Starting phenix.real_space_refine on Fri Aug 22 22:07:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwc_27752/08_2025/8dwc_27752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwc_27752/08_2025/8dwc_27752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dwc_27752/08_2025/8dwc_27752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwc_27752/08_2025/8dwc_27752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dwc_27752/08_2025/8dwc_27752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwc_27752/08_2025/8dwc_27752.map" } resolution = 2.87 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= 0.022 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 56 5.16 5 C 5318 2.51 5 N 1413 2.21 5 O 1511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8298 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 109 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2480 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1925 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 1.57, per 1000 atoms: 0.19 Number of scatterers: 8298 At special positions: 0 Unit cell: (104.72, 115.28, 118.8, 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 56 16.00 O 1511 8.00 N 1413 7.00 C 5318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 315.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.667A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.559A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.503A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.565A pdb=" N GLY R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 removed outlier: 3.686A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.991A pdb=" N ILE R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Proline residue: R 100 - end of helix removed outlier: 4.759A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE R 107 " --> pdb=" O MET R 103 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 161 Processing helix chain 'R' and resid 170 through 204 removed outlier: 3.807A pdb=" N GLN R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER R 176 " --> pdb=" O TRP R 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 227 Processing helix chain 'R' and resid 230 through 239 removed outlier: 3.607A pdb=" N ILE R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 253 Processing helix chain 'R' and resid 253 through 273 Proline residue: R 269 - end of helix Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.191A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.518A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.997A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.622A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.965A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.779A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.133A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.620A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.533A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.729A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.180A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.896A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.011A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.657A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.647A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.538A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.648A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.515A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.663A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS E 96 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY E 114 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR E 94 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR E 116 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA E 92 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.556A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.597A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1176 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: 0.90 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2603 1.33 - 1.45: 1529 1.45 - 1.57: 4274 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8482 Sorted by residual: bond pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.29e-02 6.01e+03 6.29e+00 bond pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.19e+00 bond pdb=" N THR B 221 " pdb=" CA THR B 221 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.37e-02 5.33e+03 4.69e+00 bond pdb=" N ALA B 218 " pdb=" CA ALA B 218 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.33e-02 5.65e+03 3.86e+00 bond pdb=" CG1 ILE B 49 " pdb=" CD1 ILE B 49 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.46e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11113 1.47 - 2.95: 362 2.95 - 4.42: 54 4.42 - 5.90: 12 5.90 - 7.37: 4 Bond angle restraints: 11545 Sorted by residual: angle pdb=" N THR B 221 " pdb=" CA THR B 221 " pdb=" C THR B 221 " ideal model delta sigma weight residual 113.72 109.31 4.41 1.30e+00 5.92e-01 1.15e+01 angle pdb=" N ALA B 218 " pdb=" CA ALA B 218 " pdb=" C ALA B 218 " ideal model delta sigma weight residual 113.23 109.46 3.77 1.24e+00 6.50e-01 9.26e+00 angle pdb=" N VAL B 219 " pdb=" CA VAL B 219 " pdb=" C VAL B 219 " ideal model delta sigma weight residual 112.80 109.75 3.05 1.15e+00 7.56e-01 7.03e+00 angle pdb=" CA ASP B 220 " pdb=" C ASP B 220 " pdb=" O ASP B 220 " ideal model delta sigma weight residual 120.92 118.34 2.58 1.14e+00 7.69e-01 5.13e+00 angle pdb=" C ASP B 42 " pdb=" N ASN B 43 " pdb=" CA ASN B 43 " ideal model delta sigma weight residual 124.82 128.66 -3.84 1.78e+00 3.16e-01 4.66e+00 ... (remaining 11540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4465 15.94 - 31.87: 379 31.87 - 47.81: 78 47.81 - 63.74: 10 63.74 - 79.68: 3 Dihedral angle restraints: 4935 sinusoidal: 1742 harmonic: 3193 Sorted by residual: dihedral pdb=" CA MET E 128 " pdb=" C MET E 128 " pdb=" N THR E 129 " pdb=" CA THR E 129 " ideal model delta harmonic sigma weight residual 180.00 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP C 258 " pdb=" C ASP C 258 " pdb=" N GLN C 259 " pdb=" CA GLN C 259 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 125.65 -32.65 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 872 0.042 - 0.084: 349 0.084 - 0.126: 109 0.126 - 0.168: 9 0.168 - 0.210: 3 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CB VAL B 109 " pdb=" CA VAL B 109 " pdb=" CG1 VAL B 109 " pdb=" CG2 VAL B 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU B 143 " pdb=" CB LEU B 143 " pdb=" CD1 LEU B 143 " pdb=" CD2 LEU B 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA VAL B 219 " pdb=" N VAL B 219 " pdb=" C VAL B 219 " pdb=" CB VAL B 219 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1339 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 217 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C CYS B 217 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS B 217 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 218 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO C 194 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 209 " 0.012 2.00e-02 2.50e+03 1.37e-02 2.82e+00 pdb=" CG HIS B 209 " -0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS B 209 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 209 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 209 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 209 " 0.004 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 111 2.66 - 3.22: 7580 3.22 - 3.78: 12389 3.78 - 4.34: 17741 4.34 - 4.90: 29887 Nonbonded interactions: 67708 Sorted by model distance: nonbonded pdb=" OH TYR R 130 " pdb=" OH TYR B 243 " model vdw 2.095 3.040 nonbonded pdb=" NH2 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.123 3.120 nonbonded pdb=" O SER B 44 " pdb=" ND2 ASN B 144 " model vdw 2.149 3.120 nonbonded pdb=" OD2 ASP R 177 " pdb=" NE1 TRP R 241 " model vdw 2.229 3.120 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.232 3.040 ... (remaining 67703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.770 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 0.073 8484 Z= 0.325 Angle : 0.646 7.370 11549 Z= 0.355 Chirality : 0.047 0.210 1342 Planarity : 0.004 0.044 1448 Dihedral : 12.543 79.679 2867 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: -1.14 (0.24), residues: 1082 helix: -1.16 (0.24), residues: 365 sheet: 0.11 (0.31), residues: 