Starting phenix.real_space_refine on Wed Mar 4 21:03:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lqh_0945/03_2026/6lqh_0945.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lqh_0945/03_2026/6lqh_0945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lqh_0945/03_2026/6lqh_0945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lqh_0945/03_2026/6lqh_0945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lqh_0945/03_2026/6lqh_0945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lqh_0945/03_2026/6lqh_0945.map" } resolution = 2.94 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= 0.001 sd= 0.006 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 54 5.16 5 C 10503 2.51 5 N 2853 2.21 5 O 3213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16623 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "a" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B, C, D, E, F, G, H, I, b, c, d, e, f, g, h, i Time building chain proxies: 1.74, per 1000 atoms: 0.10 Number of scatterers: 16623 At special positions: 0 Unit cell: (112, 111, 115, 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 54 16.00 O 3213 8.00 N 2853 7.00 C 10503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 761.5 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 26.2% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 226 through 249 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 226 through 249 Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 226 through 249 Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 226 through 249 Processing helix chain 'F' and resid 81 through 90 Processing helix chain 'F' and resid 100 through 115 Processing helix chain 'F' and resid 226 through 249 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 226 through 249 Processing helix chain 'H' and resid 81 through 90 Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 226 through 249 Processing helix chain 'I' and resid 81 through 90 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'a' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA a 39 " --> pdb=" O PRO a 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE a 40 " --> pdb=" O ASN a 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA b 39 " --> pdb=" O PRO b 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE b 40 " --> pdb=" O ASN b 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA c 39 " --> pdb=" O PRO c 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE c 40 " --> pdb=" O ASN c 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA d 39 " --> pdb=" O PRO d 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE d 40 " --> pdb=" O ASN d 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA e 39 " --> pdb=" O PRO e 35 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE e 40 " --> pdb=" O ASN e 36 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA f 39 " --> pdb=" O PRO f 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE f 40 " --> pdb=" O ASN f 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 47 removed outlier: 4.334A pdb=" N ALA g 39 " --> pdb=" O PRO g 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE g 40 " --> pdb=" O ASN g 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA h 39 " --> pdb=" O PRO h 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE h 40 " --> pdb=" O ASN h 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 47 removed outlier: 4.335A pdb=" N ALA i 39 " --> pdb=" O PRO i 35 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE i 40 " --> pdb=" O ASN i 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A 149 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 207 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE B 186 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN B 180 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 163 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 155 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR B 165 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY B 153 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR B 167 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER B 151 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 169 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN B 171 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER B 147 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA B 173 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR B 145 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN B 175 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 143 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG B 177 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER B 141 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 179 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU B 139 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 136 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 52 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 96 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 51 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL B 149 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG E 213 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E 207 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 186 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN E 180 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA E 163 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY E 155 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR E 165 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY E 153 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR E 167 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER E 151 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU E 169 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN E 171 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER E 147 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA E 173 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR E 145 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN E 175 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 143 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG E 177 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER E 141 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL E 179 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU E 139 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE E 136 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER E 52 " --> pdb=" O ILE E 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL E 149 " --> pdb=" O ASN H 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG H 213 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG H 207 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE H 186 " --> pdb=" O ASN H 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN H 180 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA H 163 " --> pdb=" O GLY H 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY H 155 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR H 165 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY H 153 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR H 167 " --> pdb=" O SER H 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER H 151 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 169 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN H 171 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER H 147 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA H 173 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR H 145 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN H 175 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE H 143 " --> pdb=" O ASN H 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG H 177 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER H 141 " --> pdb=" O ARG H 177 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL H 179 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU H 139 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE H 136 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 52 " --> pdb=" O ILE H 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 56 through 57 removed outlier: 