Starting phenix.real_space_refine on Mon Jul 28 14:47:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ka3_22757/07_2025/7ka3_22757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ka3_22757/07_2025/7ka3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ka3_22757/07_2025/7ka3_22757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ka3_22757/07_2025/7ka3_22757.map" model { file = "/net/cci-nas-00/data/ceres_data/7ka3_22757/07_2025/7ka3_22757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ka3_22757/07_2025/7ka3_22757.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, D Time building chain proxies: 5.97, per 1000 atoms: 0.57 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: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.30 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: 3.16 Time building geometry restraints manager: 3.34 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.440 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.003 TRP A 295 HIS 0.003 0.001 HIS B 245 PHE 0.016 0.002 PHE C 144 TYR 0.014 0.002 TYR A 213 ARG 0.003 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.14922 ( 524) hydrogen bonds : angle 6.18886 ( 1536) covalent geometry : bond 0.00422 (10672) covalent geometry : angle 0.76079 (14464) *********************** 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 : 1.112 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: 0.6757 (tpt) outliers start: 4 outliers final: 4 residues processed: 213 average time/residue: 0.2589 time to fit residues: 74.2699 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 : 1.155 ------------------------------------------------------------------------------- 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 114 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN D 50 ASN D 60 GLN D 125 GLN D 274 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119000 restraints weight = 12895.943| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.04 r_work: 0.3297 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10672 Z= 0.122 Angle : 0.515 6.692 14464 Z= 0.267 Chirality : 0.040 0.129 1644 Planarity : 0.004 0.039 1880 Dihedral : 4.316 15.906 1476 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.35 % Allowed : 10.16 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1364 helix: 0.90 (0.18), residues: 684 sheet: -2.03 (0.35), residues: 204 loop : -0.52 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 147 HIS 0.002 0.001 HIS B 156 PHE 0.008 0.001 PHE B 144 TYR 0.012 0.001 TYR A 213 ARG 0.006 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 524) hydrogen bonds : angle 4.08836 ( 1536) covalent geometry : bond 0.00275 (10672) covalent geometry : angle 0.51477 (14464) *********************** 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 : 1.272 Fit side-chains REVERT: B 56 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7440 (ttt-90) REVERT: B 95 GLN cc_start: 0.8333 (tp-100) cc_final: 0.8088 (mm-40) REVERT: B 250 MET cc_start: 0.8284 (tpp) cc_final: 0.7905 (tpt) REVERT: A 56 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7456 (ttt-90) REVERT: A 95 GLN cc_start: 0.8347 (tp-100) cc_final: 0.8063 (mm-40) REVERT: A 193 ASP cc_start: 0.8681 (m-30) cc_final: 0.8082 (p0) REVERT: C 56 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7407 (ttt-90) REVERT: C 95 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8038 (mm-40) REVERT: C 193 ASP cc_start: 0.8697 (m-30) cc_final: 0.8055 (p0) REVERT: C 250 MET cc_start: 0.8339 (tpp) cc_final: 0.8003 (tpt) REVERT: D 44 GLN cc_start: 0.8551 (tt0) cc_final: 0.8316 (tm-30) REVERT: D 56 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7395 (ttt-90) REVERT: D 250 MET cc_start: 0.8341 (tpp) cc_final: 0.7969 (tpt) outliers start: 15 outliers final: 6 residues processed: 187 average time/residue: 0.2645 time to fit residues: 67.3987 Evaluate side-chains 169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 126 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN A 324 GLN C 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118274 restraints weight = 13027.779| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.05 r_work: 0.3308 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10672 Z= 0.110 Angle : 0.469 5.669 14464 Z= 0.243 Chirality : 0.039 0.119 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.080 15.123 1472 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.44 % Allowed : 12.