282 loop : -0.78 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 31 TYR 0.026 0.002 TYR C 59 PHE 0.020 0.003 PHE B 215 TRP 0.012 0.002 TRP C 63 HIS 0.016 0.002 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00769 ( 8482) covalent geometry : angle 0.64545 (11545) SS BOND : bond 0.00579 ( 2) SS BOND : angle 0.80699 ( 4) hydrogen bonds : bond 0.25147 ( 415) hydrogen bonds : angle 8.30183 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.281 Fit side-chains REVERT: C 163 ASP cc_start: 0.7475 (p0) cc_final: 0.7192 (p0) REVERT: C 188 MET cc_start: 0.7933 (mmp) cc_final: 0.7514 (mmp) REVERT: B 25 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 114 ASP cc_start: 0.7198 (t70) cc_final: 0.6969 (t70) REVERT: B 229 ASN cc_start: 0.8236 (m-40) cc_final: 0.7986 (m-40) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.4722 time to fit residues: 101.8347 Evaluate side-chains 188 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098422 restraints weight = 11850.409| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.72 r_work: 0.3147 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8484 Z= 0.137 Angle : 0.558 8.170 11549 Z= 0.297 Chirality : 0.043 0.153 1342 Planarity : 0.005 0.039 1448 Dihedral : 4.480 16.655 1181 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.83 % Allowed : 9.92 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.26 (0.25), residues: 1082 helix: 1.12 (0.26), residues: 349 sheet: 0.40 (0.31), residues: 283 loop : -0.67 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 32 TYR 0.016 0.001 TYR E 178 PHE 0.015 0.001 PHE C 199 TRP 0.013 0.001 TRP C 211 HIS 0.009 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8482) covalent geometry : angle 0.55746 (11545) SS BOND : bond 0.00626 ( 2) SS BOND : angle 0.84145 ( 4) hydrogen bonds : bond 0.04989 ( 415) hydrogen bonds : angle 4.96825 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 0.331 Fit side-chains REVERT: C 234 PHE cc_start: 0.8622 (m-80) cc_final: 0.8409 (m-80) REVERT: C 259 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: R 85 LEU cc_start: 0.8145 (mt) cc_final: 0.7925 (mm) REVERT: R 211 LEU cc_start: 0.8231 (mp) cc_final: 0.7928 (tp) REVERT: R 227 LEU cc_start: 0.8430 (pp) cc_final: 0.8195 (mt) REVERT: E 69 THR cc_start: 0.8589 (p) cc_final: 0.8339 (t) REVERT: E 192 SER cc_start: 0.8351 (t) cc_final: 0.8123 (t) REVERT: B 9 ASP cc_start: 0.7679 (m-30) cc_final: 0.7351 (m-30) REVERT: B 25 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 229 ASN cc_start: 0.8400 (m-40) cc_final: 0.8170 (m-40) outliers start: 7 outliers final: 2 residues processed: 186 average time/residue: 0.4728 time to fit residues: 93.8017 Evaluate side-chains 184 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 0.0770 chunk 72 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 132 ASN C 176 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS B 22 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097806 restraints weight = 11765.905| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.72 r_work: 0.3144 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8484 Z= 0.148 Angle : 0.533 7.683 11549 Z= 0.281 Chirality : 0.042 0.144 1342 Planarity : 0.004 0.041 1448 Dihedral : 4.262 16.075 1181 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.94 % Allowed : 14.05 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.66 (0.26), residues: 1082 helix: 1.85 (0.27), residues: 349 sheet: 0.47 (0.30), residues: 289 loop : -0.68 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 32 TYR 0.014 0.001 TYR E 178 PHE 0.016 0.001 PHE C 199 TRP 0.013 0.001 TRP C 211 HIS 0.008 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8482) covalent geometry : angle 0.53265 (11545) SS BOND : bond 0.00629 ( 2) SS BOND : angle 0.71493 ( 4) hydrogen bonds : bond 0.04354 ( 415) hydrogen bonds : angle 4.59349 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 0.204 Fit side-chains REVERT: C 186 ASP cc_start: 0.7966 (m-30) cc_final: 0.7745 (m-30) REVERT: C 223 THR cc_start: 0.8132 (p) cc_final: 0.7903 (t) REVERT: C 249 THR cc_start: 0.8658 (p) cc_final: 0.8435 (t) REVERT: C 307 VAL cc_start: 0.8802 (t) cc_final: 0.8522 (p) REVERT: R 85 LEU cc_start: 0.8091 (mt) cc_final: 0.7885 (mm) REVERT: R 144 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8338 (t) REVERT: R 211 LEU cc_start: 0.8208 (mp) cc_final: 0.7885 (tp) REVERT: E 69 THR cc_start: 0.8579 (p) cc_final: 0.8289 (t) REVERT: E 83 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7964 (mtt) REVERT: E 192 SER cc_start: 0.8357 (t) cc_final: 0.8143 (t) REVERT: B 20 ASP cc_start: 0.7745 (m-30) cc_final: 0.7543 (m-30) REVERT: B 25 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 29 LYS cc_start: 0.8191 (mttt) cc_final: 0.7975 (mtmt) REVERT: B 196 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 229 ASN cc_start: 0.8385 (m-40) cc_final: 0.8133 (m-40) outliers start: 8 outliers final: 2 residues processed: 192 average time/residue: 0.4453 time to fit residues: 91.1897 Evaluate side-chains 188 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 176 GLN B 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097358 restraints weight = 12012.797| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.74 r_work: 0.3132 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8484 Z= 0.169 Angle : 0.536 7.647 11549 Z= 0.282 Chirality : 0.043 0.143 1342 Planarity : 0.004 0.039 1448 Dihedral : 4.235 16.101 1181 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.65 % Allowed : 15.70 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.83 (0.26), residues: 1082 helix: 2.13 (0.27), residues: 349 sheet: 0.49 (0.30), residues: 294 loop : -0.69 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.014 0.002 TYR E 178 PHE 0.017 0.002 PHE C 199 TRP 0.013 0.001 TRP C 211 HIS 0.007 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8482) covalent geometry : angle 0.53582 (11545) SS BOND : bond 0.00649 ( 2) SS BOND : angle 0.72353 ( 4) hydrogen bonds : bond 0.04228 ( 415) hydrogen bonds : angle 4.47202 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.337 Fit side-chains REVERT: C 59 TYR cc_start: 0.8071 (m-80) cc_final: 0.7567 (m-80) REVERT: C 75 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8172 (mm110) REVERT: C 223 THR cc_start: 0.8173 (p) cc_final: 0.7933 (t) REVERT: C 249 THR cc_start: 0.8681 (p) cc_final: 0.8456 (t) REVERT: C 307 VAL cc_start: 0.8801 (t) cc_final: 0.8550 (p) REVERT: R 144 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8359 (t) REVERT: R 211 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7881 (tp) REVERT: E 69 THR cc_start: 0.8591 (p) cc_final: 0.8256 (t) REVERT: E 83 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.8022 (mtt) REVERT: E 192 SER cc_start: 0.8364 (t) cc_final: 0.8141 (t) REVERT: B 20 ASP cc_start: 0.7759 (m-30) cc_final: 0.7543 (m-30) REVERT: B 25 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 29 LYS cc_start: 0.8202 (mttt) cc_final: 0.7926 (mtmt) REVERT: B 196 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 229 ASN cc_start: 0.8423 (m-40) cc_final: 0.8195 (m-40) outliers start: 14 outliers final: 5 residues processed: 200 average time/residue: 0.4522 time to fit residues: 96.9124 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN R 67 ASN B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098294 restraints weight = 11931.708| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.74 r_work: 0.3123 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8484 Z= 0.201 Angle : 0.550 8.340 11549 Z= 0.290 Chirality : 0.043 0.142 1342 Planarity : 0.004 0.044 1448 Dihedral : 4.313 16.253 1181 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.13 % Allowed : 16.53 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.83 (0.26), residues: 1082 helix: 2.14 (0.27), residues: 347 sheet: 0.52 (0.30), residues: 292 loop : -0.70 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 52 TYR 0.014 0.002 TYR E 178 PHE 0.018 0.002 PHE C 199 TRP 0.013 0.002 TRP C 211 HIS 0.007 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 8482) covalent geometry : angle 0.54960 (11545) SS BOND : bond 0.00711 ( 2) SS BOND : angle 0.69387 ( 4) hydrogen bonds : bond 0.04347 ( 415) hydrogen bonds : angle 4.47970 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.297 Fit side-chains REVERT: C 59 TYR cc_start: 0.8112 (m-80) cc_final: 0.7564 (m-80) REVERT: C 163 ASP cc_start: 0.7714 (p0) cc_final: 0.7431 (p0) REVERT: C 223 THR cc_start: 0.8203 (p) cc_final: 0.7969 (t) REVERT: C 249 THR cc_start: 0.8699 (p) cc_final: 0.8391 (t) REVERT: C 251 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8288 (mtt90) REVERT: C 259 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: C 307 VAL cc_start: 0.8789 (t) cc_final: 0.8578 (p) REVERT: R 144 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (t) REVERT: R 211 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7912 (tp) REVERT: R 250 PHE cc_start: 0.8102 (t80) cc_final: 0.7867 (t80) REVERT: E 69 THR cc_start: 0.8598 (p) cc_final: 0.8246 (t) REVERT: E 192 SER cc_start: 0.8354 (t) cc_final: 0.8129 (t) REVERT: B 20 ASP cc_start: 0.7777 (m-30) cc_final: 0.7559 (m-30) REVERT: B 25 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 29 LYS cc_start: 0.8219 (mttt) cc_final: 0.7925 (mtmt) REVERT: B 196 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 229 ASN cc_start: 0.8434 (m-40) cc_final: 0.8199 (m-40) outliers start: 18 outliers final: 8 residues processed: 206 average time/residue: 0.4327 time to fit residues: 95.4605 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097624 restraints weight = 11842.771| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.77 r_work: 0.3112 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8484 Z= 0.222 Angle : 0.574 10.220 11549 Z= 0.298 Chirality : 0.044 0.140 1342 Planarity : 0.004 0.046 1448 Dihedral : 4.383 16.832 1181 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.07 % Allowed : 15.70 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.83 (0.26), residues: 1082 helix: 2.09 (0.27), residues: 349 sheet: 0.52 (0.30), residues: 294 loop : -0.68 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 32 TYR 0.014 0.002 TYR E 59 PHE 0.019 0.002 PHE C 199 TRP 0.013 0.002 TRP C 211 HIS 0.007 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 8482) covalent geometry : angle 0.57366 (11545) SS BOND : bond 0.00747 ( 2) SS BOND : angle 0.74251 ( 4) hydrogen bonds : bond 0.04459 ( 415) hydrogen bonds : angle 4.50760 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.241 Fit side-chains REVERT: C 59 TYR cc_start: 0.8122 (m-80) cc_final: 0.7522 (m-80) REVERT: C 75 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8211 (mm110) REVERT: C 223 THR cc_start: 0.8250 (p) cc_final: 0.8038 (t) REVERT: C 249 THR cc_start: 0.8713 (p) cc_final: 0.8366 (t) REVERT: C 251 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8227 (mtt90) REVERT: C 259 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: R 144 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8356 (t) REVERT: R 211 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7956 (tp) REVERT: E 192 SER cc_start: 0.8356 (t) cc_final: 0.8123 (t) REVERT: B 20 ASP cc_start: 0.7770 (m-30) cc_final: 0.7568 (m-30) REVERT: B 25 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 29 LYS cc_start: 0.8247 (mttt) cc_final: 0.7931 (mtmt) REVERT: B 196 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 229 ASN cc_start: 0.8447 (m-40) cc_final: 0.8202 (m-40) outliers start: 26 outliers final: 13 residues processed: 204 average time/residue: 0.4218 time to fit residues: 92.2160 Evaluate side-chains 213 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099334 restraints weight = 11969.618| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.75 r_work: 0.3138 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8484 Z= 0.135 Angle : 0.514 9.229 11549 Z= 0.271 Chirality : 0.042 0.139 1342 Planarity : 0.004 0.050 1448 Dihedral : 4.161 16.115 1181 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.13 % Allowed : 17.24 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.01 (0.26), residues: 1082 helix: 2.42 (0.28), residues: 349 sheet: 0.53 (0.30), residues: 293 loop : -0.67 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 32 TYR 0.016 0.001 TYR E 178 PHE 0.016 0.001 PHE C 199 TRP 0.013 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8482) covalent geometry : angle 0.51362 (11545) SS BOND : bond 0.00613 ( 2) SS BOND : angle 0.59686 ( 4) hydrogen bonds : bond 0.03847 ( 415) hydrogen bonds : angle 4.34102 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.212 Fit