Starting phenix.real_space_refine on Sun Aug 24 14:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1o_39732/08_2025/8z1o_39732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1o_39732/08_2025/8z1o_39732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1o_39732/08_2025/8z1o_39732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1o_39732/08_2025/8z1o_39732.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1o_39732/08_2025/8z1o_39732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1o_39732/08_2025/8z1o_39732.cif" } resolution = 3.6 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= 0.009 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 72 5.16 5 C 13110 2.51 5 N 3630 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20802 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3467 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 441} Chain: "B" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3467 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 441} Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3467 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 441} Chain: "D" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3467 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 441} Chain: "E" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3467 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 441} Chain: "F" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3467 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 441} Time building chain proxies: 4.82, per 1000 atoms: 0.23 Number of scatterers: 20802 At special positions: 0 Unit cell: (118.68, 125.58, 118.68, 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 72 16.00 O 3990 8.00 N 3630 7.00 C 13110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 812.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4860 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 21 sheets defined 54.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 23 Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.787A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 107 removed outlier: 3.516A pdb=" N LEU A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.721A pdb=" N LYS A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.815A pdb=" N GLY A 188 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 214 Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.807A pdb=" N GLU A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 4.075A pdb=" N GLY A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.714A pdb=" N VAL A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.800A pdb=" N ALA A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 380 through 396 Processing helix chain 'A' and resid 400 through 427 Processing helix chain 'A' and resid 436 through 456 Processing helix chain 'B' and resid 7 through 23 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 32 through 41 removed outlier: 4.257A pdb=" N ALA B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 107 removed outlier: 3.842A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 141 Processing helix chain 'B' and resid 158 through 173 removed outlier: 3.717A pdb=" N LYS B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 removed outlier: 4.230A pdb=" N GLY B 188 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 195 through 213 Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.677A pdb=" N GLU B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 4.032A pdb=" N GLY B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 336 removed outlier: 3.572A pdb=" N VAL B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.800A pdb=" N ALA B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'B' and resid 380 through 396 Processing helix chain 'B' and resid 400 through 427 Processing helix chain 'B' and resid 436 through 457 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 41 removed outlier: 3.519A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 107 removed outlier: 3.845A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 158 through 171 removed outlier: 3.665A pdb=" N LYS C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.837A pdb=" N GLY C 188 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 214 removed outlier: 4.596A pdb=" N THR C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY C 198 " --> pdb=" O PRO C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 266 through 279 Processing helix chain 'C' and resid 283 through 288 removed outlier: 3.868A pdb=" N GLY C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 336 Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.797A pdb=" N ALA C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 380 through 396 Processing helix chain 'C' and resid 400 through 427 removed outlier: 3.536A pdb=" N VAL C 404 " --> pdb=" O THR C 400 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 456 Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 32 through 41 removed outlier: 4.360A pdb=" N ALA D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 107 removed outlier: 3.839A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 141 removed outlier: 3.520A pdb=" N GLU D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'D' and resid 184 through 188 removed outlier: 3.811A pdb=" N GLY D 188 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 213 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 266 through 279 removed outlier: 3.995A pdb=" N GLN D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 288 removed outlier: 4.115A pdb=" N GLY D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 350 through 364 Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.703A pdb=" N ALA D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.519A pdb=" N ALA D 378 " --> pdb=" O PRO D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 396 Processing helix chain 'D' and resid 400 through 427 removed outlier: 3.500A pdb=" N VAL D 404 " --> pdb=" O THR D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'E' and resid 7 through 23 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 32 through 41 removed outlier: 4.259A pdb=" N ALA E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 107 removed outlier: 3.843A pdb=" N PHE E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 141 removed outlier: 3.651A pdb=" N GLU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 173 removed outlier: 3.515A pdb=" N VAL E 162 " --> pdb=" O THR E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 removed outlier: 4.252A pdb=" N GLY E 188 " --> pdb=" O GLY E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 214 Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 266 through 279 removed outlier: 3.713A pdb=" N LEU E 272 " --> pdb=" O GLU E 268 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU E 279 " --> pdb=" O GLN E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 288 removed outlier: 3.985A pdb=" N GLY E 288 " --> pdb=" O ALA E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 Processing helix chain 'E' and resid 350 through 364 Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.774A pdb=" N ALA E 368 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 379 removed outlier: 3.508A pdb=" N ALA E 378 " --> pdb=" O PRO E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 396 Processing helix chain 'E' and resid 400 through 427 removed outlier: 3.545A pdb=" N ARG E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 409 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 456 Processing helix chain 'F' and resid 7 through 23 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 32 through 41 removed outlier: 4.339A pdb=" N ALA F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 107 removed outlier: 3.873A pdb=" N PHE F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 141 removed outlier: 3.704A pdb=" N GLU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 173 Processing helix chain 'F' and resid 184 through 188 removed outlier: 3.805A pdb=" N GLY F 188 " --> pdb=" O GLY F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 214 Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 266 through 279 removed outlier: 3.628A pdb=" N LEU F 272 " --> pdb=" O GLU F 268 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 288 removed outlier: 4.148A pdb=" N GLY F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 337 removed outlier: 3.573A pdb=" N GLY F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 365 through 369 removed outlier: 3.817A pdb=" N ALA F 368 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 379 Processing helix chain 'F' and resid 380 through 396 Processing helix chain 'F' and resid 400 through 427 Processing helix chain 'F' and resid 436 through 456 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.100A pdb=" N ARG A 82 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY A 112 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY E 112 " --> pdb=" O PHE E 70 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ARG E 82 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.915A pdb=" N TYR A 77 " --> pdb=" O VAL A 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 247 removed outlier: 6.231A pdb=" N ALA A 316 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 341 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 249 through 252 Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.136A pdb=" N ARG B 82 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLY B 112 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 70 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY D 112 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG D 82 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.791A pdb=" N TYR B 77 " --> pdb=" O VAL B 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 247 removed outlier: 6.316A pdb=" N ALA B 316 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 341 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AA9, first strand: chain 'C' and resid 81 through 83 removed outlier: 6.159A pdb=" N ARG C 82 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY C 112 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY F 112 " --> pdb=" O PHE F 70 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG F 82 " --> pdb=" O SER F 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 78 removed outlier: 7.006A pdb=" N TYR C 77 " --> pdb=" O VAL C 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 247 removed outlier: 6.278A pdb=" N ALA C 316 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 249 through 251 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 78 removed outlier: 6.779A pdb=" N TYR D 77 " --> pdb=" O VAL D 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 246 through 247 removed outlier: 6.107A pdb=" N ALA D 316 " --> pdb=" O ALA D 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 249 through 252 Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 78 removed outlier: 7.038A pdb=" N TYR E 77 " --> pdb=" O VAL E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 246 through 247 removed outlier: 6.558A pdb=" N ILE E 341 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 249 through 251 Processing sheet with id=AC1, first strand: chain 'F' and resid 77 through 78 removed outlier: 7.060A pdb=" N TYR F 77 " --> pdb=" O VAL F 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 246 through 247 removed outlier: 3.665A pdb=" N SER F 227 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA F 316 " --> pdb=" O ALA F 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 249 through 251 1179 hydrogen bonds defined for protein. 