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1364 helix: 1.72 (0.19), residues: 696 sheet: -2.13 (0.32), residues: 224 loop : -0.15 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 147 HIS 0.002 0.000 HIS D 220 PHE 0.007 0.001 PHE B 144 TYR 0.011 0.001 TYR B 213 ARG 0.003 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 524) hydrogen bonds : angle 3.67929 ( 1536) covalent geometry : bond 0.00249 (10672) covalent geometry : angle 0.46883 (14464) *********************** 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 189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.220 Fit side-chains REVERT: B 56 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7421 (ttt-90) REVERT: B 95 GLN cc_start: 0.8308 (tp-100) cc_final: 0.8018 (mm-40) REVERT: B 250 MET cc_start: 0.8301 (tpp) cc_final: 0.7910 (tpt) REVERT: A 56 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7510 (ttt-90) REVERT: A 95 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8017 (mm-40) REVERT: A 193 ASP cc_start: 0.8708 (m-30) cc_final: 0.8068 (p0) REVERT: C 56 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7492 (ttt-90) REVERT: C 95 GLN cc_start: 0.8321 (tp-100) cc_final: 0.8004 (mm-40) REVERT: C 193 ASP cc_start: 0.8680 (m-30) cc_final: 0.8038 (p0) REVERT: C 250 MET cc_start: 0.8352 (tpp) cc_final: 0.7969 (tpt) REVERT: D 44 GLN cc_start: 0.8552 (tt0) cc_final: 0.8342 (tm-30) REVERT: D 56 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7497 (ttt-90) REVERT: D 95 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8119 (mm-40) REVERT: D 250 MET cc_start: 0.8341 (tpp) cc_final: 0.7937 (tpt) outliers start: 16 outliers final: 11 residues processed: 178 average time/residue: 0.2697 time to fit residues: 64.8124 Evaluate side-chains 170 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 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 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 52 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.143701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115804 restraints weight = 13142.862| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.04 r_work: 0.3267 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.146 Angle : 0.483 6.333 14464 Z= 0.250 Chirality : 0.040 0.122 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.062 16.197 1472 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.62 % Allowed : 13.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1364 helix: 2.08 (0.19), residues: 688 sheet: -2.21 (0.32), residues: 224 loop : -0.15 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 147 HIS 0.002 0.001 HIS A 156 PHE 0.008 0.001 PHE A 144 TYR 0.014 0.001 TYR A 213 ARG 0.003 0.001 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 524) hydrogen bonds : angle 3.53739 ( 1536) covalent geometry : bond 0.00347 (10672) covalent geometry : angle 0.48276 (14464) *********************** 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 182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.388 Fit side-chains REVERT: B 42 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.6838 (mtt90) REVERT: B 56 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7617 (ttt-90) REVERT: B 250 MET cc_start: 0.8360 (tpp) cc_final: 0.7986 (tpt) REVERT: A 56 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7533 (ttt-90) REVERT: A 193 ASP cc_start: 0.8735 (m-30) cc_final: 0.8014 (p0) REVERT: A 329 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7630 (ptmt) REVERT: C 56 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7508 (ttt-90) REVERT: C 193 ASP cc_start: 0.8694 (m-30) cc_final: 0.8002 (p0) REVERT: C 250 MET cc_start: 0.8401 (tpp) cc_final: 0.7991 (tpt) REVERT: D 44 GLN cc_start: 0.8578 (tt0) cc_final: 0.8361 (tm-30) REVERT: D 56 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7554 (ttt-90) REVERT: D 95 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7977 (mm-40) REVERT: D 250 MET cc_start: 0.8392 (tpp) cc_final: 0.8025 (tpt) REVERT: D 329 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7603 (ptmt) outliers start: 18 outliers final: 15 residues processed: 171 average time/residue: 0.2876 time to fit residues: 66.0490 Evaluate side-chains 173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 45 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 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 83 optimal weight: 0.3980 chunk 134 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 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 = 0.3785 r_free = 0.3785 target = 0.146034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118227 restraints weight = 12999.155| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.01 r_work: 0.3295 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2312 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= 0.102 Angle : 0.453 7.081 14464 Z= 0.233 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.033 1880 Dihedral : 3.880 15.201 1472 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.89 % Allowed : 14.12 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1364 helix: 2.39 (0.19), residues: 688 sheet: -2.14 (0.32), residues: 224 loop : -0.05 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.001 0.000 HIS D 