side-chains REVERT: C 45 MET cc_start: 0.8812 (mtt) cc_final: 0.8543 (mtt) REVERT: C 59 TYR cc_start: 0.8110 (m-80) cc_final: 0.7623 (m-80) REVERT: C 75 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8162 (mm-40) REVERT: C 223 THR cc_start: 0.8219 (p) cc_final: 0.7983 (t) REVERT: C 249 THR cc_start: 0.8629 (p) cc_final: 0.8405 (t) REVERT: C 251 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8438 (mtt90) REVERT: C 259 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8422 (pm20) REVERT: R 144 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8351 (t) REVERT: R 211 LEU cc_start: 0.8180 (mp) cc_final: 0.7950 (tp) REVERT: E 69 THR cc_start: 0.8582 (p) cc_final: 0.8246 (t) REVERT: E 192 SER cc_start: 0.8333 (t) cc_final: 0.8109 (t) REVERT: B 20 ASP cc_start: 0.7763 (m-30) cc_final: 0.7543 (m-30) REVERT: B 25 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 29 LYS cc_start: 0.8183 (mttt) cc_final: 0.7867 (mtmt) REVERT: B 196 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 229 ASN cc_start: 0.8424 (m-40) cc_final: 0.8181 (m-40) outliers start: 18 outliers final: 7 residues processed: 204 average time/residue: 0.4291 time to fit residues: 93.7864 Evaluate side-chains 204 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.099748 restraints weight = 11933.061| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.78 r_work: 0.3138 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8484 Z= 0.130 Angle : 0.511 8.251 11549 Z= 0.268 Chirality : 0.041 0.138 1342 Planarity : 0.004 0.045 1448 Dihedral : 4.088 16.281 1181 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.01 % Allowed : 17.00 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.11 (0.26), residues: 1082 helix: 2.58 (0.28), residues: 348 sheet: 0.51 (0.30), residues: 293 loop : -0.61 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 32 TYR 0.015 0.001 TYR E 178 PHE 0.017 0.001 PHE E 68 TRP 0.012 0.001 TRP C 211 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8482) covalent geometry : angle 0.51129 (11545) SS BOND : bond 0.00589 ( 2) SS BOND : angle 0.56458 ( 4) hydrogen bonds : bond 0.03738 ( 415) hydrogen bonds : angle 4.26278 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.312 Fit side-chains REVERT: C 59 TYR cc_start: 0.8104 (m-80) cc_final: 0.7633 (m-80) REVERT: C 75 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8217 (mm-40) REVERT: C 223 THR cc_start: 0.8216 (p) cc_final: 0.7981 (t) REVERT: C 249 THR cc_start: 0.8634 (p) cc_final: 0.8415 (t) REVERT: C 251 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8429 (mtt90) REVERT: C 259 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: R 144 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8362 (t) REVERT: E 68 PHE cc_start: 0.8000 (m-10) cc_final: 0.7798 (m-10) REVERT: E 192 SER cc_start: 0.8324 (t) cc_final: 0.8102 (t) REVERT: B 20 ASP cc_start: 0.7763 (m-30) cc_final: 0.7542 (m-30) REVERT: B 25 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 29 LYS cc_start: 0.8192 (mttt) cc_final: 0.7876 (mtmt) REVERT: B 196 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 229 ASN cc_start: 0.8436 (m-40) cc_final: 0.8198 (m-40) outliers start: 17 outliers final: 9 residues processed: 200 average time/residue: 0.4453 time to fit residues: 95.3729 Evaluate side-chains 202 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098442 restraints weight = 11968.381| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.75 r_work: 0.3140 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8484 Z= 0.136 Angle : 0.511 8.237 11549 Z= 0.269 Chirality : 0.042 0.138 1342 Planarity : 0.004 0.042 1448 Dihedral : 4.063 16.212 1181 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.89 % Allowed : 17.47 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.14 (0.26), residues: 1082 helix: 2.62 (0.27), residues: 348 sheet: 0.53 (0.31), residues: 280 loop : -0.57 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.015 0.001 TYR E 178 PHE 0.016 0.001 PHE C 199 TRP 0.012 0.001 TRP C 211 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8482) covalent geometry : angle 0.51119 (11545) SS BOND : bond 0.00599 ( 2) SS BOND : angle 0.55481 ( 4) hydrogen bonds : bond 0.03754 ( 415) hydrogen