3459 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: 4.29 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7031 1.34 - 1.46: 4635 1.46 - 1.58: 9448 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 21228 Sorted by residual: bond pdb=" CB GLN E 275 " pdb=" CG GLN E 275 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" C GLY E 115 " pdb=" N GLY E 116 " ideal model delta sigma weight residual 1.329 1.316 0.012 9.60e-03 1.09e+04 1.66e+00 bond pdb=" CB MET C 110 " pdb=" CG MET C 110 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" C ALA B 152 " pdb=" N GLY B 153 " ideal model delta sigma weight residual 1.329 1.344 -0.016 1.39e-02 5.18e+03 1.29e+00 bond pdb=" C ALA E 152 " pdb=" N GLY E 153 " ideal model delta sigma weight residual 1.329 1.344 -0.016 1.39e-02 5.18e+03 1.26e+00 ... (remaining 21223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 28237 1.93 - 3.87: 388 3.87 - 5.80: 66 5.80 - 7.74: 13 7.74 - 9.67: 6 Bond angle restraints: 28710 Sorted by residual: angle pdb=" CA GLN E 275 " pdb=" CB GLN E 275 " pdb=" CG GLN E 275 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C LYS A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta sigma weight residual 120.31 115.11 5.20 1.52e+00 4.33e-01 1.17e+01 angle pdb=" CB MET B 412 " pdb=" CG MET B 412 " pdb=" SD MET B 412 " ideal model delta sigma weight residual 112.70 122.14 -9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" CB GLN E 275 " pdb=" CG GLN E 275 " pdb=" CD GLN E 275 " ideal model delta sigma weight residual 112.60 117.93 -5.33 1.70e+00 3.46e-01 9.84e+00 angle pdb=" CB MET E 412 " pdb=" CG MET E 412 " pdb=" SD MET E 412 " ideal model delta sigma weight residual 112.70 121.26 -8.56 3.00e+00 1.11e-01 8.14e+00 ... (remaining 28705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10939 17.66 - 35.31: 1186 35.31 - 52.97: 287 52.97 - 70.63: 51 70.63 - 88.29: 29 Dihedral angle restraints: 12492 sinusoidal: 4824 harmonic: 7668 Sorted by residual: dihedral pdb=" CA GLU C 195 " pdb=" C GLU C 195 " pdb=" N ALA C 196 " pdb=" CA ALA C 196 " ideal model delta harmonic sigma weight residual -180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA SER E 249 " pdb=" C SER E 249 " pdb=" N LEU E 250 " pdb=" CA LEU E 250 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA MET B 110 " pdb=" C MET B 110 " pdb=" N GLY B 111 " pdb=" CA GLY B 111 " ideal model delta harmonic sigma weight residual -180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 12489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1784 0.030 - 0.061: 892 0.061 - 0.091: 259 0.091 - 0.121: 140 0.121 - 0.151: 15 Chirality restraints: 3090 Sorted by residual: chirality pdb=" CA ILE D 144 " pdb=" N ILE D 144 " pdb=" C ILE D 144 " pdb=" CB ILE D 144 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CG LEU B 180 " pdb=" CB LEU B 180 " pdb=" CD1 LEU B 180 " pdb=" CD2 LEU B 180 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE A 144 " pdb=" N ILE A 144 " pdb=" C ILE A 144 " pdb=" CB ILE A 144 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 3087 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 150 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO D 151 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 151 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 151 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 84 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO E 85 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 85 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 85 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 150 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO B 151 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " -0.029 5.00e-02 4.00e+02 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 434 2.68 - 3.24: 20722 3.24 - 3.79: 33316 3.79 - 4.35: 43372 4.35 - 4.90: 73092 Nonbonded interactions: 170936 Sorted by model distance: nonbonded pdb=" OE2 GLU C 343 " pdb=" OH TYR C 372 " model vdw 2.130 3.040 nonbonded pdb=" OG SER B 326 " pdb=" OE1 GLU B 329 " model vdw 2.165 3.040 nonbonded pdb=" O LYS A 183 " pdb=" NH2 ARG A 193 " model vdw 2.168 3.120 nonbonded pdb=" OE1 GLU F 44 " pdb=" OH TYR F 77 " model vdw 2.224 3.040 nonbonded pdb=" O ILE B 144 " pdb=" NH1 ARG B 173 " model vdw 2.225 3.120 ... (remaining 170931 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.560 Find NCS groups from input model: 0.370 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 0.042 21228 Z= 0.193 Angle : 0.610 9.673 28710 Z= 0.322 Chirality : 0.042 0.151 3090 Planarity : 0.004 0.058 3804 Dihedral : 15.873 88.287 7632 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.27 % Favored : 97.51 % Rotamer: Outliers : 0.19 % Allowed : 20.38 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.16), residues: 2736 helix: 1.70 (0.14), residues: 1296 sheet: 0.41 (0.27), residues: 330 loop : -0.42 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 173 TYR 0.016 0.001 TYR A 203 PHE 0.023 0.002 PHE D 357 TRP 0.015 0.002 TRP A 53 HIS 0.005 0.001 HIS F 309 Details of bonding type rmsd covalent geometry : bond 0.00439 (21228) covalent geometry : angle 0.60975 (28710) hydrogen bonds : bond 0.20687 ( 1179) hydrogen bonds : angle 6.60353 ( 3459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 390 MET cc_start: 0.7064 (mmm) cc_final: 0.6787 (tpt) REVERT: F 343 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7511 (mt-10) outliers start: 4 outliers final: 1 residues processed: 159 average time/residue: 0.1069 time to fit residues: 29.2976 Evaluate side-chains 149 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN B 360 HIS D 175 GLN E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104134 restraints weight = 31056.