7.099A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL H 149 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 207 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE F 186 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN F 180 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA F 163 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY F 155 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR F 165 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY F 153 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR F 167 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER F 151 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 169 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN F 171 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER F 147 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA F 173 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR F 145 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN F 175 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE F 143 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ARG F 177 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER F 141 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL F 179 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU F 139 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE F 136 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 52 " --> pdb=" O ILE F 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 149 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 207 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE D 186 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN D 180 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 163 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY D 155 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 165 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY D 153 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR D 167 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER D 151 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU D 169 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN D 171 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER D 147 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA D 173 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR D 145 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN D 175 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE D 143 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG D 177 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER D 141 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL D 179 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU D 139 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D 136 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 52 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL D 149 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 207 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 186 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN C 180 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C 163 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY C 155 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR C 165 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY C 153 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR C 167 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 151 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 169 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN C 171 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER C 147 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA C 173 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 145 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN C 175 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 143 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG C 177 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER C 141 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 179 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU C 139 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C 136 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 52 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 96 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 51 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 149 " --> pdb=" O ASN G 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG G 213 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG G 207 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE G 186 " --> pdb=" O ASN G 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN G 180 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA G 163 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY G 155 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR G 165 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY G 153 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR G 167 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER G 151 " --> pdb=" O TYR G 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU G 169 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN G 171 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER G 147 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA G 173 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR G 145 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN G 175 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE G 143 " --> pdb=" O ASN G 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG G 177 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER G 141 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL G 179 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU G 139 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE G 136 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER G 52 " --> pdb=" O ILE G 136 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE G 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU G 96 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL G 51 " --> pdb=" O LEU G 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 56 through 57 removed outlier: 7.100A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL G 149 " --> pdb=" O ASN I 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG I 207 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE I 186 " --> pdb=" O ASN I 180 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN I 180 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA I 163 " --> pdb=" O GLY I 155 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY I 155 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR I 165 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY I 153 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR I 167 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER I 151 " --> pdb=" O TYR I 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU I 169 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN I 171 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER I 147 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA I 173 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR I 145 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN I 175 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE I 143 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG I 177 " --> pdb=" O SER I 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER I 141 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL I 179 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU I 139 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE I 136 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER I 52 " --> pdb=" O ILE I 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 56 through 57 removed outlier: 7.099A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL I 149 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 207 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 186 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN A 180 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 163 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY A 155 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR A 165 