156 PHE 0.014 0.001 PHE C 79 TYR 0.009 0.001 TYR B 213 ARG 0.003 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 524) hydrogen bonds : angle 3.35686 ( 1536) covalent geometry : bond 0.00236 (10672) covalent geometry : angle 0.45342 (14464) *********************** 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 192 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.219 Fit side-chains REVERT: B 56 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7535 (ttt-90) REVERT: B 95 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8096 (mm-40) REVERT: B 250 MET cc_start: 0.8308 (tpp) cc_final: 0.7931 (tpt) REVERT: B 329 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7606 (ptmt) REVERT: A 56 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7629 (ttt-90) REVERT: A 95 GLN cc_start: 0.8313 (tp-100) cc_final: 0.8091 (mm-40) REVERT: A 193 ASP cc_start: 0.8667 (m-30) cc_final: 0.7998 (p0) REVERT: C 56 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7625 (ttt-90) REVERT: C 193 ASP cc_start: 0.8662 (m-30) cc_final: 0.7972 (p0) REVERT: C 250 MET cc_start: 0.8368 (tpp) cc_final: 0.7962 (tpt) REVERT: C 329 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7553 (ptmt) REVERT: D 56 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7545 (ttt-90) REVERT: D 95 GLN cc_start: 0.8308 (tp-100) cc_final: 0.7997 (mm-40) REVERT: D 250 MET cc_start: 0.8340 (tpp) cc_final: 0.7948 (tpt) outliers start: 21 outliers final: 14 residues processed: 180 average time/residue: 0.2734 time to fit residues: 66.1915 Evaluate side-chains 166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET 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 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 308 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 132 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118309 restraints weight = 13116.191| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.04 r_work: 0.3306 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2444 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= 0.106 Angle : 0.453 6.435 14464 Z= 0.233 Chirality : 0.039 0.119 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.807 15.450 1472 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.89 % Allowed : 13.04 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 688 sheet: -2.10 (0.34), residues: 204 loop : -0.10 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 147 HIS 0.001 0.000 HIS B 156 PHE 0.011 0.001 PHE C 79 TYR 0.011 0.001 TYR A 213 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 524) hydrogen bonds : angle 3.27130 ( 1536) covalent geometry : bond 0.00245 (10672) covalent geometry : angle 0.45340 (14464) *********************** 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 181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.215 Fit side-chains REVERT: B 56 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7525 (ttt-90) REVERT: B 95 GLN cc_start: 0.8337 (tp-100) cc_final: 0.7940 (mm-40) REVERT: B 250 MET cc_start: 0.8252 (tpp) cc_final: 0.7863 (tpt) REVERT: A 56 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7643 (ttt-90) REVERT: A 95 GLN cc_start: 0.8345 (tp-100) cc_final: 0.8061 (mm-40) REVERT: A 193 ASP cc_start: 0.8712 (m-30) cc_final: 0.7986 (p0) REVERT: A 250 MET cc_start: 0.8155 (tpt) cc_final: 0.7929 (tpt) REVERT: A 329 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7640 (ptmt) REVERT: C 56 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7628 (ttt-90) REVERT: C 193 ASP cc_start: 0.8705 (m-30) cc_final: 0.7960 (p0) REVERT: C 250 MET cc_start: 0.8313 (tpp) cc_final: 0.7964 (tpt) REVERT: D 56 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7563 (ttt-90) REVERT: D 95 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7934 (mm-40) REVERT: D 250 MET cc_start: 0.8338 (tpp) cc_final: 0.7952 (tpt) REVERT: D 329 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7551 (ptmt) outliers start: 21 outliers final: 17 residues processed: 169 average time/residue: 0.2913 time to fit residues: 65.2580 Evaluate side-chains 161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116663 restraints weight = 13323.752| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.04 r_work: 0.3225 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.132 Angle : 0.475 5.667 14464 Z= 0.245 Chirality : 0.040 0.120 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.831 15.372 1472 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.89 % Allowed : 14.21 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1364 helix: 2.30 (0.19), residues: 712 sheet: -2.02 (0.33), residues: 200 loop : -0.04 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.002 0.000 HIS B 220 PHE 0.011 0.001 PHE C 79 TYR 0.014 0.001 TYR A 213 ARG 0.003 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 524) hydrogen bonds : angle 