=" O MET e 69 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU e 70 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 49 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO D 50 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Z 196 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO Z 197 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO Z 197 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO Z 197 " -0.020 5.00e-02 4.00e+02 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2417 2.81 - 3.33: 10131 3.33 - 3.85: 14181 3.85 - 4.38: 15833 4.38 - 4.90: 26096 Nonbonded interactions: 68658 Sorted by model distance: nonbonded pdb=" O ASN E 122 " pdb=" OD1 ASN E 122 " model vdw 2.281 3.040 nonbonded pdb=" O ASP Z 153 " pdb=" OD1 ASP Z 153 " model vdw 2.325 3.040 nonbonded pdb=" O LYS e 71 " pdb=" OD1 ASN e 75 " model vdw 2.418 3.040 nonbonded pdb=" O ALA E 79 " pdb=" OD1 ASP E 82 " model vdw 2.438 3.040 nonbonded pdb=" N GLU Z 181 " pdb=" OE1 GLU Z 181 " model vdw 2.450 3.120 ... (remaining 68653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 2 through 3 or resid 14 through 119 or resid 125 through 2 \ 06 or resid 212 through 223)) selection = (chain 'E' and (resid 2 through 3 or resid 14 through 119 or resid 125 through 2 \ 06 or resid 212 through 223)) selection = (chain 'X' and (resid 2 through 3 or resid 14 through 119 or resid 125 through 2 \ 06 or resid 212 through 223)) selection = (chain 'Z' and (resid 2 through 3 or resid 14 through 119 or resid 125 through 2 \ 06 or resid 212 through 223)) selection = (chain 'a' and (resid 2 through 3 or resid 14 through 119 or resid 125 through 2 \ 06 or resid 212 through 223)) selection = (chain 'e' and (resid 2 through 206 or resid 212 through 223)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.100 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.950 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: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.003 0.036 9395 Z= 0.138 Angle : 0.555 5.587 12735 Z= 0.295 Chirality : 0.039 0.163 1451 Planarity : 0.005 0.048 1628 Dihedral : 14.069 89.987 3527 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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: 0.81 (0.25), residues: 1136 helix: 0.87 (0.19), residues: 737 sheet: None (None), residues: 0 loop : 0.11 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 133 TYR 0.012 0.002 TYR D 131 PHE 0.013 0.001 PHE a 162 TRP 0.008 0.001 TRP Z 118 HIS 0.002 0.001 HIS X 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9395) covalent geometry : angle 0.55495 / 0.30 (12735) hydrogen bonds : bond 0.15210 / 10.06 ( 493) hydrogen bonds : angle 5.11144 / 3.59 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.304 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: symmetry clash revert: symmetry clash REVERT: D 14 GLN cc_start: 0.8286 (tp40) cc_final: 0.8080 (tp-100) REVERT: D 71 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7973 (ttpp) REVERT: D 115 GLN cc_start: 0.8431 (mt0) cc_final: 0.8146 (mp10) REVERT: D 147 SER cc_start: 0.8363 (m) cc_final: 0.8119 (t) REVERT: D 171 LYS cc_start: 0.8643 (tttp) cc_final: 0.7127 (mptt) REVERT: D 216 MET cc_start: 0.8038 (mmt) cc_final: 0.7684 (mmt) REVERT: E 144 ARG cc_start: 0.8486 (tpp-160) cc_final: 0.8205 (tpm170) REVERT: E 145 MET cc_start: 0.7243 (tpt) cc_final: 0.6980 (tpt) REVERT: E 203 LEU cc_start: 0.8773 (mt) cc_final: 0.8487 (tt) REVERT: e 68 GLN cc_start: 0.6440 (tt0) cc_final: 0.5642 (mm-40) REVERT: e 77 GLU cc_start: 0.6151 (mm-30) cc_final: 0.4802 (mm-30) REVERT: e 130 ILE cc_start: 0.8118 (pt) cc_final: 0.5726 (pt) REVERT: e 132 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8451 (tttt) REVERT: X 114 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8337 (mp0) REVERT: X 122 ASN cc_start: 0.8465 (p0) cc_final: 0.7958 (t0) REVERT: X 153 ASP cc_start: 0.7805 (t0) cc_final: 0.7535 (t0) REVERT: Z 40 MET cc_start: 0.6687 (tpp) cc_final: 0.6295 (mmt) REVERT: Z 71 LYS cc_start: 0.8427 (mtpp) cc_final: 0.7894 (mmtt) REVERT: Z 142 ILE cc_start: 0.8539 (pt) cc_final: 0.8295 (pt) REVERT: a 83 ARG cc_start: 0.8813 (ptp90) cc_final: 0.8606 (ptm-80) REVERT: a 131 TYR cc_start: 0.8493 (t80) cc_final: 0.8291 (t80) REVERT: a 132 LYS cc_start: 0.9100 (ttmt) cc_final: 0.8719 (tttt) REVERT: a 133 ARG cc_start: 0.8864 (ttp-110) cc_final: 0.8441 (mtm110) REVERT: a 140 ASN cc_start: 0.8568 (m-40) cc_final: 0.8227 (t0) REVERT: a 144 ARG cc_start: 0.7439 (tpm170) cc_final: 0.7126 (tpm170) REVERT: a 215 MET cc_start: 0.8120 (mpp) cc_final: 0.7692 (mpp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1155 time to fit residues: 32.9722 Evaluate side-chains 160 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 194 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 ASN Z 115 GLN a 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.100241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079601 restraints weight = 31312.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.081491 restraints weight = 20425.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082726 restraints weight = 15520.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083551 restraints weight = 13039.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.083922 restraints weight = 11656.550| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9395 Z= 0.170 Angle : 0.594 7.035 12735 Z= 0.310 Chirality : 0.042 0.141 1451 Planarity : 0.005 0.048 1628 Dihedral : 4.730 18.904 1229 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1136 helix: 0.86 (0.19), residues: 735 sheet: None (None), residues: 0 loop : 0.18 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 133 TYR 0.012 0.002 TYR Z 131 PHE 0.017 0.002 PHE a 162 TRP 0.011 0.001 TRP E 24 HIS 0.003 0.001 HIS e 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 9395) covalent geometry : angle 0.59362 / 0.31 (12735) hydrogen bonds : bond 0.04582 / 2.99 ( 493) hydrogen bonds : angle 4.28224 / 3.05 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.249 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7885 (ttpp) REVERT: D 115 GLN cc_start: 0.8431 (mt0) cc_final: 0.7915 (mp10) REVERT: D 147 SER cc_start: 0.8344 (m) cc_final: 0.8089 (t) REVERT: D 171 LYS cc_start: 0.8709 (tttp) cc_final: 0.7190 (mptt) REVERT: D 216 MET cc_start: 0.7896 (mmt) cc_final: 0.7571 (mmt) REVERT: E 215 MET cc_start: 0.8999 (mtp) cc_final: 0.8796 (mtp) REVERT: e 68 GLN cc_start: 0.6299 (tt0) cc_final: 0.5483 (mm-40) REVERT: e 77 GLU cc_start: 0.6280 (mm-30) cc_final: 0.6065 (mm-30) REVERT: e 119 MET cc_start: 0.7322 (mmp) cc_final: 0.7092 (mtt) REVERT: e 142 ILE cc_start: 0.8748 (pt) cc_final: 0.8541 (tp) REVERT: X 122 ASN cc_start: 0.8496 (p0) cc_final: 0.7990 (t0) REVERT: Z 40 MET cc_start: 0.6629 (tpp) cc_final: 0.6179 (tpt) REVERT: Z 71 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7936 (mmtt) REVERT: Z 142 ILE cc_start: 0.8455 (pt) cc_final: 0.8135 (pt) REVERT: Z 174 ARG cc_start: 0.6851 (ttt180) cc_final: 0.6607 (ttp-170) REVERT: a 67 MET cc_start: 0.8025 (mmt) cc_final: 0.7756 (mmm) REVERT: a 82 ASP cc_start: 0.7925 (m-30) cc_final: 0.7680 (m-30) REVERT: a 83 ARG cc_start: 0.8811 (ptp90) cc_final: 0.8606 (ptm-80) REVERT: a 132 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8744 (tttt) REVERT: a 133 ARG cc_start: 0.8913 (ttp-110) cc_final: 0.8468 (mtm180) REVERT: a 140 ASN cc_start: 0.8557 (m-40) cc_final: 0.8044 (t0) REVERT: a 179 SER cc_start: 0.9208 (t) cc_final: 0.8932 (t) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1098 time to fit residues: 29.2018 Evaluate side-chains 159 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 0.0040 chunk 26 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080955 restraints weight = 31470.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082926 restraints weight = 20194.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084236 restraints weight = 15203.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085061 restraints weight = 12667.