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104968 restraints weight = 29768.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106016 restraints weight = 30870.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106467 restraints weight = 20208.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106876 restraints weight = 18260.081| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21228 Z= 0.187 Angle : 0.561 6.719 28710 Z= 0.297 Chirality : 0.043 0.140 3090 Planarity : 0.004 0.051 3804 Dihedral : 3.917 25.744 2929 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.72 % Favored : 98.06 % Rotamer: Outliers : 3.29 % Allowed : 18.12 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.16), residues: 2736 helix: 1.71 (0.14), residues: 1410 sheet: 0.59 (0.33), residues: 270 loop : -0.76 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 173 TYR 0.016 0.001 TYR B 199 PHE 0.017 0.002 PHE A 119 TRP 0.018 0.002 TRP A 53 HIS 0.003 0.001 HIS F 309 Details of bonding type rmsd covalent geometry : bond 0.00436 (21228) covalent geometry : angle 0.56067 (28710) hydrogen bonds : bond 0.05025 ( 1179) hydrogen bonds : angle 4.53795 ( 3459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 166 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7811 (ptt) cc_final: 0.7562 (ptt) REVERT: A 158 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 390 MET cc_start: 0.6830 (tmm) cc_final: 0.6499 (tpp) REVERT: B 259 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8038 (tp) REVERT: B 371 TRP cc_start: 0.8729 (OUTLIER) cc_final: 0.8100 (t60) REVERT: C 343 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: C 390 MET cc_start: 0.7120 (mmm) cc_final: 0.6890 (tpt) REVERT: D 279 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: E 131 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8496 (tpp80) REVERT: F 272 LEU cc_start: 0.7959 (mt) cc_final: 0.7422 (tt) REVERT: F 333 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9024 (mm) outliers start: 70 outliers final: 45 residues processed: 221 average time/residue: 0.1133 time to fit residues: 41.2648 Evaluate side-chains 194 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 399 TRP Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 399 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 155 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN B 360 HIS E 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100909 restraints weight = 31408.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101552 restraints weight = 31681.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102300 restraints weight = 33265.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103213 restraints weight = 20830.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105061 restraints weight = 18495.771| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21228 Z= 0.260 Angle : 0.606 10.574 28710 Z= 0.317 Chirality : 0.045 0.160 3090 Planarity : 0.004 0.048 3804 Dihedral : 4.163 27.938 2929 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.52 % Favored : 97.26 % Rotamer: Outliers : 4.93 % Allowed : 17.28 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.16), residues: 2736 helix: 1.77 (0.14), residues: 1368 sheet: 0.64 (0.33), residues: 252 loop : -0.88 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 130 TYR 0.013 0.001 TYR A 203 PHE 0.019 0.002 PHE D 119 TRP 0.017 0.002 TRP D 53 HIS 0.004 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00612 (21228) covalent geometry : angle 0.60567 (28710) hydrogen bonds : bond 0.05412 ( 1179) hydrogen bonds : angle 4.43800 ( 3459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 151 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8456 (m-80) cc_final: 0.8162 (m-80) REVERT: B 110 MET cc_start: 0.8533 (ppp) cc_final: 0.8309 (ptm) REVERT: B 371 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.8156 (t60) REVERT: C 343 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: C 390 MET cc_start: 0.7453 (mmm) cc_final: 0.7179 (tpt) REVERT: D 70 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: D 279 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: D 300 TYR cc_start: 0.7666 (t80) cc_final: 0.7437 (t80) REVERT: E 131 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8611 (tpp80) REVERT: E 371 TRP cc_start: 0.8803 (OUTLIER) cc_final: 0.8055 (t60) REVERT: F 272 LEU cc_start: 0.8203 (mt) cc_final: 0.7501 (tt) REVERT: F 333 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8969 (mm) REVERT: F 409 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8267 (ttmm) outliers start: 105 outliers final: 66 residues processed: 241 average time/residue: 0.1191 time to fit residues: 47.5876 Evaluate side-chains 210 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 136 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 409 LYS Chi-restraints excluded: chain F residue 438 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 163 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS E 282 GLN E 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104952 restraints weight = 31115.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105867 restraints weight = 31174.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106628 restraints weight = 32107.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.107450 restraints weight = 20173.