3.29664 ( 1536) covalent geometry : bond 0.00316 (10672) covalent geometry : angle 0.47452 (14464) *********************** 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 178 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.166 Fit side-chains REVERT: B 56 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7551 (ttt-90) REVERT: B 95 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7920 (mm-40) REVERT: B 250 MET cc_start: 0.8295 (tpp) cc_final: 0.7924 (tpt) REVERT: B 329 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7561 (ptmt) REVERT: A 56 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7681 (ttt-90) REVERT: A 95 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8063 (mm-40) REVERT: A 193 ASP cc_start: 0.8714 (m-30) cc_final: 0.7912 (p0) REVERT: A 250 MET cc_start: 0.8287 (tpt) cc_final: 0.8054 (tpt) REVERT: C 56 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7657 (ttt-90) REVERT: C 95 GLN cc_start: 0.8321 (tp-100) cc_final: 0.8052 (mm-40) REVERT: C 164 MET cc_start: 0.8552 (tmm) cc_final: 0.8312 (ptt) REVERT: C 193 ASP cc_start: 0.8712 (m-30) cc_final: 0.7917 (p0) REVERT: C 250 MET cc_start: 0.8351 (tpp) cc_final: 0.7989 (tpt) REVERT: C 329 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7527 (ptmt) REVERT: D 56 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7600 (ttt-90) REVERT: D 95 GLN cc_start: 0.8382 (tp-100) cc_final: 0.7938 (mm-40) REVERT: D 231 ASN cc_start: 0.9120 (p0) cc_final: 0.8871 (p0) REVERT: D 250 MET cc_start: 0.8288 (tpp) cc_final: 0.7910 (tpt) outliers start: 21 outliers final: 17 residues processed: 166 average time/residue: 0.3020 time to fit residues: 67.1677 Evaluate side-chains 164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 121 optimal weight: 0.0050 chunk 119 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117986 restraints weight = 13130.673| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.02 r_work: 0.3302 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.108 Angle : 0.460 5.630 14464 Z= 0.238 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.754 15.064 1472 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.62 % Allowed : 14.84 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1364 helix: 2.60 (0.19), residues: 688 sheet: -2.00 (0.33), residues: 200 loop : -0.03 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 147 HIS 0.001 0.000 HIS A 220 PHE 0.009 0.001 PHE C 79 TYR 0.019 0.001 TYR A 213 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 524) hydrogen bonds : angle 3.21988 ( 1536) covalent geometry : bond 0.00252 (10672) covalent geometry : angle 0.46035 (14464) *********************** 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 174 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.131 Fit side-chains REVERT: B 56 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7550 (ttt-90) REVERT: B 95 GLN cc_start: 0.8382 (tp-100) cc_final: 0.7926 (mm-40) REVERT: B 250 MET cc_start: 0.8243 (tpp) cc_final: 0.7872 (tpt) REVERT: B 329 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7511 (ptmt) REVERT: A 56 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7682 (ttt-90) REVERT: A 95 GLN cc_start: 0.8398 (tp-100) cc_final: 0.7958 (mm-40) REVERT: A 193 ASP cc_start: 0.8720 (m-30) cc_final: 0.7883 (p0) REVERT: C 56 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7654 (ttt-90) REVERT: C 95 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8040 (mm-40) REVERT: C 193 ASP cc_start: 0.8712 (m-30) cc_final: 0.7907 (p0) REVERT: C 250 MET cc_start: 0.8308 (tpp) cc_final: 0.7942 (tpt) REVERT: C 329 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7484 (ptmt) REVERT: D 56 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7597 (ttt-90) REVERT: D 95 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7904 (mm-40) REVERT: D 231 ASN cc_start: 0.9154 (p0) cc_final: 0.8900 (p0) REVERT: D 250 MET cc_start: 0.8245 (tpp) cc_final: 0.7880 (tpt) REVERT: D 329 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7529 (ptmt) outliers start: 18 outliers final: 17 residues processed: 163 average time/residue: 0.2893 time to fit residues: 62.6318 Evaluate side-chains 163 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117072 restraints weight = 13276.849| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.02 r_work: 0.3290 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.123 Angle : 0.473 5.771 14464 Z= 0.244 Chirality : 0.040 0.118 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.775 15.259 1472 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.53 % Allowed : 15.83 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1364 helix: 2.35 (0.19), residues: 712 sheet: -2.02 (0.33), residues: 200 loop : 0.04 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.002 0.000 HIS B 220 PHE 0.010 0.001 PHE C 79 TYR 0.016 0.001 TYR A 