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085600 restraints weight = 11295.781| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9395 Z= 0.125 Angle : 0.550 6.021 12735 Z= 0.281 Chirality : 0.040 0.138 1451 Planarity : 0.005 0.047 1628 Dihedral : 4.511 17.105 1229 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1136 helix: 1.02 (0.19), residues: 736 sheet: None (None), residues: 0 loop : 0.33 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 144 TYR 0.017 0.002 TYR a 131 PHE 0.013 0.001 PHE a 162 TRP 0.009 0.001 TRP e 118 HIS 0.003 0.001 HIS D 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 9395) covalent geometry : angle 0.54973 / 0.28 (12735) hydrogen bonds : bond 0.03910 / 2.57 ( 493) hydrogen bonds : angle 4.00530 / 2.85 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.358 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: symmetry clash revert: symmetry clash REVERT: D 71 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7888 (ttpp) REVERT: D 115 GLN cc_start: 0.8514 (mt0) cc_final: 0.8017 (mp10) REVERT: D 171 LYS cc_start: 0.8652 (tttp) cc_final: 0.7075 (mptt) REVERT: D 216 MET cc_start: 0.7913 (mmt) cc_final: 0.7623 (mmt) REVERT: E 133 ARG cc_start: 0.8953 (mtp-110) cc_final: 0.8630 (ttp-110) REVERT: e 68 GLN cc_start: 0.6059 (tt0) cc_final: 0.5227 (mm-40) REVERT: X 114 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8242 (mt-10) REVERT: X 122 ASN cc_start: 0.8452 (p0) cc_final: 0.7948 (t0) REVERT: X 134 TRP cc_start: 0.7923 (m-10) cc_final: 0.7651 (m-10) REVERT: Z 40 MET cc_start: 0.6218 (tpp) cc_final: 0.5801 (tpt) REVERT: Z 71 LYS cc_start: 0.8347 (mtpp) cc_final: 0.7891 (mmtt) REVERT: Z 119 MET cc_start: 0.7015 (mmt) cc_final: 0.6690 (mmp) REVERT: Z 174 ARG cc_start: 0.6839 (ttt180) cc_final: 0.6122 (ttp-170) REVERT: Z 186 MET cc_start: 0.8301 (mtm) cc_final: 0.7930 (mtp) REVERT: a 82 ASP cc_start: 0.8098 (m-30) cc_final: 0.7838 (m-30) REVERT: a 114 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8877 (mt-10) REVERT: a 132 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8770 (tttt) REVERT: a 133 ARG cc_start: 0.8867 (ttp-110) cc_final: 0.8495 (mtm110) REVERT: a 140 ASN cc_start: 0.8528 (m-40) cc_final: 0.8104 (t0) REVERT: a 145 MET cc_start: 0.8190 (tpp) cc_final: 0.7921 (tpp) REVERT: a 215 MET cc_start: 0.8105 (mpp) cc_final: 0.7575 (mpp) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1040 time to fit residues: 29.8596 Evaluate side-chains 168 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 115 optimal weight: 0.0370 chunk 108 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081515 restraints weight = 31508.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083446 restraints weight = 20238.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084778 restraints weight = 15284.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085649 restraints weight = 12706.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086130 restraints weight = 11255.032| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9395 Z= 0.120 Angle : 0.543 6.206 12735 Z= 0.275 Chirality : 0.040 0.139 1451 Planarity : 0.005 0.046 1628 Dihedral : 4.404 16.430 1229 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1136 helix: 1.15 (0.20), residues: 730 sheet: None (None), residues: 0 loop : 0.50 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 83 TYR 0.009 0.001 TYR Z 131 PHE 0.013 0.001 PHE e 41 TRP 0.012 0.001 TRP e 118 HIS 0.002 0.001 HIS e 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9395) covalent geometry : angle 0.54288 / 0.27 (12735) hydrogen bonds : bond 0.03566 / 2.35 ( 493) hydrogen bonds : angle 3.87476 / 2.75 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.253 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7790 (ttpp) REVERT: D 115 GLN cc_start: 0.8498 (mt0) cc_final: 0.7917 (mp10) REVERT: D 171 LYS cc_start: 0.8621 (tttp) cc_final: 0.7047 (mptt) REVERT: D 219 CYS cc_start: 0.7997 (m) cc_final: 0.7171 (t) REVERT: e 68 GLN cc_start: 0.5789 (tt0) cc_final: 0.4889 (mm-40) REVERT: e 77 GLU cc_start: 0.6825 (mm-30) cc_final: 