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY A 153 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR A 167 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 151 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 169 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 171 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER A 147 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA A 173 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR A 145 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN A 175 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 143 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A 177 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER A 141 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 179 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU A 139 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 136 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 52 " --> pdb=" O ILE A 136 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5597 1.34 - 1.45: 2474 1.45 - 1.57: 8732 1.57 - 1.68: 0 1.68 - 1.80: 99 Bond restraints: 16902 Sorted by residual: bond pdb=" CG PRO C 67 " pdb=" CD PRO C 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.17e+00 bond pdb=" CG PRO H 67 " pdb=" CD PRO H 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.17e+00 bond pdb=" CG PRO I 67 " pdb=" CD PRO I 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.14e+00 bond pdb=" CG PRO G 67 " pdb=" CD PRO G 67 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.14e+00 bond pdb=" CG PRO D 67 " pdb=" CD PRO D 67 " ideal model delta sigma weight residual 1.512 1.473 0.039 2.70e-02 1.37e+03 2.10e+00 ... (remaining 16897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 21972 1.75 - 3.49: 780 3.49 - 5.24: 126 5.24 - 6.99: 18 6.99 - 8.73: 27 Bond angle restraints: 22923 Sorted by residual: angle pdb=" N GLY d 33 " pdb=" CA GLY d 33 " pdb=" C GLY d 33 " ideal model delta sigma weight residual 113.18 121.91 -8.73 2.37e+00 1.78e-01 1.36e+01 angle pdb=" N GLY g 33 " pdb=" CA GLY g 33 " pdb=" C GLY g 33 " ideal model delta sigma weight residual 113.18 121.89 -8.71 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY f 33 " pdb=" CA GLY f 33 " pdb=" C GLY f 33 " ideal model delta sigma weight residual 113.18 121.88 -8.70 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY a 33 " pdb=" CA GLY a 33 " pdb=" C GLY a 33 " ideal model delta sigma weight residual 113.18 121.88 -8.70 2.37e+00 1.78e-01 1.35e+01 angle pdb=" N GLY h 33 " pdb=" CA GLY h 33 " pdb=" C GLY h 33 " ideal model delta sigma weight residual 113.18 121.87 -8.69 2.37e+00 1.78e-01 1.35e+01 ... (remaining 22918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 8668 15.68 - 31.37: 899 31.37 - 47.05: 243 47.05 - 62.73: 189 62.73 - 78.42: 36 Dihedral angle restraints: 10035 sinusoidal: 3888 harmonic: 6147 Sorted by residual: dihedral pdb=" CA GLN A 99 " pdb=" C GLN A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLN E 99 " pdb=" C GLN E 99 " pdb=" N GLY E 100 " pdb=" CA GLY E 100 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLN H 99 " pdb=" C GLN H 99 " pdb=" N GLY H 100 " pdb=" CA GLY H 100 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 10032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1410 0.037 - 0.074: 842 0.074 - 0.111: 244 0.111 - 0.148: 89 0.148 - 0.185: 16 Chirality restraints: 2601 Sorted by residual: chirality pdb=" CA PHE h 31 " pdb=" N PHE h 31 " pdb=" C PHE h 31 " pdb=" CB PHE h 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA PHE d 31 " pdb=" N PHE d 31 " pdb=" C PHE d 31 " pdb=" CB PHE d 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA PHE c 31 " pdb=" N PHE c 31 " pdb=" C PHE c 31 " pdb=" CB PHE c 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 2598 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE f 31 " 0.014 2.00e-02 2.50e+03 1.31e-02 3.02e+00 pdb=" CG PHE f 31 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE f 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE f 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE f 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE f 31 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE f 31 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE h 31 " 0.014 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE h 31 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE h 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE h 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE h 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE h 31 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE h 31 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE b 31 " -0.014 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE b 31 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE b 31 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE b 31 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE b 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE b 31 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE b 31 " -0.002 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4554 2.79 - 3.32: 15055 3.32 - 3.85: 29376 3.85 - 4.37: 35899 4.37 - 4.90: 62728 Nonbonded interactions: 147612 Sorted by model distance: nonbonded pdb=" O SER e 50 " pdb=" OG SER e 50 " model vdw 2.268 3.040 nonbonded pdb=" O SER f 50 " pdb=" OG SER f 50 " model vdw 2.268 3.040 nonbonded pdb=" O SER d 50 " pdb=" OG SER d 50 " model vdw 2.269 3.040 nonbonded pdb=" O SER b 50 " pdb=" OG SER b 50 " model vdw 2.269 3.040 nonbonded pdb=" O SER c 50 " pdb=" OG SER c 50 " model vdw 2.269 3.040 ... (remaining 147607 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.850 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.008 0.041 16902 Z= 0.371 Angle : 0.825 8.734 22923 Z= 0.461 Chirality : 0.051 0.185 2601 Planarity : 0.004 0.027 3024 Dihedral : 17.093 78.418 6111 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 9.05 % Allowed : 11.56 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.16), residues: 2124 helix: -1.15 (0.17), residues: 576 sheet: -0.81 (0.21), residues: 666 loop : -3.05 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG c 27 TYR 0.013 0.002 TYR E 158 PHE 0.031 0.002 PHE f 31 TRP 0.010 0.003 TRP A 252 Details of bonding type rmsd covalent geometry : bond 0.00825 (16902) covalent geometry : angle 0.82527 (22923) hydrogen bonds : bond 0.13207 ( 774) hydrogen bonds : angle 7.29299 ( 2295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 427 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8917 (mttp) cc_final: 0.8704 (mttt) REVERT: A 109 LYS cc_start: 0.8794 (mttp) cc_final: 0.8560 (mttt) REVERT: A 232 MET cc_start: 0.7953 (tpt) cc_final: 0.7439 (tpt) REVERT: B 70 ASN cc_start: 0.8422 (m-40) cc_final: 0.8152 (m-40) REVERT: B 170 ASP cc_start: 0.8106 (m-30) cc_final: 0.7904 (m-30) REVERT: C 70 ASN cc_start: 0.8420 (m-40) cc_final: 0.8019 (m-40) REVERT: C 166 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: C 185 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: D 70 ASN cc_start: 0.8450 (m-40) cc_final: 0.8060 (m-40) REVERT: D 88 LYS cc_start: 0.8891 (tptp) cc_final: 0.8678 (tptm) REVERT: D 109 LYS cc_start: 0.8838 (mttp) cc_final: 0.8538 (mtmt) REVERT: D 137 MET cc_start: 0.8463 (ttm) cc_final: 0.8124 (ttp) REVERT: D 141 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8908 (p) REVERT: D 166 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 170 ASP cc_start: 0.8182 (m-30) cc_final: 0.7971 (m-30) REVERT: E 109 LYS cc_start: 0.8863 (mttp) cc_final: 0.8661 (mttp) REVERT: E 166 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: E 170 ASP cc_start: 0.8192 (m-30) cc_final: 0.7931 (m-30) REVERT: E 185 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: F 70 ASN cc_start: 0.8410 (m-40) cc_final: 0.8144 (m110) REVERT: F 102 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7771 (tp40) REVERT: F 137 MET cc_start: 0.8380 (ttm) cc_final: 0.8083 (ttp) REVERT: F 141 SER cc_start: 0.9180 (OUTLIER) cc_final: 0.8899 (p) REVERT: F 166 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: F 213 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.7917 (mmt180) REVERT: F 240 ILE cc_start: 0.8779 (mt) cc_final: 0.8549 (mp) REVERT: G 59 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7540 (mt-10) REVERT: G 88 LYS cc_start: 0.8909 (tptp) cc_final: 0.8581 (mtpp) REVERT: G 109 LYS cc_start: 0.8799 (mttp) cc_final: 0.8527 (mttt) REVERT: G 166 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: H 59 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7641 (mt-10) REVERT: H 109 LYS cc_start: 0.8825 (mttp) cc_final: 0.8594 (mttt) REVERT: H 141 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8942 (p) REVERT: H 185 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: H 193 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8469 (t) REVERT: H 200 GLU cc_start: 0.7820 (tt0) cc_final: 0.7604 (tt0) REVERT: I 64 LYS cc_start: 0.8904 (mttp) cc_final: 0.8660 (mttt) REVERT: I 70 ASN cc_start: 0.8486 (m-40) cc_final: 0.8274 (m110) REVERT: I 88 LYS cc_start: 0.8909 (tptp) cc_final: 0.8596 (mtpp) REVERT: I 109 LYS cc_start: 0.8795 (mttp) cc_final: 0.8573 (mttp) REVERT: I 167 TYR cc_start: 0.8685 (p90) cc_final: 0.8439 (p90) REVERT: I 185 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: e 44 SER cc_start: 0.8427 (p) cc_final: 0.8192 (p) REVERT: h 44 SER cc_start: 0.8536 (p) cc_final: 0.8316 (p) outliers start: 162 outliers final: 57 residues processed: 559 average time/residue: 0.6143 time to fit residues: 378.2944 Evaluate side-chains 375 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 252 TRP Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain d residue 50 SER Chi-restraints excluded: chain e residue 50 SER Chi-restraints excluded: chain f residue 50 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 148 ASN A 212 GLN B 62 GLN B 148 ASN C 62 GLN C 180 ASN D 62 GLN D 77 GLN D 148 ASN D 180 ASN E 62 GLN E 148 ASN E 171 GLN F 62 GLN F 77 GLN F 148 ASN F 212 GLN G 62 GLN G 70 ASN G 77 GLN G 180 ASN H 62 GLN I 62 GLN I 77 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.138214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111688 restraints weight = 18174.249| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.37 r_work: 0.3102 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16902 Z= 0.186 Angle : 0.678 8.124 22923 Z= 0.356 Chirality : 0.047 0.143 2601 Planarity : 0.004 0.024 3024 Dihedral : 9.303 82.244 2422 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.69 % Allowed : 17.64 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.52 (0.17), residues: 2124 helix: 0.64 (0.20), residues: 585 sheet: -0.69 (0.22), residues: 612 loop : -2.34 (0.16), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 207 TYR 0.010 0.001 TYR C 199 PHE 0.022 0.002 PHE d 31 TRP 0.008 0.002 TRP F 92 Details of bonding type rmsd covalent geometry : bond 0.00426 (16902) covalent geometry : angle 0.67779 (22923) hydrogen bonds : bond 0.03091 ( 774) hydrogen bonds : angle 5.32648 ( 2295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 308 time to evaluate : 0.681 Fit side-chains REVERT: A 64 LYS cc_start: 0.9033 (mttp) cc_final: 0.8814 (mttt) REVERT: A 66 TYR cc_start: 0.8737 (t80) cc_final: 0.8461 (t80) REVERT: A 109 LYS cc_start: 0.8945 (mttp) cc_final: 0.8734 (mttt) REVERT: B 70 ASN cc_start: 0.8591 (m-40) cc_final: 0.8281 (m-40) REVERT: B 146 GLU cc_start: 0.7759 (tp30) cc_final: 0.7395 (mm-30) REVERT: B 213 ARG cc_start: 0.7927 (mmt-90) cc_final: 0.7576 (mmt180) REVERT: B 249 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7400 (ptp90) REVERT: C 59 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8010 (mt-10) REVERT: C 70 ASN cc_start: 0.8573 (m-40) cc_final: 0.8249 (m-40) REVERT: C 185 GLU cc_start: 0.8388 (tt0) cc_final: 0.8149 (pt0) REVERT: C 249 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6991 (ptm-80) REVERT: D 70 ASN cc_start: 0.8666 (m-40) cc_final: 0.8333 (m-40) REVERT: D 88 LYS cc_start: 0.8778 (tptp) cc_final: 0.8523 (tptm) REVERT: D 137 MET cc_start: 0.9038 (ttm) cc_final: 0.8682 (ttp) REVERT: D 146 GLU cc_start: 0.7957 (tp30) cc_final: 0.7556 (mm-30) REVERT: D 166 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: D 249 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6911 (ptm-80) REVERT: E 59 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7868 (mt-10) REVERT: E 109 LYS cc_start: 0.8947 (mttp) cc_final: 0.8736 (mttp) REVERT: E 185 GLU cc_start: 0.8368 (tt0) cc_final: 0.8130 (pt0) REVERT: F 70 ASN cc_start: 0.8589 (m-40) cc_final: 0.8376 (m-40) REVERT: F 166 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: F 213 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7836 (mmt-90) REVERT: F 219 VAL cc_start: 0.9005 (t) cc_final: 0.8694 (p) REVERT: F 249 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7231 (ptm-80) REVERT: G 59 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7919 (mt-10) REVERT: G 88 LYS cc_start: 0.8785 (tptp) cc_final: 0.8415 (mtpp) REVERT: H 59 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8035 (mt-10) REVERT: H 146 GLU cc_start: 0.7746 (tp30) cc_final: 0.7440 (mm-30) REVERT: H 249 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7006 (ptm160) REVERT: I 59 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8080 (mt-10) REVERT: I 70 ASN cc_start: 0.8680 (m-40) cc_final: 0.8476 (m-40) REVERT: I 146 GLU cc_start: 0.7669 (tp30) cc_final: 0.7435 (mm-30) REVERT: I 185 GLU cc_start: 0.8496 (tt0) cc_final: 0.8255 (pt0) REVERT: b 44 SER cc_start: 0.8358 (p) cc_final: 0.8010 (p) REVERT: e 44 SER cc_start: 0.8111 (p) cc_final: 0.7756 (p) REVERT: f 44 SER cc_start: 0.8294 (p) cc_final: 0.7954 (p) REVERT: h 44 SER cc_start: 0.8087 (p) cc_final: 0.7837 (p) outliers start: 66 outliers final: 31 residues processed: 359 average time/residue: 0.6683 time to fit residues: 262.6491 Evaluate side-chains 315 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 180 ASN B 148 ASN B 180 ASN C 148 ASN D 148 ASN D 166 GLN E 148 ASN E 180 ASN F 180 ASN H 57 GLN H 180 ASN I 148 ASN I 180 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.136121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109531 restraints weight = 18419.744| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.36 r_work: 0.3075 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 16902 Z= 0.240 Angle : 0.691 8.083 22923 Z= 0.360 Chirality : 0.048 0.147 2601 Planarity : 0.004 0.027 3024 Dihedral : 8.335 74.443 2363 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.08 % Allowed : 17.92 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.18 (0.18), residues: 2124 helix: 1.14 (0.20), residues: 585 sheet: -0.55 (0.21), residues: 702 loop : -2.40 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 249 TYR 0.014 0.001 TYR C 199 PHE 0.025 0.002 PHE d 31 TRP 0.011 0.002 TRP F 92 Details of bonding type rmsd covalent geometry : bond 0.00566 (16902) covalent geometry : angle 0.69102 (22923) hydrogen bonds : bond 0.03181 ( 774) hydrogen bonds : angle 5.17295 ( 2295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 298 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8733 (t80) cc_final: 0.8488 (t80) REVERT: A 97 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: A 109 LYS cc_start: 0.8919 (mttp) cc_final: 0.8719 (mttp) REVERT: A 249 ARG cc_start: 0.7454 (ptt-90) cc_final: 0.6830 (ptm-80) REVERT: B 70 ASN cc_start: 0.8700 (m-40) cc_final: 0.8415 (m-40) REVERT: B 146 GLU cc_start: 0.7762 (tp30) cc_final: 0.7347 (mm-30) REVERT: B 213 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7474 (mmt180) REVERT: B 249 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6964 (ptm-80) REVERT: C 70 ASN cc_start: 0.8621 (m-40) cc_final: 0.8333 (m-40) REVERT: C 146 GLU cc_start: 0.7821 (tp30) cc_final: 0.7333 (tp30) REVERT: C 185 GLU cc_start: 0.8430 (tt0) cc_final: 0.8162 (pt0) REVERT: C 249 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7007 (ptm-80) REVERT: D 70 ASN cc_start: 0.8740 (m-40) cc_final: 0.8386 (m-40) REVERT: D 88 LYS cc_start: 0.8775 (tptp) cc_final: 0.8487 (tptm) REVERT: D 137 MET cc_start: 0.9040 (ttm) cc_final: 0.8673 (ttp) REVERT: D 146 GLU cc_start: 0.7930 (tp30) cc_final: 0.7516 (mm-30) REVERT: D 249 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6966 (ptm-80) REVERT: E 59 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 109 LYS cc_start: 0.8964 (mttp) cc_final: 0.8750 (mttt) REVERT: E 146 GLU