Starting phenix.real_space_refine on Wed Mar 4 03:21:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ka3_22757/03_2026/7ka3_22757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ka3_22757/03_2026/7ka3_22757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ka3_22757/03_2026/7ka3_22757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ka3_22757/03_2026/7ka3_22757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ka3_22757/03_2026/7ka3_22757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ka3_22757/03_2026/7ka3_22757.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s 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: 10472 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Restraints were copied for chains: A, C, D Time building chain proxies: 2.15, per 1000 atoms: 0.21 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.37, 80.99, 105.56, 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 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 520.3 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 55.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.599A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.522A pdb=" N VAL B 69 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.511A pdb=" N GLN B 85 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.993A pdb=" N LYS B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 removed outlier: 3.703A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.503A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.946A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'A' and resid 8 through 23 removed outlier: 3.600A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.522A pdb=" N VAL A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.512A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.993A pdb=" N LYS A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.703A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.502A pdb=" N ALA A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.946A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 340 Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.601A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 47 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.521A pdb=" N VAL C 69 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.512A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.993A pdb=" N LYS C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 removed outlier: 3.703A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.594A pdb=" N THR C 226 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.502A pdb=" N ALA C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.947A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.600A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.521A pdb=" N VAL D 69 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.511A pdb=" N GLN D 85 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.993A pdb=" N LYS D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.704A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.503A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.946A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 340 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.460A pdb=" N GLY B 28 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE B 77 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 30 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.460A pdb=" N GLY A 28 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE A 77 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 30 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 31 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.461A pdb=" N GLY C 28 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE C 77 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 30 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE C 185 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 31 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.460A pdb=" N GLY D 28 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE D 77 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 30 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 31 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 524 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3479 1.34 - 1.46: 1920 1.46 - 1.58: 5217 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.52e+00 bond pdb=" C ASN B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.334 1.397 -0.064 2.34e-02 1.83e+03 7.37e+00 bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.28e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.28e+00 bond pdb=" C PHE C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.94e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 14042 1.89 - 3.78: 358 3.78 - 5.67: 56 5.67 - 7.56: 4 7.56 - 9.45: 4 Bond angle restraints: 14464 Sorted by residual: angle pdb=" C ASN D 319 " pdb=" N LEU D 320 " pdb=" CA LEU D 320 " ideal model delta sigma weight residual 121.19 127.32 -6.13 1.59e+00 3.96e-01 1.49e+01 angle pdb=" C ASN A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta sigma weight residual 121.19 127.29 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" C ASN B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta sigma weight residual 121.19 127.29 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" C ASN C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta sigma weight residual 121.19 127.28 -6.09 1.59e+00 3.96e-01 1.46e+01 angle pdb=" CA LEU B 61 " pdb=" CB LEU B 61 " pdb=" CG LEU B 61 " ideal model delta sigma weight residual 116.30 125.75 -9.45 3.50e+00 8.16e-02 7.30e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5912 17.48 - 34.95: 485 34.95 - 52.43: 83 52.43 - 69.91: 12 69.91 - 87.38: 12 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU D 270 " pdb=" C LEU D 270 " pdb=" N SER D 271 " pdb=" CA SER D 271 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU B 270 " pdb=" C LEU B 270 " pdb=" N SER B 271 " pdb=" CA SER B 271 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 960 0.029 - 0.059: 395 0.059 - 0.088: 177 0.088 - 0.117: 96 0.117 - 0.146: 16 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA VAL D 113 " pdb=" N VAL D 113 " pdb=" C VAL D 113 " pdb=" CB VAL D 113 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA VAL C 113 " pdb=" N VAL C 113 " pdb=" C VAL C 113 " pdb=" CB VAL C 113 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA VAL B 113 " pdb=" N VAL B 113 " pdb=" C VAL B 113 " pdb=" CB VAL B 113 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 329 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C LYS C 329 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS C 329 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 330 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 329 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C LYS B 329 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 329 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 330 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 329 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" C LYS A 329 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 329 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 330 " -0.015 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3100 2.82 - 3.34: 9356 3.34 - 3.86: 18013 3.86 - 4.38: 20884 4.38 - 4.90: 36001 Nonbonded interactions: 87354 Sorted by model distance: nonbonded pdb=" O ILE B 248 " pdb=" OG1 THR B 252 " model vdw 2.294 3.040 nonbonded pdb=" O ILE A 248 " pdb=" OG1 THR A 252 " model vdw 2.294 3.040 nonbonded pdb=" O ILE C 248 " pdb=" OG1 THR C 252 " model vdw 2.294 3.040 nonbonded pdb=" O ILE D 248 " pdb=" OG1 THR D 252 " model vdw 2.295 3.040 nonbonded pdb=" OE2 GLU D 277 " pdb=" OH TYR D 342 " model vdw 2.347 3.040 ... (remaining 87349 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.990 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.004 0.064 10672 Z= 0.200 Angle : 0.761 9.454 14464 Z= 0.441 Chirality : 0.043 0.146 1644 Planarity : 0.008 0.059 1880 Dihedral : 13.663 87.383 3984 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.36 % Allowed : 7.82 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.21 (0.19), residues: 1364 helix: -1.29 (0.15), residues: 672 sheet: -2.19 (0.33), residues: 204 loop : -1.04 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.014 0.002 TYR A 213 PHE 0.016 0.002 PHE C 144 TRP 0.014 0.003 TRP A 295 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00422 (10672) covalent geometry : angle 0.76079 (14464) hydrogen bonds : bond 0.14922 ( 524) hydrogen bonds : angle 6.18886 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 0.398 Fit side-chains REVERT: B 250 MET cc_start: 0.7093 (tpp) cc_final: 0.6732 (tpt) REVERT: A 193 ASP cc_start: 0.8246 (m-30) cc_final: 0.7996 (p0) REVERT: A 250 MET cc_start: 0.7243 (tpp) cc_final: 0.7020 (tpt) REVERT: A 278 GLU cc_start: 0.6947 (pt0) cc_final: 0.6740 (pt0) REVERT: C 193 ASP cc_start: 0.8251 (m-30) cc_final: 0.7861 (p0) REVERT: C 250 MET cc_start: 0.7250 (tpp) cc_final: 0.7017 (tpt) REVERT: C 278 GLU