0.5274 (mm-30) REVERT: X 114 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8196 (mt-10) REVERT: X 122 ASN cc_start: 0.8513 (p0) cc_final: 0.7984 (t0) REVERT: X 145 MET cc_start: 0.6997 (ttm) cc_final: 0.6690 (ttm) REVERT: Z 40 MET cc_start: 0.6107 (tpp) cc_final: 0.5652 (tpt) REVERT: Z 71 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7830 (mmtt) REVERT: Z 119 MET cc_start: 0.7057 (mmt) cc_final: 0.6850 (mmt) REVERT: Z 174 ARG cc_start: 0.6803 (ttt180) cc_final: 0.6473 (ttp-170) REVERT: Z 183 LYS cc_start: 0.8310 (mttt) cc_final: 0.8102 (mttp) REVERT: Z 186 MET cc_start: 0.8262 (mtm) cc_final: 0.7957 (mtp) REVERT: a 82 ASP cc_start: 0.7895 (m-30) cc_final: 0.7652 (m-30) REVERT: a 132 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8786 (tttt) REVERT: a 133 ARG cc_start: 0.8893 (ttp-110) cc_final: 0.8556 (mtm110) REVERT: a 140 ASN cc_start: 0.8426 (m-40) cc_final: 0.8053 (t0) REVERT: a 145 MET cc_start: 0.8143 (tpp) cc_final: 0.7852 (tpp) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1069 time to fit residues: 30.0411 Evaluate side-chains 161 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 99 optimal weight: 0.0570 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 140 ASN D 177 GLN X 58 ASN Z 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081526 restraints weight = 31106.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083450 restraints weight = 20056.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084777 restraints weight = 15168.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085620 restraints weight = 12609.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086176 restraints weight = 11204.903| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9395 Z= 0.140 Angle : 0.569 6.453 12735 Z= 0.289 Chirality : 0.040 0.142 1451 Planarity : 0.005 0.046 1628 Dihedral : 4.398 17.154 1229 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.26), residues: 1136 helix: 1.12 (0.19), residues: 732 sheet: None (None), residues: 0 loop : 0.48 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 133 TYR 0.017 0.002 TYR D 165 PHE 0.014 0.002 PHE a 162 TRP 0.015 0.001 TRP e 24 HIS 0.002 0.001 HIS X 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9395) covalent geometry : angle 0.56859 / 0.29 (12735) hydrogen bonds : bond 0.03644 / 2.39 ( 493) hydrogen bonds : angle 3.92178 / 2.79 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.247 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: symmetry clash REVERT: D 71 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7876 (ttpp) REVERT: D 115 GLN cc_start: 0.8563 (mt0) cc_final: 0.8148 (mp10) REVERT: D 171 LYS cc_start: 0.8688 (tttp) cc_final: 0.7088 (mptt) REVERT: D 216 MET cc_start: 0.7698 (mmt) cc_final: 0.7382 (mmt) REVERT: D 219 CYS cc_start: 0.7900 (m) cc_final: 0.7175 (t) REVERT: E 133 ARG cc_start: 0.8922 (mtp-110) cc_final: 0.8589 (ttp-110) REVERT: E 203 LEU cc_start: 0.8870 (mt) cc_final: 0.8496 (tt) REVERT: E 216 MET cc_start: 0.7546 (mtt) cc_final: 0.7340 (mtm) REVERT: e 68 GLN cc_start: 0.5870 (tt0) cc_final: 0.4971 (mm-40) REVERT: e 77 GLU cc_start: 0.6710 (mm-30) cc_final: 0.5227 (mm-30) REVERT: e 114 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8360 (tt0) REVERT: e 132 LYS cc_start: 0.9070 (tmtt) cc_final: 0.8549 (tttt) REVERT: X 122 ASN cc_start: 0.8497 (p0) cc_final: 0.7943 (t0) REVERT: Z 40 MET cc_start: 0.6137 (tpp) cc_final: 0.5678 (tpt) REVERT: Z 71 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7865 (mmtm) REVERT: Z 174 ARG cc_start: 0.6845 (ttt180) cc_final: 0.6081 (ttp-170) REVERT: Z 186 MET cc_start: 0.8245 (mtm) cc_final: 0.7950 (mtp) REVERT: a 82 ASP cc_start: 0.7944 (m-30) cc_final: 0.7687 (m-30) REVERT: a 132 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8788 (tttt) REVERT: a 133 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.8530 (mtm110) REVERT: a 140 ASN cc_start: 0.8441 (m-40) cc_final: 0.8094 (t0) REVERT: a 145 MET cc_start: 0.8180 (tpp) cc_final: 0.7941 (tpp) REVERT: a 215 MET cc_start: 0.8162 (mpp) cc_final: 0.7643 (mpp) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.1015 time to fit residues: 28.1513 Evaluate side-chains 164 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 57 optimal weight: 30.0000 chunk 40 optimal weight: 0.0970 chunk 86 optimal weight: 0.3980 chunk 45 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.102662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082477 restraints weight = 31962.