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109458 restraints weight = 18117.425| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21228 Z= 0.118 Angle : 0.502 9.380 28710 Z= 0.259 Chirality : 0.041 0.139 3090 Planarity : 0.003 0.043 3804 Dihedral : 3.680 20.882 2929 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.54 % Favored : 98.25 % Rotamer: Outliers : 3.33 % Allowed : 19.01 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.16), residues: 2736 helix: 2.06 (0.14), residues: 1374 sheet: 0.15 (0.32), residues: 282 loop : -0.72 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.017 0.001 TYR B 199 PHE 0.013 0.001 PHE A 119 TRP 0.014 0.001 TRP D 176 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00269 (21228) covalent geometry : angle 0.50171 (28710) hydrogen bonds : bond 0.03798 ( 1179) hydrogen bonds : angle 4.06456 ( 3459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 160 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 MET cc_start: 0.8542 (ppp) cc_final: 0.8243 (ptt) REVERT: B 176 TRP cc_start: 0.3817 (OUTLIER) cc_final: 0.2912 (m100) REVERT: B 208 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7728 (ttp) REVERT: C 259 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7788 (mm) REVERT: C 390 MET cc_start: 0.7394 (mmm) cc_final: 0.7150 (tpt) REVERT: D 70 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: D 176 TRP cc_start: 0.4637 (OUTLIER) cc_final: 0.3460 (m100) REVERT: E 131 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8561 (tpp80) REVERT: E 259 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8627 (mm) REVERT: E 272 LEU cc_start: 0.8816 (mt) cc_final: 0.8073 (tt) REVERT: F 272 LEU cc_start: 0.8291 (mt) cc_final: 0.7584 (tt) REVERT: F 275 GLN cc_start: 0.7950 (pp30) cc_final: 0.7694 (pp30) REVERT: F 333 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9000 (mm) REVERT: F 456 GLN cc_start: 0.8853 (mt0) cc_final: 0.8462 (mt0) outliers start: 71 outliers final: 47 residues processed: 218 average time/residue: 0.1268 time to fit residues: 45.5812 Evaluate side-chains 200 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 41 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 175 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 256 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 225 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN B 360 HIS E 282 GLN E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101191 restraints weight = 31857.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100324 restraints weight = 28858.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102150 restraints weight = 24125.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103061 restraints weight = 18424.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103521 restraints weight = 16610.199| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21228 Z= 0.103 Angle : 0.483 8.275 28710 Z= 0.247 Chirality : 0.040 0.131 3090 Planarity : 0.003 0.042 3804 Dihedral : 3.435 21.850 2929 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.86 % Favored : 97.92 % Rotamer: Outliers : 3.76 % Allowed : 18.40 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.17), residues: 2736 helix: 2.28 (0.14), residues: 1374 sheet: 0.10 (0.30), residues: 360 loop : -0.47 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.018 0.001 TYR A 235 PHE 0.011 0.001 PHE F 101 TRP 0.014 0.001 TRP C 176 HIS 0.003 0.000 HIS F 309 Details of bonding type rmsd covalent geometry : bond 0.00233 (21228) covalent geometry : angle 0.48328 (28710) hydrogen bonds : bond 0.03530 ( 1179) hydrogen bonds : angle 3.89920 ( 3459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 165 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8375 (ptp) REVERT: B 176 TRP cc_start: 0.3655 (OUTLIER) cc_final: 0.2673 (m100) REVERT: B 208 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7838 (ttp) REVERT: B 259 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7897 (mm) REVERT: C 176 TRP cc_start: 0.3971 (OUTLIER) cc_final: 0.2999 (m100) REVERT: C 275 GLN cc_start: 0.7700 (pp30) cc_final: 0.7405 (pp30) REVERT: C 343 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: C 390 MET cc_start: 0.7497 (mmm) cc_final: 0.7217 (tpt) REVERT: D 70 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: D 176 TRP cc_start: 0.4284 (OUTLIER) cc_final: 0.3145 (m100) REVERT: D 390 MET cc_start: 0.7126 (tpt) cc_final: 0.6895 (tpp) REVERT: E 131 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8583 (tpp80) REVERT: E 259 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8504 (mm) REVERT: E 371 TRP cc_start: 0.8598 (OUTLIER) cc_final: 0.8080 (t60) REVERT: F 271 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7757 (tm-30) REVERT: F 272 LEU cc_start: 0.8370 (mt) cc_final: 0.7283 (tt) REVERT: F 275 GLN cc_start: 0.8011 (pp30) cc_final: 0.7755 (pp30) REVERT: F 297 LYS cc_start: 0.7345 (tppt) cc_final: 0.7070 (tppp) REVERT: F 333 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8967 (mm) REVERT: F 409 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8240 (ttmm) REVERT: F 456 GLN cc_start: 0.8847 (mt0) cc_final: 0.8418 (mt0) outliers start: 80 outliers final: 51 residues processed: 228 average time/residue: 0.1142 time to fit residues: 43.1851 Evaluate side-chains 213 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 156 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 116 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100815 restraints weight = 31599.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100521 restraints weight = 27032.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101769 restraints weight = 23694.