cc_start: 0.7987 (tp30) cc_final: 0.7587 (tp30) REVERT: E 166 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: E 185 GLU cc_start: 0.8306 (tt0) cc_final: 0.8104 (pt0) REVERT: F 131 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8484 (mp) REVERT: F 170 ASP cc_start: 0.8536 (m-30) cc_final: 0.8294 (m-30) REVERT: F 219 VAL cc_start: 0.8990 (t) cc_final: 0.8722 (p) REVERT: F 249 ARG cc_start: 0.7654 (ptt-90) cc_final: 0.7112 (ptm160) REVERT: G 88 LYS cc_start: 0.8838 (tptp) cc_final: 0.8439 (mtpp) REVERT: G 146 GLU cc_start: 0.7998 (tp30) cc_final: 0.7548 (mm-30) REVERT: G 200 GLU cc_start: 0.8405 (tt0) cc_final: 0.8030 (tt0) REVERT: H 59 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8117 (mt-10) REVERT: H 146 GLU cc_start: 0.7822 (tp30) cc_final: 0.7428 (mm-30) REVERT: H 249 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6917 (ptm160) REVERT: I 70 ASN cc_start: 0.8749 (m-40) cc_final: 0.8522 (m-40) REVERT: I 97 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: I 146 GLU cc_start: 0.7695 (tp30) cc_final: 0.7347 (mm-30) REVERT: I 170 ASP cc_start: 0.8686 (m-30) cc_final: 0.8479 (m-30) REVERT: I 185 GLU cc_start: 0.8494 (tt0) cc_final: 0.8272 (pt0) REVERT: e 44 SER cc_start: 0.8072 (p) cc_final: 0.7755 (p) REVERT: f 44 SER cc_start: 0.8219 (p) cc_final: 0.7915 (p) REVERT: h 44 SER cc_start: 0.8060 (p) cc_final: 0.7810 (p) outliers start: 73 outliers final: 39 residues processed: 358 average time/residue: 0.6875 time to fit residues: 269.4537 Evaluate side-chains 327 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 168 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 46 optimal weight: 0.0070 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN D 148 ASN E 148 ASN F 148 ASN G 148 ASN H 57 GLN H 148 ASN I 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116486 restraints weight = 18318.364| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.41 r_work: 0.3174 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16902 Z= 0.120 Angle : 0.586 7.502 22923 Z= 0.304 Chirality : 0.045 0.137 2601 Planarity : 0.003 0.030 3024 Dihedral : 7.070 68.436 2350 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.02 % Allowed : 18.65 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.69 (0.19), residues: 2124 helix: 2.06 (0.22), residues: 585 sheet: -0.66 (0.21), residues: 738 loop : -2.18 (0.18), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 249 TYR 0.011 0.001 TYR C 199 PHE 0.016 0.001 PHE h 31 TRP 0.009 0.002 TRP C 252 Details of bonding type rmsd covalent geometry : bond 0.00284 (16902) covalent geometry : angle 0.58620 (22923) hydrogen bonds : bond 0.02392 ( 774) hydrogen bonds : angle 4.65512 ( 2295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 273 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8625 (t80) cc_final: 0.8314 (t80) REVERT: A 219 VAL cc_start: 0.8852 (t) cc_final: 0.8595 (p) REVERT: A 249 ARG cc_start: 0.7643 (ptt-90) cc_final: 0.6880 (ptm160) REVERT: B 88 LYS cc_start: 0.8485 (tptm) cc_final: 0.8212 (tptp) REVERT: B 109 LYS cc_start: 0.8846 (mttp) cc_final: 0.8561 (mtmt) REVERT: B 146 GLU cc_start: 0.7560 (tp30) cc_final: 0.7186 (mm-30) REVERT: B 213 ARG cc_start: 0.7750 (mmt-90) cc_final: 0.7304 (mmt180) REVERT: B 219 VAL cc_start: 0.8835 (t) cc_final: 0.8565 (p) REVERT: B 249 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6827 (ptm-80) REVERT: C 146 GLU cc_start: 0.7353 (tp30) cc_final: 0.6911 (tp30) REVERT: C 185 GLU cc_start: 0.8424 (tt0) cc_final: 0.8172 (pt0) REVERT: C 249 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6817 (ptm160) REVERT: D 70 ASN cc_start: 0.8632 (m-40) cc_final: 0.8294 (m-40) REVERT: D 88 LYS cc_start: 0.8575 (tptp) cc_final: 0.8269 (tptm) REVERT: D 109 LYS cc_start: 0.8712 (mttt) cc_final: 0.8461 (mtmt) REVERT: D 137 MET cc_start: 0.9009 (ttm) cc_final: 0.8624 (ttp) REVERT: D 146 GLU cc_start: 0.7726 (tp30) cc_final: 0.7289 (mm-30) REVERT: D 249 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6948 (ptm160) REVERT: E 146 GLU cc_start: 0.7566 (tp30) cc_final: 0.7232 (mm-30) REVERT: E 185 GLU cc_start: 0.8256 (tt0) cc_final: 0.8035 (pt0) REVERT: E 219 VAL cc_start: 0.8631 (t) cc_final: 0.8377 (p) REVERT: F 146 GLU cc_start: 0.7705 (tp30) cc_final: 0.7325 (mm-30) REVERT: F 170 ASP cc_start: 0.8489 (m-30) cc_final: 0.8264 (m-30) REVERT: F 213 ARG cc_start: 0.7885 (mmt-90) cc_final: 0.7651 (mmt-90) REVERT: F 219 VAL cc_start: 0.8909 (t) cc_final: 0.8623 (p) REVERT: F 249 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7188 (ptm160) REVERT: G 88 LYS cc_start: 0.8629 (tptp) cc_final: 0.8254 (mtpp) REVERT: G 146 GLU cc_start: 0.7586 (tp30) cc_final: 0.7191 (mm-30) REVERT: H 59 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7957 (mt-10) REVERT: H 146 GLU cc_start: 0.7504 (tp30) cc_final: 0.7076 (mm-30) REVERT: H 232 MET cc_start: 0.8352 (tpt) cc_final: 0.8086 (tpp) REVERT: H 249 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6973 (ptm-80) REVERT: I 131 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8245 (mp) REVERT: I 146 GLU cc_start: 0.7450 (tp30) cc_final: 0.7204 (mm-30) REVERT: I 185 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: f 44 SER cc_start: 0.7876 (p) cc_final: 0.7638 (p) REVERT: h 44 SER cc_start: 0.7633 (p) cc_final: 0.7406 (p) outliers start: 72 outliers final: 34 residues processed: 325 average time/residue: 0.6397 time to fit residues: 228.3239 Evaluate side-chains 288 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 252 TRP Chi-restraints excluded: chain f residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.2980 chunk 202 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 212 GLN D 148 ASN F 148 ASN G 70 ASN H 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110213 restraints weight = 18502.502| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.36 r_work: 0.3065 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16902 Z= 0.266 Angle : 0.693 8.356 22923 Z= 0.364 Chirality : 0.049 0.144 2601 Planarity : 0.004 0.027 3024 Dihedral : 7.631 80.990 2347 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.91 % Allowed : 19.32 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.71 (0.18), residues: 2124 helix: 1.63 (0.21), residues: 585 sheet: -0.19 (0.21), residues: 702 loop : -2.30 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 207 TYR 0.015 0.002 TYR C 199 PHE 0.025 0.002 PHE d 31 TRP 0.013 0.003 TRP B 92 Details of bonding type rmsd covalent geometry : bond 0.00624 (16902) covalent geometry : angle 0.69259 (22923) hydrogen bonds : bond 0.03201 ( 774) hydrogen bonds : angle 5.01275 ( 2295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 282 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8680 (t80) cc_final: 0.8350 (t80) REVERT: A 97 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: A 219 VAL cc_start: 0.8866 (t) cc_final: 0.8573 (p) REVERT: A 249 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6947 (ptm-80) REVERT: B 70 ASN cc_start: 0.8722 (m-40) cc_final: 0.8433 (m-40) REVERT: B 146 GLU cc_start: 0.7781 (tp30) cc_final: 0.7439 (mm-30) REVERT: B 213 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7766 (mmt180) REVERT: B 219 VAL cc_start: 0.8918 (t) cc_final: 0.8664 (p) REVERT: B 249 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6976 (ptm-80) REVERT: C 70 ASN cc_start: 0.8654 (m-40) cc_final: 0.8395 (m-40) REVERT: C 146 GLU cc_start: 0.7647 (tp30) cc_final: 0.7284 (mm-30) REVERT: C 185 GLU cc_start: 0.8349 (tt0) cc_final: 0.8101 (pt0) REVERT: C 249 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7071 (ptm160) REVERT: D 59 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8384 (pt0) REVERT: D 70 ASN cc_start: 0.8759 (m-40) cc_final: 0.8414 (m-40) REVERT: D 88 LYS cc_start: 0.8776 (tptp) cc_final: 0.8484 (tptm) REVERT: D 109 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8563 (mtmt) REVERT: D 137 MET cc_start: 0.9028 (ttm) cc_final: 0.8662 (ttp) REVERT: D 146 GLU cc_start: 0.7911 (tp30) cc_final: 0.7556 (mm-30) REVERT: D 219 VAL cc_start: 0.8926 (t) cc_final: 0.8594 (p) REVERT: D 249 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7003 (ptm160) REVERT: E 59 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7898 (mt-10) REVERT: E 146 