Starting phenix.real_space_refine on Wed Jun 18 04:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1o_39732/06_2025/8z1o_39732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1o_39732/06_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_39732/06_2025/8z1o_39732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1o_39732/06_2025/8z1o_39732.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1o_39732/06_2025/8z1o_39732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1o_39732/06_2025/8z1o_39732.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.09, per 1000 atoms: 0.58 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: 4.61 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.59 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: 7.77 Time building geometry restraints manager: 5.56 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: 0.04 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: 0.590 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: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 47.820 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.560 ------------------------------------------------------------------------------- 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 : 9.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (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 TRP 0.015 0.002 TRP A 53 HIS 0.005 0.001 HIS F 309 PHE 0.023 0.002 PHE D 357 TYR 0.016 0.001 TYR A 203 ARG 0.006 0.001 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.20687 ( 1179) hydrogen bonds : angle 6.60353 ( 3459) covalent geometry : bond 0.00439 (21228) covalent geometry : angle 0.60975 (28710) *********************** 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 : 2.264 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: 0.2690 time to fit residues: 73.0048 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 : 2.151 ------------------------------------------------------------------------------- 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 227 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3655 r_free = 0.3655 target = 0.133860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101111 restraints weight = 31158.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101230 restraints weight = 31508.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102351 restraints weight = 30302.298| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 21228 Z= 0.278 Angle : 0.625 6.730 28710 Z= 0.332 Chirality : 0.045 0.143 3090 Planarity : 0.005 0.054 3804 Dihedral : 4.224 30.797 2929 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.23 % Favored : 97.55 % Rotamer: Outliers : 4.27 % Allowed : 17.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2736 helix: 1.48 (0.14), residues: 1410 sheet: 0.31 (0.28), residues: 330 loop : -0.74 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 53 HIS 0.004 0.001 HIS D 207 PHE 0.020 0.002 PHE A 119 TYR 0.017 0.002 TYR A 372 ARG 0.006 0.001 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.05567 ( 1179) hydrogen bonds : angle 4.63250 ( 3459) covalent geometry : bond 0.00656 (21228) covalent geometry : angle 0.62505 (28710) *********************** 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 250 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 159 time to evaluate : 2.310 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: 0.8056 (ptt) cc_final: 0.7755 (ptm) REVERT: B 78 LYS cc_start: 0.7633 (tptt) cc_final: 0.7385 (tptm) REVERT: B 110 MET cc_start: 0.8580 (ppp) cc_final: 0.8250 (ptt) REVERT: B 371 TRP cc_start: 0.8785 (OUTLIER) cc_final: 0.8142 (t60) REVERT: C 343 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: C 390 MET cc_start: 0.7189 (mmm) cc_final: 0.6976 (tpt) REVERT: D 70 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: D 279 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: E 131 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8604 (tpp80) REVERT: E 371 TRP cc_start: 0.8777 (OUTLIER) cc_final: 0.8102 (t60) REVERT: F 272 LEU cc_start: 0.8117 (mt) cc_final: 0.7300 (tt) outliers start: 91 outliers final: 56 residues processed: 234 average time/residue: 0.2943 time to fit residues: 111.9897 Evaluate side-chains 201 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 139 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 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 355 ASP Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 399 TRP 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 282 GLN Chi-restraints excluded: chain B residue 283 LEU 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 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 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 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 371 TRP Chi-restraints excluded: chain D residue 404 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 259 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 371 TRP 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 399 TRP Chi-restraints excluded: chain F residue 438 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 195 optimal weight: 0.3980 chunk 140 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 225 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS E 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.139189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101423 restraints weight = 31539.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102947 restraints weight = 23045.