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103246 restraints weight = 18154.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103490 restraints weight = 16053.002| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21228 Z= 0.107 Angle : 0.480 9.009 28710 Z= 0.244 Chirality : 0.040 0.129 3090 Planarity : 0.003 0.039 3804 Dihedral : 3.373 21.981 2929 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.54 % Favored : 98.25 % Rotamer: Outliers : 3.62 % Allowed : 18.73 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.17), residues: 2736 helix: 2.42 (0.14), residues: 1368 sheet: 0.18 (0.30), residues: 360 loop : -0.43 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.021 0.001 TYR A 235 PHE 0.011 0.001 PHE A 119 TRP 0.012 0.001 TRP D 176 HIS 0.003 0.000 HIS F 309 Details of bonding type rmsd covalent geometry : bond 0.00246 (21228) covalent geometry : angle 0.48025 (28710) hydrogen bonds : bond 0.03530 ( 1179) hydrogen bonds : angle 3.85426 ( 3459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 157 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 TRP cc_start: 0.3654 (OUTLIER) cc_final: 0.2602 (m100) REVERT: B 208 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7796 (ttp) REVERT: B 259 ILE cc_start: 0.8109 (tp) cc_final: 0.7849 (mm) REVERT: C 176 TRP cc_start: 0.3855 (OUTLIER) cc_final: 0.2861 (m100) REVERT: C 343 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: C 390 MET cc_start: 0.7503 (mmm) cc_final: 0.7256 (tpt) REVERT: D 70 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: D 176 TRP cc_start: 0.4293 (OUTLIER) cc_final: 0.3161 (m100) REVERT: D 390 MET cc_start: 0.7138 (tpt) cc_final: 0.6900 (tpp) REVERT: E 110 MET cc_start: 0.7713 (ttm) cc_final: 0.7481 (tpp) REVERT: E 131 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8556 (tpp80) REVERT: E 259 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8467 (mm) REVERT: E 371 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.8095 (t60) REVERT: F 271 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7807 (tp30) REVERT: F 272 LEU cc_start: 0.8330 (mt) cc_final: 0.7405 (tt) REVERT: F 297 LYS cc_start: 0.7266 (tppt) cc_final: 0.7010 (tppp) REVERT: F 333 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8965 (mm) REVERT: F 456 GLN cc_start: 0.8851 (mt0) cc_final: 0.8402 (mt0) outliers start: 77 outliers final: 56 residues processed: 220 average time/residue: 0.1049 time to fit residues: 38.2436 Evaluate side-chains 217 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 151 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 211 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 200 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.134472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092460 restraints weight = 31925.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095678 restraints weight = 19717.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096887 restraints weight = 14920.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097666 restraints weight = 13927.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097639 restraints weight = 12650.195| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21228 Z= 0.155 Angle : 0.517 8.976 28710 Z= 0.265 Chirality : 0.041 0.134 3090 Planarity : 0.003 0.043 3804 Dihedral : 3.551 25.287 2929 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.23 % Favored : 97.55 % Rotamer: Outliers : 3.76 % Allowed : 18.92 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.16), residues: 2736 helix: 2.32 (0.14), residues: 1368 sheet: 0.68 (0.32), residues: 300 loop : -0.68 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 82 TYR 0.015 0.001 TYR A 203 PHE 0.014 0.002 PHE D 119 TRP 0.016 0.001 TRP D 176 HIS 0.002 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00365 (21228) covalent geometry : angle 0.51746 (28710) hydrogen bonds : bond 0.04165 ( 1179) hydrogen bonds : angle 3.93043 ( 3459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 149 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 TRP cc_start: 0.4254 (OUTLIER) cc_final: 0.3479 (m100) REVERT: B 259 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7934 (mm) REVERT: B 371 TRP cc_start: 0.8755 (OUTLIER) cc_final: 0.8088 (t60) REVERT: C 176 TRP cc_start: 0.3567 (OUTLIER) cc_final: 0.3007 (m100) REVERT: C 256 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8287 (p) REVERT: C 343 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: C 390 MET cc_start: 0.7515 (mmm) cc_final: 0.7253 (tpt) REVERT: D 70 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: D 176 TRP cc_start: 0.4477 (OUTLIER) cc_final: 0.3323 (m100) REVERT: D 390 MET cc_start: 0.7231 (tpt) cc_final: 0.7006 (tpp) REVERT: D 412 MET cc_start: 0.9041 (mmm) cc_final: 0.8799 (mmt) REVERT: E 131 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8662 (tpp80) REVERT: E 259 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8389 (mm) REVERT: E 272 LEU cc_start: 0.8940 (mt) cc_final: 0.8407 (tt) REVERT: E 329 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8718 (mp0) REVERT: E 371 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.8033 (t60) REVERT: F 78 LYS cc_start: 0.7567 (tttt) cc_final: 0.7047 (tttp) REVERT: F 110 MET cc_start: 0.7607 (mtm) cc_final: 0.7229 (mtt) REVERT: F 129 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.9003 (tt) REVERT: F 271 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7833 (tm-30) REVERT: F 272 LEU cc_start: 0.8340 (mt) cc_final: 0.7623 (tt) REVERT: F 275 GLN cc_start: 0.8232 (pp30) cc_final: 0.8017 (pp30) REVERT: F 297 LYS cc_start: 0.7211 (tppt) cc_final: 0.6943 (tppp) REVERT: F 333 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8897 (mm) REVERT: F 386 SER cc_start: 0.8212 (m) cc_final: 0.7906 (p) REVERT: F 409 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8210 (ttmm) outliers start: 80 outliers final: 59 residues processed: 217 average time/residue: 0.1137 time to fit residues: 40.6333 Evaluate side-chains 218 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 144 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 390 MET Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 225 optimal weight: 0.0370 chunk 28 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.134505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097814 restraints weight = 31837.