GLU cc_start: 0.7877 (tp30) cc_final: 0.7432 (tp30) REVERT: E 166 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: E 185 GLU cc_start: 0.8300 (tt0) cc_final: 0.8072 (pt0) REVERT: E 218 GLU cc_start: 0.7698 (tp30) cc_final: 0.7403 (tp30) REVERT: E 251 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6907 (mp) REVERT: F 170 ASP cc_start: 0.8542 (m-30) cc_final: 0.8304 (m-30) REVERT: F 213 ARG cc_start: 0.8068 (mmt-90) cc_final: 0.7813 (mmt-90) REVERT: F 219 VAL cc_start: 0.8972 (t) cc_final: 0.8728 (p) REVERT: F 228 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8247 (ptt) REVERT: F 249 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7199 (ptm160) REVERT: G 59 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8096 (mt-10) REVERT: G 88 LYS cc_start: 0.8812 (tptp) cc_final: 0.8426 (mtpp) REVERT: G 146 GLU cc_start: 0.7856 (tp30) cc_final: 0.7413 (mm-30) REVERT: G 170 ASP cc_start: 0.8402 (m-30) cc_final: 0.8185 (m-30) REVERT: G 200 GLU cc_start: 0.8376 (tt0) cc_final: 0.8051 (tt0) REVERT: H 59 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8145 (mt-10) REVERT: H 146 GLU cc_start: 0.7748 (tp30) cc_final: 0.7327 (mm-30) REVERT: H 249 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6996 (ptm160) REVERT: I 59 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8062 (mt-10) REVERT: I 97 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: I 146 GLU cc_start: 0.7675 (tp30) cc_final: 0.7426 (mm-30) REVERT: I 185 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: e 44 SER cc_start: 0.7875 (p) cc_final: 0.7609 (p) REVERT: h 44 SER cc_start: 0.7838 (p) cc_final: 0.7593 (p) outliers start: 70 outliers final: 35 residues processed: 332 average time/residue: 0.6797 time to fit residues: 246.7450 Evaluate side-chains 314 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Chi-restraints excluded: chain f residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 201 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN C 148 ASN D 148 ASN E 148 ASN F 148 ASN H 57 GLN I 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.141578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114833 restraints weight = 18236.639| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.38 r_work: 0.3131 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16902 Z= 0.137 Angle : 0.615 8.630 22923 Z= 0.322 Chirality : 0.046 0.168 2601 Planarity : 0.003 0.028 3024 Dihedral : 7.191 78.589 2346 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.85 % Allowed : 19.77 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.32 (0.19), residues: 2124 helix: 2.18 (0.22), residues: 585 sheet: -0.30 (0.21), residues: 702 loop : -1.92 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 249 TYR 0.011 0.001 TYR F 199 PHE 0.018 0.001 PHE d 31 TRP 0.011 0.002 TRP C 92 Details of bonding type rmsd covalent geometry : bond 0.00319 (16902) covalent geometry : angle 0.61511 (22923) hydrogen bonds : bond 0.02539 ( 774) hydrogen bonds : angle 4.68238 ( 2295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8563 (t80) cc_final: 0.8246 (t80) REVERT: A 207 ARG cc_start: 0.7697 (ptm-80) cc_final: 0.7479 (ptm-80) REVERT: A 219 VAL cc_start: 0.8783 (t) cc_final: 0.8537 (p) REVERT: A 249 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6822 (ptm160) REVERT: B 109 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8417 (mtmt) REVERT: B 146 GLU cc_start: 0.7652 (tp30) cc_final: 0.7192 (mm-30) REVERT: B 213 ARG cc_start: 0.7711 (mmt-90) cc_final: 0.7489 (mmt180) REVERT: B 219 VAL cc_start: 0.8767 (t) cc_final: 0.8515 (p) REVERT: B 249 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6821 (ptm160) REVERT: C 146 GLU cc_start: 0.7441 (tp30) cc_final: 0.6816 (tp30) REVERT: C 170 ASP cc_start: 0.8546 (m-30) cc_final: 0.8313 (m-30) REVERT: C 185 GLU cc_start: 0.8321 (tt0) cc_final: 0.8044 (pt0) REVERT: C 219 VAL cc_start: 0.8686 (t) cc_final: 0.8268 (p) REVERT: C 249 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6817 (ptm160) REVERT: D 59 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8269 (pt0) REVERT: D 70 ASN cc_start: 0.8695 (m-40) cc_final: 0.8305 (m-40) REVERT: D 88 LYS cc_start: 0.8418 (tptp) cc_final: 0.8143 (mtpp) REVERT: D 109 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8348 (mtmt) REVERT: D 137 MET cc_start: 0.9021 (ttm) cc_final: 0.8513 (ttp) REVERT: D 146 GLU cc_start: 0.7687 (tp30) cc_final: 0.7151 (mm-30) REVERT: D 202 GLN cc_start: 0.8580 (mt0) cc_final: 0.7921 (tt0) REVERT: D 219 VAL cc_start: 0.8829 (t) cc_final: 0.8447 (p) REVERT: D 249 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6868 (ptm160) REVERT: E 146 GLU cc_start: 0.7593 (tp30) cc_final: 0.7096 (mm-30) REVERT: E 166 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: E 185 GLU cc_start: 0.8222 (tt0) cc_final: 0.7986 (pt0) REVERT: E 207 ARG cc_start: 0.7878 (ptm-80) cc_final: 0.7678 (ptm-80) REVERT: E 219 VAL cc_start: 0.8562 (t) cc_final: 0.8361 (p) REVERT: F 146 GLU cc_start: 0.7671 (tp30) cc_final: 0.7288 (mm-30) REVERT: F 170 ASP cc_start: 0.8531 (m-30) cc_final: 0.8281 (m-30) REVERT: F 213 ARG cc_start: 0.7841 (mmt-90) cc_final: 0.7607 (mmt-90) REVERT: F 219 VAL cc_start: 0.8836 (t) cc_final: 0.8585 (p) REVERT: F 249 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7026 (ptm160) REVERT: G 88 LYS cc_start: 0.8501 (tptp) cc_final: 0.8151 (mtpp) REVERT: G 146 GLU cc_start: 0.7642 (tp30) cc_final: 0.7146 (mm-30) REVERT: G 170 ASP cc_start: 0.8415 (m-30) cc_final: 0.8138 (m-30) REVERT: H 59 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7896 (mt-10) REVERT: H 146 GLU cc_start: 0.7549 (tp30) cc_final: 0.6974 (mm-30) REVERT: H 249 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6862 (ptm160) REVERT: I 59 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7919 (mt-10) REVERT: I 88 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8212 (mtpp) REVERT: I 146 GLU cc_start: 0.7546 (tp30) cc_final: 0.7196 (mm-30) REVERT: I 170 ASP cc_start: 0.8716 (m-30) cc_final: 0.8512 (m-30) REVERT: I 185 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: e 28 ASN cc_start: 0.7537 (m-40) cc_final: 0.7318 (t0) REVERT: e 44 SER cc_start: 0.7356 (p) cc_final: 0.7147 (p) outliers start: 69 outliers final: 39 residues processed: 317 average time/residue: 0.7157 time to fit residues: 247.6758 Evaluate side-chains 309 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 169 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN F 148 ASN H 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110569 restraints weight = 18355.455| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.35 r_work: 0.3069 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 16902 Z= 0.263 Angle : 0.684 8.329 22923 Z= 0.359 Chirality : 0.049 0.149 2601 Planarity : 0.004 0.035 3024 Dihedral : 7.723 87.817 2346 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.46 % Allowed : 20.83 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.56 (0.18), residues: 2124 helix: 1.72 (0.21), residues: 585 sheet: 0.00 (0.21), residues: 702 loop : -2.30 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 249 TYR 0.017 0.002 TYR C 199 PHE 0.024 0.002 PHE d 31 TRP 0.015 0.003 TRP E 92 Details of bonding type rmsd covalent geometry : bond 0.00617 (16902) covalent geometry : angle 0.68395 (22923) hydrogen bonds : bond 0.03188 ( 774) hydrogen bonds : angle 4.99299 ( 2295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 274 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8667 (t80) cc_final: 0.8349 (t80) REVERT: A 97 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: A 207 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7695 (ptm-80) REVERT: A 219 VAL cc_start: 0.8878 (t) cc_final: 0.8619 (p) REVERT: A 249 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6924 (ptm160) REVERT: B 70 ASN cc_start: 0.8724 (m-40) cc_final: 0.8426 (m-40) REVERT: B 146 GLU cc_start: 0.7753 (tp30) cc_final: 0.7434 (mm-30) REVERT: B 213 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.7795 (mmt180) REVERT: B 219 VAL cc_start: 0.8864 (t) cc_final: 0.8646 (p) REVERT: B 249 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6987 (ptm160) REVERT: C 146 GLU cc_start: 0.7700 (tp30) cc_final: 0.7132 (mm-30) REVERT: C 185 GLU cc_start: 0.8376 (tt0) cc_final: 0.8117 (pt0) REVERT: C 219 VAL cc_start: 0.8811 (t) cc_final: 0.8441 (p) REVERT: C 249 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7000 (ptm160) REVERT: D 59 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8470 (mt-10) REVERT: D 70 ASN cc_start: 0.8771 (m-40) cc_final: 0.8396 (m-40) REVERT: D 88 LYS cc_start: 0.8780 (tptp) cc_final: 0.8484 (tptm) REVERT: D 109 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8559 (mtmt) REVERT: D 137 MET cc_start: 0.9026 (ttm) cc_final: 0.8653 (ttp) REVERT: D 146 GLU cc_start: 0.7902 (tp30) cc_final: 0.7517 (mm-30) REVERT: D 219 VAL cc_start: 0.8920 (t) cc_final: 0.8611 (p) REVERT: D 249 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7013 (ptm160) REVERT: E 146 GLU cc_start: 0.7833 (tp30) cc_final: 0.7374 (tp30) REVERT: E 166 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: E 185 GLU cc_start: 0.8305 (tt0) cc_final: 0.8076 (pt0) REVERT: E 218 GLU cc_start: 0.7705 (tp30) cc_final: 0.7426 (tp30) REVERT: F 131 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8531 (mp) REVERT: F 170 ASP cc_start: 0.8548 (m-30) cc_final: 0.8315 (m-30) REVERT: F 213 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7763 (mmt-90) REVERT: F 219 VAL cc_start: 0.8951 (t) cc_final: 0.8715 (p) REVERT: F 249 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7161 (ptm160) REVERT: G 59 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8113 (mt-10) REVERT: G 88 LYS cc_start: 0.8860 (tptp) cc_final: 0.8444 (mtpp) REVERT: G 146 GLU cc_start: 0.7853 (tp30) cc_final: 0.7433 (mm-30) REVERT: G 170 ASP cc_start: 0.8442 (m-30) cc_final: 0.8227 (m-30) REVERT: G 200 GLU cc_start: 0.8354 (tt0) cc_final: 0.8056 (tt0) REVERT: H 59 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8149 (mt-10) REVERT: H 249 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7047 (ptm-80) REVERT: I 97 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: I 146 GLU cc_start: 0.7754 (tp30) cc_final: 0.7470 (mm-30) REVERT: I 185 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8278 (pt0) REVERT: I 249 ARG cc_start: 0.7007 (ptm-80) cc_final: 0.6502 (ppt170) REVERT: e 44 SER cc_start: 0.7813 (p) cc_final: 0.7583 (p) outliers start: 62 outliers final: 34 residues processed: 321 average time/residue: 0.6930 time to fit residues: 242.8272 Evaluate side-chains 303 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 142 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN E 148 ASN F 148 ASN H 57 GLN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114401 restraints weight = 18223.244| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.38 r_work: 0.3126 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16902 Z= 0.153 Angle : 0.609 9.017 22923 Z= 0.319 Chirality : 0.046 0.139 2601 Planarity : 0.003 0.030 3024 Dihedral : 7.377 87.448 2346 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.41 % Allowed : 21.78 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.25 (0.19), residues: 2124 helix: 2.20 (0.21), residues: 585 sheet: -0.15 (0.22), residues: 702 loop : -1.96 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 249 TYR 0.013 0.001 TYR F 199 PHE 0.017 0.001 PHE b 31 TRP 0.012 0.002 TRP E 92 Details of bonding type rmsd covalent geometry : bond 0.00356 (16902) covalent geometry : angle 0.60904 (22923) hydrogen bonds : bond 0.02590 ( 774) hydrogen bonds : angle 4.68625 ( 2295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8534 (t80) cc_final: 0.8195 (t80) REVERT: A 219 VAL cc_start: 0.8739 (t) cc_final: 0.8520 (p) REVERT: A 249 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6732 (ptm160) REVERT: B 70 ASN cc_start: 0.8664 (m-40) cc_final: 0.8383 (m-40) REVERT: B 146 GLU cc_start: 0.7648 (tp30) cc_final: 0.7203 (mm-30) REVERT: B 213 ARG cc_start: 0.7799 (mmt-90) cc_final: 0.7551 (mmt180) REVERT: B 219 VAL cc_start: 0.8730 (t) cc_final: 0.8513 (p) REVERT: B 249 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6868 (ptm160) REVERT: C 146 GLU cc_start: 0.7495 (tp30) cc_final: 0.6820 (mm-30) REVERT: C 219 VAL cc_start: 0.8703 (t) cc_final: 0.8365 (p) REVERT: C 249 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6810 (ptm160) REVERT: D 70 ASN cc_start: 0.8705 (m-40) cc_final: 0.8325 (m-40) REVERT: D 88 LYS cc_start: 0.8441 (tptp) cc_final: 0.8197 (mtpp) REVERT: D 109 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8401 (mtmt) REVERT: D 137 MET cc_start: 0.8998 (ttm) cc_final: 0.8581 (ttp) REVERT: D 146 GLU cc_start: 0.7635 (tp30) cc_final: 0.7177 (mm-30) REVERT: D 219 VAL cc_start: 0.8812 (t) cc_final: 0.8516 (p) REVERT: D 249 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6817 (ptm160) REVERT: E 146 GLU cc_start: 0.7611 (tp30) cc_final: 0.7101 (tp30) REVERT: E 166 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: E 185 GLU cc_start: 0.8246 (tt0) cc_final: 0.7970 (pt0) REVERT: E 219 VAL cc_start: 0.8591 (t) cc_final: 0.8386 (p) REVERT: F 146 GLU cc_start: 0.7706 (tp30) cc_final: 0.7315 (mm-30) REVERT: F 170 ASP cc_start: 0.8553 (m-30) cc_final: 0.8286 (m-30) REVERT: F 213 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7617 (mmt-90) REVERT: F 219 VAL cc_start: 0.8844 (t) cc_final: 0.8606 (p) REVERT: F 249 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7016 (ptm160) REVERT: G 88 LYS cc_start: 0.8538 (tptp) cc_final: 0.8198 (mtpp) REVERT: G 146 GLU cc_start: 0.7653 (tp30) cc_final: 0.7175 (mm-30) REVERT: G 170 ASP cc_start: 0.8440 (m-30) cc_final: 0.8156 (m-30) REVERT: G 219 VAL cc_start: 0.8713 (t) cc_final: 0.8412 (p) REVERT: H 59 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7909 (mt-10) REVERT: H 146 GLU cc_start: 0.7561 (tp30) cc_final: 0.7275 (tp30) REVERT: H 249 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6880 (ptm-80) REVERT: I 88 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8320 (mtpp) REVERT: I 146 GLU cc_start: 0.7586 (tp30) cc_final: 0.7242 (mm-30) REVERT: I 185 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: I 219 VAL cc_start: 0.8680 (t) cc_final: 0.8346 (p) REVERT: I 249 ARG cc_start: 0.6939 (ptm-80) cc_final: 0.6535 (ptm-80) outliers start: 61 outliers final: 40 residues processed: 297 average time/residue: 0.6755 time to fit residues: 219.6484 Evaluate side-chains 298 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 197 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 148 optimal weight: 0.0970 chunk 143 optimal weight: 0.0570 chunk 51 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 overall best weight: 3.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.136143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.108596 restraints weight = 18313.312| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.46 r_work: 0.3030 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 16902 Z= 0.266 Angle : 0.681 9.937 22923 Z= 0.359 Chirality : 0.049 0.143 2601 Planarity : 0.004 0.037 3024 Dihedral : 7.826 85.749 2346 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.62 % Allowed : 22.56 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.37 (0.18), residues: 2124 helix: 1.80 (0.20), residues: 585 sheet: 0.24 (0.22), residues: 666 loop : -2.15 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 249 TYR 0.017 0.002 TYR F 199 PHE 0.022 0.002 PHE b 31 TRP 0.018 0.003 TRP E 92 Details of bonding type rmsd covalent geometry : bond 0.00623 (16902) covalent geometry : angle 0.68136 (22923) hydrogen bonds : bond 0.03182 ( 774) hydrogen bonds : angle 4.95569 ( 2295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8665 (t80) cc_final: 0.8369 (t80) REVERT: A 97 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: A 219 VAL cc_start: 0.8875 (t) cc_final: 0.8634 (p) REVERT: A 249 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6855 (ptm160) REVERT: B 70 ASN cc_start: 0.8744 (m-40) cc_final: 0.8445 (m-40) REVERT: B 146 GLU cc_start: 0.7847 (tp30) cc_final: 0.7453 (mm-30) REVERT: B 207 ARG cc_start: 0.7513 (mtp85) cc_final: 0.7221 (mtp85) REVERT: B 219 VAL cc_start: 0.8924 (t) cc_final: 0.8708 (p) REVERT: B 249 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6966 (ptm160) REVERT: C 146 GLU cc_start: 0.7726 (tp30) cc_final: 0.7167 (tp30) REVERT: C 219 VAL cc_start: 0.8851 (t) cc_final: 