cc_start: 0.6970 (pt0) cc_final: 0.6759 (pt0) REVERT: D 250 MET cc_start: 0.7124 (tpp) cc_final: 0.6756 (tpt) outliers start: 4 outliers final: 4 residues processed: 213 average time/residue: 0.1189 time to fit residues: 34.2728 Evaluate side-chains 154 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain D residue 252 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 125 GLN B 274 GLN B 324 GLN A 60 GLN A 125 GLN A 274 GLN A 324 GLN C 60 GLN C 125 GLN C 231 ASN C 274 GLN D 60 GLN D 125 GLN D 274 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.146881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118532 restraints weight = 12953.173| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.07 r_work: 0.3306 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.126 Angle : 0.520 6.763 14464 Z= 0.269 Chirality : 0.040 0.125 1644 Planarity : 0.004 0.039 1880 Dihedral : 4.326 15.926 1476 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.35 % Allowed : 10.07 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.22), residues: 1364 helix: 0.89 (0.18), residues: 684 sheet: -2.15 (0.33), residues: 224 loop : -0.44 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 56 TYR 0.012 0.001 TYR A 213 PHE 0.007 0.001 PHE B 144 TRP 0.012 0.001 TRP C 147 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00282 (10672) covalent geometry : angle 0.51964 (14464) hydrogen bonds : bond 0.04700 ( 524) hydrogen bonds : angle 4.09170 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.423 Fit side-chains REVERT: B 56 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7374 (ttt-90) REVERT: B 250 MET cc_start: 0.8256 (tpp) cc_final: 0.7871 (tpt) REVERT: A 56 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7422 (ttt-90) REVERT: A 95 GLN cc_start: 0.8341 (tp-100) cc_final: 0.7967 (mm-40) REVERT: A 193 ASP cc_start: 0.8689 (m-30) cc_final: 0.8045 (p0) REVERT: A 278 GLU cc_start: 0.7565 (pt0) cc_final: 0.7361 (pt0) REVERT: C 56 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7368 (ttt-90) REVERT: C 95 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7986 (mm-40) REVERT: C 193 ASP cc_start: 0.8715 (m-30) cc_final: 0.8030 (p0) REVERT: C 250 MET cc_start: 0.8312 (tpp) cc_final: 0.7977 (tpt) REVERT: D 44 GLN cc_start: 0.8534 (tt0) cc_final: 0.8288 (tm-30) REVERT: D 56 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7355 (ttt-90) REVERT: D 250 MET cc_start: 0.8324 (tpp) cc_final: 0.7942 (tpt) outliers start: 15 outliers final: 6 residues processed: 188 average time/residue: 0.1156 time to fit residues: 29.7268 Evaluate side-chains 167 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 324 GLN A 324 GLN C 231 ASN D 50 ASN D 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115415 restraints weight = 13163.327| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.06 r_work: 0.3266 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10672 Z= 0.154 Angle : 0.500 5.859 14464 Z= 0.261 Chirality : 0.040 0.123 1644 Planarity : 0.004 0.035 1880 Dihedral : 4.193 15.412 1472 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.71 % Allowed : 11.87 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.52 (0.23), residues: 1364 helix: 1.68 (0.19), residues: 692 sheet: -2.21 (0.32), residues: 224 loop : -0.22 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 56 TYR 0.015 0.001 TYR B 213 PHE 0.008 0.001 PHE B 144 TRP 0.011 0.001 TRP D 147 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00359 (10672) covalent geometry : angle 0.50002 (14464) hydrogen bonds : bond 0.04492 ( 524) hydrogen bonds : angle 3.73542 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.463 Fit side-chains REVERT: B 56 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7523 (ttt-90) REVERT: B 95 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8022 (mm-40) REVERT: B 164 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8030 (ttp) REVERT: B 250 MET cc_start: 0.8364 (tpp) cc_final: 0.8001 (tpt) REVERT: A 44 GLN cc_start: 0.8582 (tt0) cc_final: 0.8381 (tm-30) REVERT: A 56 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7551 (ttt-90) REVERT: A 193 ASP cc_start: 0.8703 (m-30) cc_final: 0.8050 (p0) REVERT: C 56 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7536 (ttt-90) REVERT: C 95 GLN cc_start: 0.8377 (tp-100) cc_final: 0.8043 (mm-40) REVERT: C 193 ASP cc_start: 0.8695 (m-30) cc_final: 0.8000 (p0) REVERT: C 250 MET cc_start: 0.8372 (tpp) cc_final: 0.8034 (tpt) REVERT: D 44 GLN cc_start: 0.8554 (tt0) cc_final: 0.8343 (tm-30) REVERT: D 56 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7539 (ttt-90) REVERT: D 95 GLN cc_start: 0.8372 (tp40) cc_final: 0.8108 (mm-40) REVERT: D 164 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8313 (ttp) REVERT: D 250 MET cc_start: 0.8363 (tpp) cc_final: 0.8016 (tpt) outliers start: 19 outliers final: 12 residues processed: 179 average time/residue: 0.1215 time to fit residues: 29.1613 Evaluate side-chains 173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN A 60 GLN C 60 GLN C 231 ASN D 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116208 restraints weight = 13256.637| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.05 r_work: 0.3209 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.121 Angle : 0.472 5.750 14464 Z= 0.245 Chirality : 0.039 0.118 1644 Planarity : 0.004 0.034 1880 Dihedral : 4.033 15.677 1472 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.80 % Allowed : 12.86 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.88 (0.23), residues: 1364 helix: 2.09 (0.19), residues: 688 sheet: -2.19 (0.32), residues: 224 loop : -0.16 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.013 0.001 TYR D 213 PHE 0.014 0.001 PHE D 79 TRP 0.008 0.001 TRP B 147 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00282 (10672) covalent geometry : angle 0.47227 (14464) hydrogen bonds : bond 0.03947 ( 524) hydrogen bonds : angle 3.53877 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.489 Fit side-chains REVERT: B 42 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.6848 (mtt90) REVERT: B 56 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7505 (ttt-90) REVERT: B 95 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7966 (mm-40) REVERT: B 250 MET cc_start: 0.8339 (tpp) cc_final: 0.7956 (tpt) REVERT: A 56 ARG cc_start: 0.7872 (ttp80) cc_final: 0.6981 (ttp80) REVERT: A 95 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8119 (mm-40) REVERT: A 193 ASP cc_start: 0.8680 (m-30) cc_final: 0.7993 (p0) REVERT: C 56 ARG cc_start: 0.7868 (ttp80) cc_final: 0.6986 (ttp80) REVERT: C 193 ASP cc_start: 0.8667 (m-30) cc_final: 0.7964 (p0) REVERT: C 250 MET cc_start: 0.8415 (tpp) cc_final: 0.8025 (tpt) REVERT: D 44 GLN cc_start: 0.8560 (tt0) cc_final: 0.8354 (tm-30) REVERT: D 56 ARG cc_start: 0.7860 (ttp80) cc_final: 0.6960 (ttp80) REVERT: D 250 MET cc_start: 0.8396 (tpp) cc_final: 0.8020 (tpt) outliers start: 20 outliers final: 14 residues processed: 177 average time/residue: 0.1276 time to fit residues: 30.5433 Evaluate side-chains 171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 127 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN C 231 ASN D 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118404 restraints weight = 13048.256| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.02 r_work: 0.3302 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10672 Z= 0.097 Angle : 0.446 7.333 14464 Z= 0.230 Chirality : 0.039 0.118 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.836 15.373 1472 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.80 % Allowed : 12.77 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.16 (0.23), residues: 1364 helix: 2.39 (0.19), residues: 692 sheet: -2.16 (0.32), residues: 224 loop : -0.12 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 56 TYR 0.009 0.001 TYR D 213 PHE 0.010 0.001 PHE A 79 TRP 0.005 0.001 TRP B 147 HIS 0.002 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00222 (10672) covalent geometry : angle 0.44626 (14464) hydrogen bonds : bond 0.03422 ( 524) hydrogen bonds : angle 3.32937 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.279 Fit side-chains REVERT: B 42 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.6866 (mtt90) REVERT: B 56 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7505 (ttt-90) REVERT: B 95 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7972 (mm-40) REVERT: B 250 MET cc_start: 0.8310 (tpp) cc_final: 0.7911 (tpt) REVERT: B 329 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7546 (ptmt) REVERT: A 56 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7576 (ttt-90) REVERT: A 95 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7976 (mm-40) REVERT: A 193 ASP cc_start: 0.8704 (m-30) cc_final: 0.7999 (p0) REVERT: A 329 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7556 (ptmt) REVERT: C 56 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7553 (ttt-90) REVERT: C 193 ASP cc_start: 0.8639 (m-30) cc_final: 0.7954 (p0) REVERT: C 250 MET cc_start: 0.8416 (tpp) cc_final: 0.7988 (tpt) REVERT: D 56 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7556 (ttt-90) REVERT: D 