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084548 restraints weight = 20094.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085919 restraints weight = 14874.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.086828 restraints weight = 12232.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087391 restraints weight = 10782.715| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9395 Z= 0.111 Angle : 0.550 6.978 12735 Z= 0.276 Chirality : 0.040 0.162 1451 Planarity : 0.005 0.045 1628 Dihedral : 4.258 16.745 1229 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1136 helix: 1.15 (0.19), residues: 737 sheet: None (None), residues: 0 loop : 0.43 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 133 TYR 0.008 0.001 TYR Z 146 PHE 0.017 0.001 PHE e 41 TRP 0.019 0.001 TRP e 118 HIS 0.001 0.000 HIS E 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9395) covalent geometry : angle 0.55044 / 0.28 (12735) hydrogen bonds : bond 0.03352 / 2.24 ( 493) hydrogen bonds : angle 3.81652 / 2.71 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.348 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 MET cc_start: 0.8459 (mmp) cc_final: 0.8098 (mmm) REVERT: D 71 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7780 (ttpp) REVERT: D 115 GLN cc_start: 0.8563 (mt0) cc_final: 0.8222 (mp10) REVERT: D 171 LYS cc_start: 0.8611 (tttp) cc_final: 0.7003 (mptt) REVERT: D 216 MET cc_start: 0.7721 (mmt) cc_final: 0.7493 (mmt) REVERT: D 219 CYS cc_start: 0.7755 (m) cc_final: 0.7199 (t) REVERT: E 203 LEU cc_start: 0.8887 (mt) cc_final: 0.8512 (tt) REVERT: e 68 GLN cc_start: 0.5361 (tt0) cc_final: 0.4525 (mm-40) REVERT: e 77 GLU cc_start: 0.6449 (mm-30) cc_final: 0.4892 (mm-30) REVERT: e 132 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8452 (tttt) REVERT: e 216 MET cc_start: 0.8147 (mtp) cc_final: 0.7943 (mtm) REVERT: X 122 ASN cc_start: 0.8446 (p0) cc_final: 0.7867 (t0) REVERT: Z 40 MET cc_start: 0.6019 (tpp) cc_final: 0.5581 (tpt) REVERT: Z 71 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7822 (mmtt) REVERT: Z 174 ARG cc_start: 0.6795 (ttt180) cc_final: 0.6118 (ttp-170) REVERT: Z 186 MET cc_start: 0.8259 (mtm) cc_final: 0.7964 (mtp) REVERT: a 82 ASP cc_start: 0.8039 (m-30) cc_final: 0.7766 (m-30) REVERT: a 132 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8761 (tttt) REVERT: a 133 ARG cc_start: 0.8904 (ttp-110) cc_final: 0.8589 (mtm180) REVERT: a 140 ASN cc_start: 0.8395 (m-40) cc_final: 0.8046 (t0) REVERT: a 145 MET cc_start: 0.8140 (tpp) cc_final: 0.7939 (tpp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1005 time to fit residues: 29.2243 Evaluate side-chains 172 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 97 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.101512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080846 restraints weight = 32152.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082814 restraints weight = 20689.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084066 restraints weight = 15621.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084926 restraints weight = 13076.