0.8516 (p) REVERT: C 249 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6896 (ptm160) REVERT: D 70 ASN cc_start: 0.8796 (m-40) cc_final: 0.8419 (m-40) REVERT: D 88 LYS cc_start: 0.8776 (tptp) cc_final: 0.8484 (mtpp) REVERT: D 137 MET cc_start: 0.9048 (ttm) cc_final: 0.8684 (ttp) REVERT: D 146 GLU cc_start: 0.7880 (tp30) cc_final: 0.7490 (mm-30) REVERT: D 219 VAL cc_start: 0.8926 (t) cc_final: 0.8596 (p) REVERT: D 249 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6962 (ptm160) REVERT: E 146 GLU cc_start: 0.7864 (tp30) cc_final: 0.7407 (tp30) REVERT: E 166 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: E 185 GLU cc_start: 0.8333 (tt0) cc_final: 0.8109 (pt0) REVERT: E 218 GLU cc_start: 0.7714 (tp30) cc_final: 0.7396 (tp30) REVERT: E 219 VAL cc_start: 0.8769 (t) cc_final: 0.8545 (p) REVERT: E 249 ARG cc_start: 0.7074 (ptm-80) cc_final: 0.6584 (ptm160) REVERT: E 251 LEU cc_start: 0.7179 (mp) cc_final: 0.6924 (mp) REVERT: F 131 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8546 (mp) REVERT: F 170 ASP cc_start: 0.8592 (m-30) cc_final: 0.8359 (m-30) REVERT: F 213 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.7820 (mmt-90) REVERT: F 219 VAL cc_start: 0.8966 (t) cc_final: 0.8725 (p) REVERT: F 249 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7162 (ptm160) REVERT: G 59 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8127 (mt-10) REVERT: G 88 LYS cc_start: 0.8830 (tptp) cc_final: 0.8426 (mtpp) REVERT: G 146 GLU cc_start: 0.7880 (tp30) cc_final: 0.7458 (mm-30) REVERT: G 170 ASP cc_start: 0.8497 (m-30) cc_final: 0.8278 (m-30) REVERT: G 200 GLU cc_start: 0.8401 (tt0) cc_final: 0.8062 (tt0) REVERT: H 59 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8176 (mt-10) REVERT: H 146 GLU cc_start: 0.7783 (tp30) cc_final: 0.7551 (tp30) REVERT: H 202 GLN cc_start: 0.8535 (mt0) cc_final: 0.8272 (mt0) REVERT: H 249 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7049 (ptm160) REVERT: I 146 GLU cc_start: 0.7815 (tp30) cc_final: 0.7522 (mm-30) REVERT: I 185 GLU cc_start: 0.8538 (tt0) cc_final: 0.8334 (pt0) REVERT: I 249 ARG cc_start: 0.7015 (ptm-80) cc_final: 0.6613 (ptm160) outliers start: 47 outliers final: 33 residues processed: 300 average time/residue: 0.7177 time to fit residues: 234.7217 Evaluate side-chains 300 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 195 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 199 optimal weight: 6.9990 chunk 127 optimal weight: 0.3980 chunk 175 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN D 148 ASN D 171 GLN G 171 GLN ** e 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.138822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112097 restraints weight = 18395.510| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.37 r_work: 0.3097 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16902 Z= 0.210 Angle : 0.656 9.865 22923 Z= 0.343 Chirality : 0.047 0.142 2601 Planarity : 0.003 0.033 3024 Dihedral : 7.795 84.906 2346 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.51 % Allowed : 22.67 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.31 (0.18), residues: 2124 helix: 1.94 (0.21), residues: 585 sheet: 0.25 (0.22), residues: 666 loop : -2.17 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 249 TYR 0.015 0.001 TYR F 199 PHE 0.021 0.002 PHE b 31 TRP 0.018 0.002 TRP G 92 Details of bonding type rmsd covalent geometry : bond 0.00490 (16902) covalent geometry : angle 0.65557 (22923) hydrogen bonds : bond 0.02936 ( 774) hydrogen bonds : angle 4.86191 ( 2295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 66 TYR cc_start: 0.8600 (t80) cc_final: 0.8295 (t80) REVERT: A 97 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: A 137 MET cc_start: 0.8959 (ttm) cc_final: 0.8737 (ttp) REVERT: A 207 ARG cc_start: 0.7582 (ptp-110) cc_final: 0.7173 (mtp85) REVERT: A 249 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6823 (ptm160) REVERT: B 70 ASN cc_start: 0.8699 (m-40) cc_final: 0.8414 (m-40) REVERT: B 146 GLU cc_start: 0.7764 (tp30) cc_final: 0.7336 (mm-30) REVERT: B 207 ARG cc_start: 0.7354 (mtp85) cc_final: 0.7006 (mtp85) REVERT: B 219 VAL cc_start: 0.8866 (t) cc_final: 0.8653 (p) REVERT: B 249 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6848 (ptm160) REVERT: C 146 GLU cc_start: 0.7603 (tp30) cc_final: 0.7004 (mm-30) REVERT: C 219 VAL cc_start: 0.8761 (t) cc_final: 0.8430 (p) REVERT: C 249 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6884 (ptm160) REVERT: D 70 ASN cc_start: 0.8749 (m-40) cc_final: 0.8383 (m-40) REVERT: D 88 LYS cc_start: 0.8658 (tptp) cc_final: 0.8391 (mtpp) REVERT: D 109 LYS cc_start: 0.8754 (mttt) cc_final: 0.8497 (mtmt) REVERT: D 137 MET cc_start: 0.9023 (ttm) cc_final: 0.8657 (ttp) REVERT: D 146 GLU cc_start: 0.7799 (tp30) cc_final: 0.7380 (mm-30) REVERT: D 219 VAL cc_start: 0.8878 (t) cc_final: 0.8544 (p) REVERT: D 249 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6919 (ptm160) REVERT: E 146 GLU cc_start: 0.7766 (tp30) cc_final: 0.7288 (tp30) REVERT: E 166 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: E 185 GLU cc_start: 0.8287 (tt0) cc_final: 0.8065 (pt0) REVERT: E 218 GLU cc_start: 0.7645 (tp30) cc_final: 0.7302 (tp30) REVERT: E 219 VAL cc_start: 0.8680 (t) cc_final: 0.8474 (p) REVERT: E 249 ARG cc_start: 0.7038 (ptm-80) cc_final: 0.6553 (ptm160) REVERT: E 251 LEU cc_start: 0.7166 (mp) cc_final: 0.6919 (mp) REVERT: F 131 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8446 (mp) REVERT: F 170 ASP cc_start: 0.8548 (m-30) cc_final: 0.8303 (m-30) REVERT: F 213 ARG cc_start: 0.8000 (mmt-90) cc_final: 0.7741 (mmt-90) REVERT: F 219 VAL cc_start: 0.8900 (t) cc_final: 0.8663 (p) REVERT: F 249 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7099 (ptm160) REVERT: G 88 LYS cc_start: 0.8726 (tptp) cc_final: 0.8358 (mtpp) REVERT: G 146 GLU cc_start: 0.7799 (tp30) cc_final: 0.7365 (mm-30) REVERT: G 170 ASP cc_start: 0.8405 (m-30) cc_final: 0.8157 (m-30) REVERT: G 219 VAL cc_start: 0.8778 (t) cc_final: 0.8492 (p) REVERT: H 59 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8040 (mt-10) REVERT: H 146 GLU cc_start: 0.7687 (tp30) cc_final: 0.7441 (tp30) REVERT: H 207 ARG cc_start: 0.8023 (ptm160) cc_final: 0.7775 (ptm-80) REVERT: H 249 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6957 (ptm160) REVERT: I 88 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8498 (mtpp) REVERT: I 97 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: I 146 GLU cc_start: 0.7685 (tp30) cc_final: 0.7391 (mm-30) REVERT: I 185 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: I 219 VAL cc_start: 0.8755 (t) cc_final: 0.8450 (p) REVERT: I 249 ARG cc_start: 0.6966 (ptm-80) cc_final: 0.6576 (ptm160) outliers start: 45 outliers final: 31 residues processed: 291 average time/residue: 0.6807 time to fit residues: 216.5482 Evaluate side-chains 292 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain D residue 252 TRP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 252 TRP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 252 TRP Chi-restraints excluded: chain H residue 249 ARG Chi-restraints excluded: chain H residue 252 TRP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 252 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112196 restraints weight = 18321.460| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.36 r_work: 0.3092 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16902 Z= 0.212 Angle : 0.655 9.881 22923 Z= 0.343 Chirality : 0.047 0.145 2601 Planarity : 0.003 0.033 3024 Dihedral : 7.841 89.954 2346 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.46 % Allowed : 22.95 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.29 (0.18), residues: 2124 helix: 1.97 (0.21), residues: 585 sheet: 0.27 (0.22), residues: 666 loop : -2.17 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 249 TYR 0.015 0.001 TYR F 199 PHE 0.019 0.002 PHE b 31 TRP 0.019 0.002 TRP C 92 Details of bonding type rmsd covalent geometry : bond 0.00495 (16902) covalent geometry : angle 0.65524 (22923) hydrogen bonds : bond 0.02936 ( 774) hydrogen bonds : angle 4.83373 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5760.86 seconds wall clock time: 98 minutes 48.76 seconds (5928.76 seconds total)