95 GLN cc_start: 0.8333 (tp40) cc_final: 0.8110 (mm-40) REVERT: D 250 MET cc_start: 0.8364 (tpp) cc_final: 0.7961 (tpt) outliers start: 20 outliers final: 16 residues processed: 176 average time/residue: 0.1317 time to fit residues: 30.9285 Evaluate side-chains 166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 90 optimal weight: 0.0770 chunk 97 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 0.0270 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN ** C 231 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 = 0.3808 r_free = 0.3808 target = 0.147996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120131 restraints weight = 13134.135| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.04 r_work: 0.3335 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10672 Z= 0.090 Angle : 0.444 6.358 14464 Z= 0.228 Chirality : 0.038 0.118 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.687 14.811 1472 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.71 % Allowed : 13.58 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.39 (0.23), residues: 1364 helix: 2.56 (0.19), residues: 692 sheet: -2.10 (0.32), residues: 224 loop : 0.05 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 56 TYR 0.009 0.001 TYR D 213 PHE 0.008 0.001 PHE D 79 TRP 0.004 0.001 TRP A 147 HIS 0.002 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00201 (10672) covalent geometry : angle 0.44350 (14464) hydrogen bonds : bond 0.03083 ( 524) hydrogen bonds : angle 3.21104 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.348 Fit side-chains REVERT: B 42 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.6830 (mtt90) REVERT: B 56 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7628 (ttt-90) REVERT: B 95 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7941 (mm-40) REVERT: B 250 MET cc_start: 0.8358 (tpp) cc_final: 0.7977 (tpt) REVERT: A 56 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7607 (ttp80) REVERT: A 95 GLN cc_start: 0.8331 (tp-100) cc_final: 0.7947 (mm-40) REVERT: A 193 ASP cc_start: 0.8727 (m-30) cc_final: 0.7979 (p0) REVERT: C 56 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7607 (ttp80) REVERT: C 193 ASP cc_start: 0.8687 (m-30) cc_final: 0.7967 (p0) REVERT: C 250 MET cc_start: 0.8382 (tpp) cc_final: 0.7957 (tpt) REVERT: D 95 GLN cc_start: 0.8376 (tp40) cc_final: 0.8057 (mm-40) REVERT: D 231 ASN cc_start: 0.9122 (p0) cc_final: 0.8872 (p0) REVERT: D 250 MET cc_start: 0.8295 (tpp) cc_final: 0.7922 (tpt) outliers start: 19 outliers final: 11 residues processed: 177 average time/residue: 0.1338 time to fit residues: 31.5373 Evaluate side-chains 164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 31 optimal weight: 0.0000 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120311 restraints weight = 12989.223| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.03 r_work: 0.3334 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10672 Z= 0.093 Angle : 0.442 5.742 14464 Z= 0.228 Chirality : 0.039 0.116 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.604 14.650 1472 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.71 % Allowed : 14.93 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.56 (0.23), residues: 1364 helix: 2.64 (0.19), residues: 696 sheet: -1.98 (0.33), residues: 220 loop : 0.17 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 42 TYR 0.011 0.001 TYR D 213 PHE 0.007 0.001 PHE C 79 TRP 0.004 0.001 TRP B 295 HIS 0.002 0.000 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00208 (10672) covalent geometry : angle 0.44161 (14464) hydrogen bonds : bond 0.02987 ( 524) hydrogen bonds : angle 3.12131 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.390 Fit side-chains REVERT: B 42 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.6835 (mtt90) REVERT: B 56 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7635 (ttt-90) REVERT: B 95 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7945 (mm-40) REVERT: B 250 MET cc_start: 0.8297 (tpp) cc_final: 0.7953 (tpt) REVERT: B 329 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7642 (ptmt) REVERT: A 95 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7993 (mm-40) REVERT: A 193 ASP cc_start: 0.8727 (m-30) cc_final: 0.7950 (p0) REVERT: A 329 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7632 (ptmt) REVERT: C 56 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7683 (ttt-90) REVERT: C 95 GLN cc_start: 0.8349 (tp40) cc_final: 0.8049 (mm-40) REVERT: C 193 ASP cc_start: 0.8743 (m-30) cc_final: 0.7956 (p0) REVERT: C 250 MET cc_start: 0.8373 (tpp) cc_final: 