213 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 524) hydrogen bonds : angle 3.23897 ( 1536) covalent geometry : bond 0.00295 (10672) covalent geometry : angle 0.47329 (14464) *********************** 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 168 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.238 Fit side-chains REVERT: B 56 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7625 (ttt-90) REVERT: B 95 GLN cc_start: 0.8389 (tp-100) cc_final: 0.7982 (mm-40) REVERT: B 250 MET cc_start: 0.8271 (tpp) cc_final: 0.7904 (tpt) REVERT: B 329 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7524 (ptmt) REVERT: A 56 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7716 (ttt-90) REVERT: A 95 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8004 (mm-40) REVERT: A 193 ASP cc_start: 0.8689 (m-30) cc_final: 0.7893 (p0) REVERT: A 329 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7614 (ptmt) REVERT: C 56 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7718 (ttt-90) REVERT: C 95 GLN cc_start: 0.8376 (tp-100) cc_final: 0.8086 (mm-40) REVERT: C 193 ASP cc_start: 0.8702 (m-30) cc_final: 0.7908 (p0) REVERT: C 250 MET cc_start: 0.8360 (tpp) cc_final: 0.7993 (tpt) REVERT: D 56 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7630 (ttt-90) REVERT: D 95 GLN cc_start: 0.8372 (tp-100) cc_final: 0.7966 (mm-40) REVERT: D 231 ASN cc_start: 0.9136 (p0) cc_final: 0.8905 (p0) REVERT: D 250 MET cc_start: 0.8267 (tpp) cc_final: 0.7892 (tpt) REVERT: D 329 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7540 (ptmt) outliers start: 17 outliers final: 17 residues processed: 157 average time/residue: 0.2967 time to fit residues: 61.9854 Evaluate side-chains 162 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116230 restraints weight = 13217.545| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.02 r_work: 0.3280 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2697 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= 0.135 Angle : 0.482 5.631 14464 Z= 0.249 Chirality : 0.040 0.121 1644 Planarity : 0.004 0.032 1880 Dihedral : 3.818 15.397 1472 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.53 % Allowed : 16.28 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1364 helix: 2.56 (0.19), residues: 688 sheet: -2.07 (0.33), residues: 200 loop : -0.05 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 147 HIS 0.002 0.000 HIS A 220 PHE 0.010 0.001 PHE C 79 TYR 0.018 0.001 TYR A 213 ARG 0.002 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 524) hydrogen bonds : angle 3.26555 ( 1536) covalent geometry : bond 0.00324 (10672) covalent geometry : angle 0.48226 (14464) ********************** 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 162 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.249 Fit side-chains REVERT: B 56 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7659 (ttt-90) REVERT: B 95 GLN cc_start: 0.8397 (tp-100) cc_final: 0.7988 (mm-40) REVERT: B 250 MET cc_start: 0.8259 (tpp) cc_final: 0.7898 (tpt) REVERT: A 56 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7731 (ttt-90) REVERT: A 95 GLN cc_start: 0.8382 (tp-100) cc_final: 0.7995 (mm-40) REVERT: A 329 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7554 (ptmt) REVERT: C 56 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7747 (ttt-90) REVERT: C 95 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8101 (mm-40) REVERT: C 250 MET cc_start: 0.8347 (tpp) cc_final: 0.7961 (tpt) REVERT: D 56 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7690 (ttt-90) REVERT: D 250 MET cc_start: 0.8250 (tpp) cc_final: 0.7876 (tpt) outliers start: 17 outliers final: 17 residues processed: 151 average time/residue: 0.3449 time to fit residues: 68.3895 Evaluate side-chains 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118324 restraints weight = 13022.742| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.02 r_work: 0.3270 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2752 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= 0.104 Angle : 0.467 6.071 14464 Z= 0.241 Chirality : 0.039 0.116 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.695 15.044 1472 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.62 % Allowed : 15.92 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.23), residues: 1364 helix: 2.65 (0.19), residues: 688 sheet: -2.04 (0.33), residues: 200 loop : -0.00 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.001 0.000 HIS C 219 PHE 0.010 0.001 PHE C 79 TYR 0.012 0.001 TYR A 213 ARG 0.002 0.000 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 524) hydrogen bonds : angle 3.18764 ( 1536) covalent geometry : bond 0.00243 (10672) covalent geometry : angle 0.46720 (14464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5739.46 seconds wall clock time: 100 minutes 59.78 seconds (6059.78 seconds total)