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085307 restraints weight = 11667.498| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9395 Z= 0.154 Angle : 0.588 6.733 12735 Z= 0.303 Chirality : 0.041 0.151 1451 Planarity : 0.005 0.046 1628 Dihedral : 4.437 17.860 1229 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1136 helix: 1.06 (0.19), residues: 734 sheet: None (None), residues: 0 loop : 0.49 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 168 TYR 0.014 0.002 TYR D 131 PHE 0.015 0.002 PHE a 162 TRP 0.020 0.001 TRP e 118 HIS 0.003 0.001 HIS X 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 9395) covalent geometry : angle 0.58812 / 0.30 (12735) hydrogen bonds : bond 0.03717 / 2.44 ( 493) hydrogen bonds : angle 3.98923 / 2.83 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.384 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: D 69 MET cc_start: 0.8459 (mmp) cc_final: 0.8158 (mmm) REVERT: D 71 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7976 (ttpp) REVERT: D 115 GLN cc_start: 0.8565 (mt0) cc_final: 0.8166 (mp10) REVERT: D 171 LYS cc_start: 0.8700 (tttp) cc_final: 0.7069 (mptt) REVERT: D 199 CYS cc_start: 0.5921 (m) cc_final: 0.5648 (m) REVERT: D 216 MET cc_start: 0.7588 (mmt) cc_final: 0.7242 (mmt) REVERT: D 219 CYS cc_start: 0.7824 (m) cc_final: 0.7212 (t) REVERT: E 203 LEU cc_start: 0.8917 (mt) cc_final: 0.8529 (tt) REVERT: e 68 GLN cc_start: 0.5608 (tt0) cc_final: 0.4857 (mm-40) REVERT: e 216 MET cc_start: 0.8408 (mtp) cc_final: 0.8201 (mtp) REVERT: X 122 ASN cc_start: 0.8519 (p0) cc_final: 0.7954 (t0) REVERT: X 186 MET cc_start: 0.7957 (mtp) cc_final: 0.7662 (mtp) REVERT: X 215 MET cc_start: 0.8964 (mtm) cc_final: 0.8758 (mtt) REVERT: Z 40 MET cc_start: 0.6162 (tpp) cc_final: 0.5731 (tpt) REVERT: Z 71 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7867 (mmtm) REVERT: Z 186 MET cc_start: 0.8226 (mtm) cc_final: 0.7985 (mtp) REVERT: a 82 ASP cc_start: 0.7824 (m-30) cc_final: 0.7620 (m-30) REVERT: a 132 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8778 (tttt) REVERT: a 133 ARG cc_start: 0.8922 (ttp-110) cc_final: 0.8527 (mtm110) REVERT: a 140 ASN cc_start: 0.8436 (m-40) cc_final: 0.8118 (t0) REVERT: a 145 MET cc_start: 0.8210 (tpp) cc_final: 0.7943 (tpp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1078 time to fit residues: 29.8480 Evaluate side-chains 168 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 97 optimal weight: 0.0170 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.102051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.081479 restraints weight = 32192.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083386 restraints weight = 20777.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084665 restraints weight = 15752.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085534 restraints weight = 13181.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085977 restraints weight = 11728.692| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9395 Z= 0.123 Angle : 0.585 5.975 12735 Z= 0.299 Chirality : 0.041 0.139 1451 Planarity : 0.005 0.045 1628 Dihedral : 4.366 17.724 1229 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1136 helix: 1.11 (0.19), residues: 737 sheet: None (None), residues: 0 loop : 0.63 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 144 TYR 0.024 0.002 TYR X 170 PHE 0.016 0.001 PHE e 41 TRP 0.022 0.001 TRP e 118 HIS 0.002 0.000 HIS X 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9395) covalent geometry : angle 0.58528 / 0.30 (12735) hydrogen bonds : bond 0.03511 / 2.27 ( 493) hydrogen bonds : angle 3.91468 / 2.79 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.382 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: D 69 MET cc_start: 0.8503 (mmp) cc_final: 0.8173 (mmm) REVERT: D 71 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7848 (ttpp) REVERT: D 115 GLN cc_start: 0.8571 (mt0) cc_final: 0.8246 (mp10) REVERT: D 171 LYS cc_start: 0.8678 (tttp) cc_final: 0.7033 (mptt) REVERT: D 199 CYS cc_start: 0.5798 (m) cc_final: 0.5542 (m) REVERT: D 216 MET cc_start: 0.7634 (mmt) cc_final: 0.7335 (mmt) REVERT: D 219 CYS cc_start: 0.7676 (m) cc_final: 0.7206 (t) REVERT: E 45 SER cc_start: 0.9123 (p) cc_final: 0.8900 (p) REVERT: E 144 ARG cc_start: 0.8376 (tpm170) cc_final: 0.7885 (tpm170) REVERT: E 203 LEU cc_start: 0.8892 (mt) cc_final: 0.8518 (tt) REVERT: e 68 GLN cc_start: 0.5603 (tt0) cc_final: 0.4792 (mm-40) REVERT: e 77 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5057 (mm-30) REVERT: e 119 MET cc_start: 0.7642 (mmt) cc_final: 0.6518 (mtt) REVERT: e 132 LYS cc_start: 0.9056 (tmtt) cc_final: 0.8466 (tptt) REVERT: X 118 TRP cc_start: 0.6802 (m-10) cc_final: 0.6417 (m-90) REVERT: X 122 ASN cc_start: 0.8510 (p0) cc_final: 0.7966 (t0) REVERT: X 186 MET cc_start: 0.8094 (mtp) cc_final: 0.7852 (mtp) REVERT: Z 40 MET cc_start: 0.6048 (tpp) cc_final: 0.5607 (tpt) REVERT: Z 71 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7845 (mmtm) REVERT: Z 174 ARG cc_start: 0.6768 (ttt180) cc_final: 0.6094 (ttp-170) REVERT: Z 186 MET cc_start: 0.8232 (mtm) cc_final: 0.7934 (mtp) REVERT: a 82 ASP cc_start: 0.8138 (m-30) cc_final: 0.7862 (m-30) REVERT: a 132 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8804 (tttt) REVERT: a 133 ARG cc_start: 0.8913 (ttp-110) cc_final: 0.8599 (mtm180) REVERT: a 140 ASN cc_start: 0.8317 (m-40) cc_final: 0.7994 (t0) REVERT: a 145 MET cc_start: 0.8079 (tpp) cc_final: 0.7872 (tpp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1050 time to fit residues: 30.4775 Evaluate side-chains 172 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080701 restraints weight = 31090.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082515 restraints weight = 20526.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083699 restraints weight = 15757.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084501 restraints weight = 13306.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085010 restraints weight = 11927.718| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9395 Z= 0.164 Angle : 0.629 7.274 12735 Z= 0.322 Chirality : 0.042 0.140 1451 Planarity : 0.005 0.046 1628 Dihedral : 4.588 22.070 1229 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1136 helix: 0.93 (0.19), residues: 727 sheet: None (None), residues: 0 loop : 0.63 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 144 TYR 0.015 0.002 TYR a 170 PHE 0.015 0.002 PHE a 162 TRP 0.024 0.001 TRP e 118 HIS 0.003 0.001 HIS X 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 9395) covalent geometry : angle 0.62904 / 0.32 (12735) hydrogen bonds : bond 0.03796 / 2.46 ( 493) hydrogen bonds : angle 4.07904 / 2.89 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 MET cc_start: 0.8521 (mmp) cc_final: 0.8174 (mmm) REVERT: D 71 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7964 (ttpp) REVERT: D 115 GLN cc_start: 0.8577 (mt0) cc_final: 0.8201 (mp10) REVERT: D 171 LYS cc_start: 0.8714 (tttp) cc_final: 0.6998 (mptt) REVERT: D 199 CYS cc_start: 0.5864 (m) cc_final: 0.5607 (m) REVERT: D 216 MET cc_start: 0.7669 (mmt) cc_final: 0.7259 (mmt) REVERT: D 219 CYS cc_start: 0.7678 (m) cc_final: 0.7186 (t) REVERT: E 51 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8627 (tm-30) REVERT: E 203 LEU cc_start: 0.8890 (mt) cc_final: 0.8521 (tt) REVERT: e 68 GLN cc_start: 0.5740 (tt0) cc_final: 0.4786 (mm-40) REVERT: e 119 MET cc_start: 0.7650 (mmt) cc_final: 0.6616 (mtt) REVERT: Z 40 MET cc_start: 0.6166 (tpp) cc_final: 0.5705 (tpt) REVERT: Z 71 LYS cc_start: 0.8405 (mtpp) cc_final: 0.7905 (mmtm) REVERT: Z 174 ARG cc_start: 0.6799 (ttt180) cc_final: 0.6100 (ttp-170) REVERT: Z 186 MET cc_start: 0.8187 (mtm) cc_final: 0.7939 (mtp) REVERT: a 82 ASP cc_start: 0.8005 (m-30) cc_final: 0.7749 (m-30) REVERT: a 132 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8791 (tttt) REVERT: a 133 ARG cc_start: 0.8915 (ttp-110) cc_final: 0.8554 (mtm110) REVERT: a 140 ASN cc_start: 0.8412 (m-40) cc_final: 0.8101 (t0) REVERT: a 145 MET cc_start: 0.8121 (tpp) cc_final: 0.7882 (tpp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1030 time to fit residues: 28.8157 Evaluate side-chains 168 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 0.0020 chunk 47 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 0.1980 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 69 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093684 restraints weight = 31601.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095723 restraints weight = 20322.