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098629 restraints weight = 24051.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100093 restraints weight = 19612.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100368 restraints weight = 16139.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103950 restraints weight = 15532.467| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21228 Z= 0.146 Angle : 0.508 9.239 28710 Z= 0.260 Chirality : 0.041 0.140 3090 Planarity : 0.003 0.041 3804 Dihedral : 3.521 23.047 2929 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.79 % Favored : 97.99 % Rotamer: Outliers : 3.57 % Allowed : 18.78 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.16), residues: 2736 helix: 2.29 (0.14), residues: 1374 sheet: 0.07 (0.29), residues: 360 loop : -0.52 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 131 TYR 0.022 0.001 TYR A 235 PHE 0.014 0.001 PHE A 119 TRP 0.014 0.001 TRP D 176 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00343 (21228) covalent geometry : angle 0.50825 (28710) hydrogen bonds : bond 0.03915 ( 1179) hydrogen bonds : angle 3.90380 ( 3459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 149 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 TRP cc_start: 0.4268 (OUTLIER) cc_final: 0.3474 (m100) REVERT: B 208 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8269 (ttp) REVERT: C 176 TRP cc_start: 0.3583 (OUTLIER) cc_final: 0.3050 (m100) REVERT: C 343 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: C 390 MET cc_start: 0.7540 (mmm) cc_final: 0.7249 (tpt) REVERT: D 70 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: D 176 TRP cc_start: 0.4633 (OUTLIER) cc_final: 0.3517 (m100) REVERT: D 390 MET cc_start: 0.7134 (tpt) cc_final: 0.6904 (tpp) REVERT: D 412 MET cc_start: 0.9133 (mmm) cc_final: 0.8854 (mmt) REVERT: E 131 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8608 (tpp80) REVERT: E 259 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8497 (mm) REVERT: E 272 LEU cc_start: 0.8952 (mt) cc_final: 0.8362 (tt) REVERT: E 371 TRP cc_start: 0.8619 (OUTLIER) cc_final: 0.8084 (t60) REVERT: F 129 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8930 (tt) REVERT: F 243 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8479 (tt) REVERT: F 259 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8176 (mm) REVERT: F 271 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7861 (tp30) REVERT: F 272 LEU cc_start: 0.8325 (mt) cc_final: 0.7896 (tt) REVERT: F 275 GLN cc_start: 0.7915 (pp30) cc_final: 0.7645 (pp30) REVERT: F 297 LYS cc_start: 0.7357 (tppt) cc_final: 0.7141 (tppp) REVERT: F 333 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8998 (mm) REVERT: F 386 SER cc_start: 0.8162 (m) cc_final: 0.7901 (p) REVERT: F 409 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8210 (ttmm) outliers start: 76 outliers final: 55 residues processed: 214 average time/residue: 0.1108 time to fit residues: 39.1834 Evaluate side-chains 209 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 140 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 390 MET Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 253 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100071 restraints weight = 31717.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099686 restraints weight = 25756.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100800 restraints weight = 23362.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102399 restraints weight = 17883.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102584 restraints weight = 15765.982| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21228 Z= 0.105 Angle : 0.488 8.385 28710 Z= 0.249 Chirality : 0.040 0.131 3090 Planarity : 0.003 0.039 3804 Dihedral : 3.385 21.270 2929 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.75 % Favored : 98.03 % Rotamer: Outliers : 3.15 % Allowed : 19.20 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.17), residues: 2736 helix: 2.41 (0.14), residues: 1374 sheet: 0.34 (0.28), residues: 402 loop : -0.41 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.013 0.001 TYR A 203 PHE 0.011 0.001 PHE B 132 TRP 0.016 0.001 TRP F 176 HIS 0.003 0.000 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00239 (21228) covalent geometry : angle 0.48814 (28710) hydrogen bonds : bond 0.03442 ( 1179) hydrogen bonds : angle 3.81861 ( 3459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 151 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 TRP cc_start: 0.4049 (OUTLIER) cc_final: 0.3342 (m100) REVERT: B 208 MET cc_start: 0.8566 (ttp) cc_final: 0.8213 (ttp) REVERT: C 129 ILE cc_start: 0.9036 (pt) cc_final: 0.8517 (mt) REVERT: C 176 TRP cc_start: 0.3790 (OUTLIER) cc_final: 0.3286 (m100) REVERT: C 343 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: C 390 MET cc_start: 0.7571 (mmm) cc_final: 0.7278 (tpt) REVERT: D 70 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: D 176 TRP cc_start: 0.4186 (OUTLIER) cc_final: 0.3318 (m100) REVERT: E 131 