bonds : angle 4.24100 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.301 Fit side-chains REVERT: C 59 TYR cc_start: 0.8099 (m-80) cc_final: 0.7569 (m-80) REVERT: C 223 THR cc_start: 0.8212 (p) cc_final: 0.7969 (t) REVERT: C 249 THR cc_start: 0.8623 (p) cc_final: 0.8421 (t) REVERT: C 259 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8415 (pm20) REVERT: R 144 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8365 (t) REVERT: E 128 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7449 (mtm) REVERT: E 192 SER cc_start: 0.8306 (t) cc_final: 0.8084 (t) REVERT: B 20 ASP cc_start: 0.7753 (m-30) cc_final: 0.7529 (m-30) REVERT: B 25 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 29 LYS cc_start: 0.8200 (mttt) cc_final: 0.7888 (mtmt) REVERT: B 196 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 229 ASN cc_start: 0.8431 (m-40) cc_final: 0.8197 (m-40) outliers start: 16 outliers final: 8 residues processed: 196 average time/residue: 0.4498 time to fit residues: 94.2838 Evaluate side-chains 201 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098169 restraints weight = 11799.816| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.74 r_work: 0.3129 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8484 Z= 0.171 Angle : 0.545 9.242 11549 Z= 0.283 Chirality : 0.043 0.139 1342 Planarity : 0.004 0.041 1448 Dihedral : 4.155 16.317 1181 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.65 % Allowed : 17.83 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.09 (0.26), residues: 1082 helix: 2.55 (0.27), residues: 348 sheet: 0.52 (0.30), residues: 289 loop : -0.61 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.014 0.002 TYR E 178 PHE 0.017 0.002 PHE C 199 TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8482) covalent geometry : angle 0.54514 (11545) SS BOND : bond 0.00653 ( 2) SS BOND : angle 0.62931 ( 4) hydrogen bonds : bond 0.04009 ( 415) hydrogen bonds : angle 4.29982 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.247 Fit side-chains REVERT: C 59 TYR cc_start: 0.8120 (m-80) cc_final: 0.7650 (m-80) REVERT: C 75 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8194 (mm-40) REVERT: C 223 THR cc_start: 0.8227 (p) cc_final: 0.7993 (t) REVERT: C 249 THR cc_start: 0.8671 (p) cc_final: 0.8397 (t) REVERT: C 251 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8328 (mtt90) REVERT: R 144 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8365 (t) REVERT: R 211 LEU cc_start: 0.8163 (mp) cc_final: 0.7957 (tp) REVERT: E 128 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7462 (mtm) REVERT: E 166 LEU cc_start: 0.8680 (tt) cc_final: 0.8452 (tm) REVERT: E 192 SER cc_start: 0.8316 (t) cc_final: 0.8097 (t) REVERT: B 20 ASP cc_start: 0.7758 (m-30) cc_final: 0.7553 (m-30) REVERT: B 25 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 29 LYS cc_start: 0.8233 (mttt) cc_final: 0.7911 (mtmt) REVERT: B 196 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 229 ASN cc_start: 0.8435 (m-40) cc_final: 0.8199 (m-40) outliers start: 14 outliers final: 9 residues processed: 198 average time/residue: 0.4313 time to fit residues: 91.5051 Evaluate side-chains 204 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101317 restraints weight = 11892.363| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.78 r_work: 0.3143 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8484 Z= 0.130 Angle : 0.514 8.976 11549 Z= 0.268 Chirality : 0.042 0.140 1342 Planarity : 0.004 0.039 1448 Dihedral : 4.060 16.168 1181 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.53 % Allowed : 18.30 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.21 (0.26), residues: 1082 helix: 2.69 (0.27), residues: 349 sheet: 0.55 (0.31), residues: 280 loop : -0.53 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.015 0.001 TYR E 178 PHE 0.020 0.001 PHE E 68 TRP 0.012 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8482) covalent geometry : angle 0.51392 (11545) SS BOND : bond 0.00580 ( 2) SS BOND : angle 0.56817 ( 4) hydrogen bonds : bond 0.03694 ( 415) hydrogen bonds : angle 4.22659 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.84 seconds wall clock time: 51 minutes 11.22 seconds (3071.22 seconds total)