0.7950 (tpt) REVERT: D 95 GLN cc_start: 0.8365 (tp40) cc_final: 0.8039 (mm-40) REVERT: D 231 ASN cc_start: 0.9093 (p0) cc_final: 0.8863 (p0) REVERT: D 250 MET cc_start: 0.8342 (tpp) cc_final: 0.7947 (tpt) REVERT: D 329 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7647 (ptmt) outliers start: 19 outliers final: 14 residues processed: 167 average time/residue: 0.1415 time to fit residues: 30.9066 Evaluate side-chains 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 129 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 117 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 231 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 = 0.3796 r_free = 0.3796 target = 0.146617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119185 restraints weight = 13036.597| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.02 r_work: 0.3307 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10672 Z= 0.106 Angle : 0.464 5.996 14464 Z= 0.240 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.642 14.796 1472 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.53 % Allowed : 15.56 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.60 (0.23), residues: 1364 helix: 2.67 (0.19), residues: 696 sheet: -1.94 (0.34), residues: 200 loop : 0.05 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 56 TYR 0.014 0.001 TYR D 213 PHE 0.008 0.001 PHE C 79 TRP 0.005 0.001 TRP C 147 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00248 (10672) covalent geometry : angle 0.46426 (14464) hydrogen bonds : bond 0.03152 ( 524) hydrogen bonds : angle 3.14995 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.397 Fit side-chains REVERT: B 42 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.6841 (mtt90) REVERT: B 56 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7637 (ttt-90) REVERT: B 95 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7956 (mm-40) REVERT: B 250 MET cc_start: 0.8319 (tpp) cc_final: 0.7974 (tpt) REVERT: B 329 LYS cc_start: 0.8011 (mtpt) cc_final: 0.7579 (ptmt) REVERT: A 95 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8017 (mm-40) REVERT: A 193 ASP cc_start: 0.8753 (m-30) cc_final: 0.7941 (p0) REVERT: A 329 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7631 (ptmt) REVERT: C 52 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: C 56 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7699 (ttt-90) REVERT: C 95 GLN cc_start: 0.8362 (tp40) cc_final: 0.8096 (mm-40) REVERT: C 193 ASP cc_start: 0.8725 (m-30) cc_final: 0.7925 (p0) REVERT: C 250 MET cc_start: 0.8373 (tpp) cc_final: 0.7951 (tpt) REVERT: C 329 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7667 (ptmt) REVERT: D 95 GLN cc_start: 0.8410 (tp40) cc_final: 0.8085 (mm-40) REVERT: D 231 ASN cc_start: 0.9113 (p0) cc_final: 0.8885 (p0) REVERT: D 250 MET cc_start: 0.8353 (tpp) cc_final: 0.7932 (tpt) REVERT: D 329 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7648 (ptmt) outliers start: 17 outliers final: 15 residues processed: 159 average time/residue: 0.1408 time to fit residues: 29.7203 Evaluate side-chains 161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN D 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118464 restraints weight = 13205.816| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.03 r_work: 0.3298 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.114 Angle : 0.469 5.799 14464 Z= 0.242 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.642 14.625 1472 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.80 % Allowed : 15.38 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.61 (0.23), residues: 1364 helix: 2.68 (0.19), residues: 696 sheet: -1.95 (0.33), residues: 200 loop : 0.06 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 56 TYR 0.018 0.001 TYR B 213 PHE 0.008 0.001 PHE C 79 TRP 0.006 0.001 TRP D 147 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00267 (10672) covalent geometry : angle 0.46921 (14464) hydrogen bonds : bond 0.03254 ( 524) hydrogen bonds : angle 3.16522 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.400 Fit side-chains REVERT: B 95 GLN cc_start: 0.8308 (tp-100) cc_final: 0.7941 (mm-40) REVERT: B 250 MET cc_start: 0.8363 (tpp) cc_final: 0.7994 (tpt) REVERT: A 52 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: A 95 GLN cc_start: 0.8362 (tp-100) cc_final: 0.8023 (mm-40) REVERT: A 193 ASP cc_start: 0.8694 (m-30) cc_final: 0.7888 (p0) REVERT: A 338 CYS cc_start: 0.7895 (t) cc_final: 0.7335 (t) REVERT: C 52 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6974 (mm-30) REVERT: C 95 GLN cc_start: 