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8581 (tpp80) REVERT: E 272 LEU cc_start: 0.8933 (mt) cc_final: 0.8361 (tt) REVERT: E 371 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.7965 (t60) REVERT: F 259 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8106 (mm) REVERT: F 271 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7887 (tp30) REVERT: F 272 LEU cc_start: 0.8279 (mt) cc_final: 0.7788 (tt) REVERT: F 275 GLN cc_start: 0.7889 (pp30) cc_final: 0.7627 (pp30) REVERT: F 333 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9021 (mm) REVERT: F 409 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8249 (ttmm) REVERT: F 456 GLN cc_start: 0.8849 (mt0) cc_final: 0.8399 (mt0) outliers start: 67 outliers final: 54 residues processed: 209 average time/residue: 0.1289 time to fit residues: 44.3108 Evaluate side-chains 207 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 143 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 176 TRP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 390 MET Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 222 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099247 restraints weight = 31919.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098909 restraints weight = 28023.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100687 restraints weight = 23227.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101339 restraints weight = 18198.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101915 restraints weight = 16296.885| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21228 Z= 0.119 Angle : 0.501 8.621 28710 Z= 0.254 Chirality : 0.041 0.134 3090 Planarity : 0.003 0.038 3804 Dihedral : 3.412 22.700 2929 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.94 % Favored : 97.84 % Rotamer: Outliers : 3.05 % Allowed : 19.34 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.16), residues: 2736 helix: 2.42 (0.14), residues: 1374 sheet: 0.59 (0.30), residues: 342 loop : -0.59 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 131 TYR 0.015 0.001 TYR A 203 PHE 0.013 0.001 PHE A 119 TRP 0.015 0.001 TRP F 176 HIS 0.006 0.001 HIS F 309 Details of bonding type rmsd covalent geometry : bond 0.00277 (21228) covalent geometry : angle 0.50102 (28710) hydrogen bonds : bond 0.03630 ( 1179) hydrogen bonds : angle 3.81457 ( 3459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 150 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8976 (mmm) cc_final: 0.8724 (mmt) REVERT: B 176 TRP cc_start: 0.4143 (OUTLIER) cc_final: 0.3349 (m100) REVERT: B 208 MET cc_start: 0.8579 (ttp) cc_final: 0.8177 (ttp) REVERT: C 78 LYS cc_start: 0.7261 (tttt) cc_final: 0.6966 (mttp) REVERT: C 129 ILE cc_start: 0.9076 (pt) cc_final: 0.8558 (mt) REVERT: C 176 TRP cc_start: 0.4134 (OUTLIER) cc_final: 0.3240 (m100) REVERT: C 259 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7911 (mm) REVERT: C 343 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: D 70 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: D 176 TRP cc_start: 0.4333 (OUTLIER) cc_final: 0.3522 (m100) REVERT: D 412 MET cc_start: 0.8910 (mmm) cc_final: 0.8680 (mmt) REVERT: E 131 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8648 (tpp80) REVERT: E 272 LEU cc_start: 0.8937 (mt) cc_final: 0.8364 (tt) REVERT: E 297 LYS cc_start: 0.7324 (tppt) cc_final: 0.6658 (mmmt) REVERT: E 371 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.8005 (t60) REVERT: F 129 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8939 (tt) REVERT: F 259 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8282 (mm) REVERT: F 271 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7882 (tp30) REVERT: F 272 LEU cc_start: 0.8286 (mt) cc_final: 0.7782 (tt) REVERT: F 275 GLN cc_start: 0.7887 (pp30) cc_final: 0.7616 (pp30) REVERT: F 333 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9032 (mm) REVERT: F 409 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8246 (ttmm) REVERT: F 456 GLN cc_start: 0.8872 (mt0) cc_final: 0.8436 (mt0) outliers start: 65 outliers final: 51 residues processed: 206 average time/residue: 0.1288 time to fit residues: 43.9186 Evaluate side-chains 207 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 144 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 145 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 266 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104302 restraints weight = 31238.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104924 restraints weight = 30380.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105655 restraints weight = 33583.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107005 restraints weight = 21230.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107860 restraints weight = 18483.797| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21228 Z= 0.111 Angle : 0.498 8.674 28710 Z= 0.252 Chirality : 0.040 0.136 3090 Planarity : 0.003 0.038 3804 Dihedral : 3.375 21.622 2929 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.97 % Favored : 97.84 % Rotamer: Outliers : 3.15 % Allowed : 19.30 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.16), residues: 2736 helix: 2.45 (0.14), residues: 1374 sheet: 0.64 (0.30), residues: 342 loop : -0.59 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 131 TYR 0.015 0.001 TYR A 203 PHE 0.011 0.001 PHE A 119 TRP 0.014 0.001 TRP F 176 HIS 0.006 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00257 (21228) covalent geometry : angle 0.49754 (28710) hydrogen bonds : bond 0.03488 ( 1179) hydrogen bonds : angle 3.80303 ( 3459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.30 seconds wall clock time: 41 minutes 1.89 seconds (2461.89 seconds total)