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097072 restraints weight = 15286.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097948 restraints weight = 12706.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.098423 restraints weight = 11292.614| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9395 Z= 0.118 Angle : 0.614 8.083 12735 Z= 0.308 Chirality : 0.041 0.141 1451 Planarity : 0.005 0.055 1628 Dihedral : 4.285 22.239 1229 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1136 helix: 1.01 (0.19), residues: 734 sheet: None (None), residues: 0 loop : 0.82 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 144 TYR 0.027 0.002 TYR e 131 PHE 0.020 0.001 PHE e 41 TRP 0.023 0.001 TRP X 118 HIS 0.002 0.000 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9395) covalent geometry : angle 0.61422 / 0.31 (12735) hydrogen bonds : bond 0.03164 / 2.07 ( 493) hydrogen bonds : angle 3.90750 / 2.78 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.367 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: symmetry clash REVERT: D 69 MET cc_start: 0.8421 (mmp) cc_final: 0.8128 (mmm) REVERT: D 115 GLN cc_start: 0.8590 (mt0) cc_final: 0.8261 (mp10) REVERT: D 171 LYS cc_start: 0.8613 (tttp) cc_final: 0.6989 (mptt) REVERT: D 179 SER cc_start: 0.7576 (t) cc_final: 0.7345 (p) REVERT: D 199 CYS cc_start: 0.6292 (m) cc_final: 0.5987 (m) REVERT: D 216 MET cc_start: 0.7525 (mmt) cc_final: 0.7312 (mmt) REVERT: D 219 CYS cc_start: 0.7571 (m) cc_final: 0.7202 (t) REVERT: E 203 LEU cc_start: 0.8827 (mt) cc_final: 0.8465 (tt) REVERT: e 68 GLN cc_start: 0.5560 (tt0) cc_final: 0.4795 (mm-40) REVERT: e 77 GLU cc_start: 0.6434 (mm-30) cc_final: 0.4927 (mm-30) REVERT: e 119 MET cc_start: 0.7679 (mmt) cc_final: 0.6601 (mtt) REVERT: e 193 GLN cc_start: 0.8170 (tp40) cc_final: 0.7907 (tm-30) REVERT: X 176 GLU cc_start: 0.8224 (tp30) cc_final: 0.8012 (tm-30) REVERT: Z 40 MET cc_start: 0.6038 (tpp) cc_final: 0.5540 (tpt) REVERT: Z 71 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7781 (mmtt) REVERT: Z 174 ARG cc_start: 0.7011 (ttt180) cc_final: 0.6398 (ttp-170) REVERT: a 68 GLN cc_start: 0.8315 (mm110) cc_final: 0.7928 (mm-40) REVERT: a 82 ASP cc_start: 0.8071 (m-30) cc_final: 0.7788 (m-30) REVERT: a 132 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8812 (tttt) REVERT: a 133 ARG cc_start: 0.8929 (ttp-110) cc_final: 0.8598 (mtm180) REVERT: a 140 ASN cc_start: 0.8319 (m-40) cc_final: 0.7967 (t0) REVERT: a 145 MET cc_start: 0.7984 (tpp) cc_final: 0.7744 (tpp) REVERT: a 215 MET cc_start: 0.8066 (mpp) cc_final: 0.7620 (mpp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1073 time to fit residues: 30.7302 Evaluate side-chains 179 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 115 GLN ** e 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.100765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080299 restraints weight = 32504.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082152 restraints weight = 21358.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083376 restraints weight = 16327.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084187 restraints weight = 13739.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084700 restraints weight = 12297.452| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9395 Z= 0.176 Angle : 0.662 7.302 12735 Z= 0.340 Chirality : 0.043 0.160 1451 Planarity : 0.005 0.054 1628 Dihedral : 4.514 25.379 1229 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1136 helix: 0.90 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.73 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG a 144 TYR 0.023 0.002 TYR e 131 PHE 0.016 0.002 PHE a 162 TRP 0.067 0.002 TRP a 118 HIS 0.004 0.001 HIS X 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 9395) covalent geometry : angle 0.66220 / 0.34 (12735) hydrogen bonds : bond 0.03760 / 2.43 ( 493) hydrogen bonds : angle 4.17824 / 2.97 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1501.13 seconds wall clock time: 26 minutes 33.90 seconds (1593.90 seconds total)