0.8394 (tp40) cc_final: 0.8045 (mm-40) REVERT: C 193 ASP cc_start: 0.8692 (m-30) cc_final: 0.7914 (p0) REVERT: C 250 MET cc_start: 0.8384 (tpp) cc_final: 0.7949 (tpt) REVERT: C 329 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7563 (ptmt) REVERT: C 338 CYS cc_start: 0.7914 (t) cc_final: 0.7316 (t) REVERT: D 95 GLN cc_start: 0.8405 (tp40) cc_final: 0.8079 (mm-40) REVERT: D 231 ASN cc_start: 0.9086 (p0) cc_final: 0.8846 (p0) REVERT: D 250 MET cc_start: 0.8356 (tpp) cc_final: 0.7927 (tpt) REVERT: D 329 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7589 (ptmt) outliers start: 20 outliers final: 16 residues processed: 161 average time/residue: 0.1361 time to fit residues: 29.1059 Evaluate side-chains 164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 0.0060 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 0.0170 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.5434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 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 = 0.3799 r_free = 0.3799 target = 0.146917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119432 restraints weight = 12982.669| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.02 r_work: 0.3323 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10672 Z= 0.101 Angle : 0.472 6.083 14464 Z= 0.244 Chirality : 0.039 0.116 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.612 14.544 1472 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.62 % Allowed : 15.47 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.65 (0.23), residues: 1364 helix: 2.71 (0.19), residues: 696 sheet: -1.93 (0.33), residues: 200 loop : 0.10 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 56 TYR 0.015 0.001 TYR A 213 PHE 0.008 0.001 PHE C 79 TRP 0.005 0.001 TRP B 295 HIS 0.002 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00234 (10672) covalent geometry : angle 0.47201 (14464) hydrogen bonds : bond 0.03072 ( 524) hydrogen bonds : angle 3.13787 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.423 Fit side-chains REVERT: B 95 GLN cc_start: 0.8340 (tp-100) cc_final: 0.7955 (mm-40) REVERT: B 250 MET cc_start: 0.8299 (tpp) cc_final: 0.7962 (tpt) REVERT: B 329 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7638 (ptmt) REVERT: A 95 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7950 (mm-40) REVERT: A 193 ASP cc_start: 0.8743 (m-30) cc_final: 0.7894 (p0) REVERT: A 278 GLU cc_start: 0.7763 (pt0) cc_final: 0.7490 (pt0) REVERT: A 329 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7701 (ptmt) REVERT: A 338 CYS cc_start: 0.7995 (t) cc_final: 0.7565 (t) REVERT: C 95 GLN cc_start: 0.8382 (tp40) cc_final: 0.8002 (mm-40) REVERT: C 193 ASP cc_start: 0.8735 (m-30) cc_final: 0.7922 (p0) REVERT: C 250 MET cc_start: 0.8371 (tpp) cc_final: 0.7940 (tpt) REVERT: C 329 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7628 (ptmt) REVERT: C 338 CYS cc_start: 0.7867 (t) cc_final: 0.7291 (t) REVERT: D 95 GLN cc_start: 0.8424 (tp40) cc_final: 0.8084 (mm-40) REVERT: D 231 ASN cc_start: 0.9159 (p0) cc_final: 0.8892 (p0) REVERT: D 250 MET cc_start: 0.8301 (tpp) cc_final: 0.7904 (tpt) REVERT: D 329 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7628 (ptmt) outliers start: 18 outliers final: 15 residues processed: 162 average time/residue: 0.1402 time to fit residues: 29.8175 Evaluate side-chains 161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 0.0670 chunk 63 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 ASN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.147454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119968 restraints weight = 13048.483| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.02 r_work: 0.3330 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10672 Z= 0.099 Angle : 0.466 6.123 14464 Z= 0.241 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.564 14.507 1472 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.44 % Allowed : 15.74 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.69 (0.23), residues: 1364 helix: 2.74 (0.19), residues: 696 sheet: -1.91 (0.33), residues: 200 loop : 0.12 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 56 TYR 0.017 0.001 TYR A 213 PHE 0.007 0.001 PHE C 79 TRP 0.005 0.001 TRP C 295 HIS 0.002 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00228 (10672) covalent geometry : angle 0.46565 (14464) hydrogen bonds : bond 0.03017 ( 524) hydrogen bonds : angle 3.12077 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2608.53 seconds wall clock time: 45 minutes 31.26 seconds (2731.26 seconds total)