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104110 restraints weight = 18140.813| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1829 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= 0.099 Angle : 0.503 9.882 28710 Z= 0.257 Chirality : 0.040 0.137 3090 Planarity : 0.003 0.046 3804 Dihedral : 3.610 18.231 2929 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.46 % Favored : 98.32 % Rotamer: Outliers : 2.77 % Allowed : 18.87 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 2736 helix: 2.14 (0.14), residues: 1368 sheet: 1.10 (0.34), residues: 252 loop : -0.75 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 53 HIS 0.003 0.000 HIS C 309 PHE 0.016 0.001 PHE F 101 TYR 0.011 0.001 TYR E 199 ARG 0.007 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1179) hydrogen bonds : angle 4.12029 ( 3459) covalent geometry : bond 0.00212 (21228) covalent geometry : angle 0.50279 (28710) *********************** 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 234 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 2.404 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: 0.8222 (ptt) cc_final: 0.8012 (ptm) REVERT: A 372 TYR cc_start: 0.8241 (t80) cc_final: 0.8026 (t80) REVERT: A 390 MET cc_start: 0.6986 (tmm) cc_final: 0.6697 (tpp) REVERT: B 110 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8273 (ptp) REVERT: C 390 MET cc_start: 0.7305 (mmm) cc_final: 0.7095 (tpt) REVERT: D 70 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: E 131 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8577 (tpp80) REVERT: E 282 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7346 (tp-100) REVERT: F 272 LEU cc_start: 0.8060 (mt) cc_final: 0.7545 (tt) REVERT: F 275 GLN cc_start: 0.8076 (pp30) cc_final: 0.7803 (pp30) REVERT: F 279 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: F 333 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8919 (mm) REVERT: F 343 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7665 (mt-10) REVERT: F 456 GLN cc_start: 0.8861 (mt0) cc_final: 0.8496 (mt0) outliers start: 59 outliers final: 44 residues processed: 220 average time/residue: 0.2837 time to fit residues: 104.7084 Evaluate side-chains 196 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 180 LEU 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 421 GLU Chi-restraints excluded: chain A residue 438 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 176 TRP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 400 THR 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 C residue 346 ASN 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 370 ILE 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 176 TRP Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 438 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 279 GLU Chi-restraints excluded: chain F residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 179 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS E 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100946 restraints weight = 31551.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.101285 restraints weight = 33135.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102380 restraints weight = 33139.455| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21228 Z= 0.243 Angle : 0.577 8.201 28710 Z= 0.302 Chirality : 0.044 0.132 3090 Planarity : 0.004 0.045 3804 Dihedral : 3.947 29.084 2929 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.23 % Favored : 97.55 % Rotamer: Outliers : 4.41 % Allowed : 18.12 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2736 helix: 1.95 (0.14), residues: 1368 sheet: 0.61 (0.33), residues: 252 loop : -0.86 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 176 HIS 0.003 0.001 HIS E 207 PHE 0.017 0.002 PHE A 132 TYR 0.026 0.001 TYR A 235 ARG 0.004 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 1179) hydrogen bonds : angle 4.28519 ( 3459) covalent geometry : bond 0.00571 (21228) covalent geometry : angle 0.57744 (28710) *********************** 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 247 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 153 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8124 (ptt) cc_final: 0.7905 (ptp) REVERT: B 110 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8239 (ptp) REVERT: B 371 TRP cc_start: 0.8801 (OUTLIER) cc_final: 0.8078 (t60) REVERT: C 176 TRP cc_start: 0.3839 (OUTLIER) cc_final: 0.3333 (m100) REVERT: C 343 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: C 390 MET cc_start: 0.7448 (mmm) cc_final: 0.7191 (tpt) REVERT: D 70 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: E 131 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8630 (tpp80) REVERT: E 259 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8650 (mm) REVERT: E 371 TRP cc_start: 0.8763 (OUTLIER) cc_final: 0.8101 (t60) REVERT: E 390 MET cc_start: 0.7492 (mmm) cc_final: 0.7164 (tpt) REVERT: E 422 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8908 (t) REVERT: F 272 LEU cc_start: 0.8139 (mt) cc_final: 0.7457 (tt) REVERT: F 333 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9016 (mm) REVERT: F 409 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8270 (ttmm) outliers start: 94 outliers final: 65 residues processed: 232 average time/residue: 0.2889 time to fit residues: 109.0638 Evaluate side-chains 210 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 134 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 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 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 180 LEU 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 315 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 438 VAL 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 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 438 VAL 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 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 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 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 282 GLN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 422 THR 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 Chi-restraints excluded: chain F residue 438 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 222 optimal weight: 0.0370 chunk 269 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS E 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099742 restraints weight = 32015.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101247 restraints weight = 24064.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102549 restraints weight = 18686.644| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21228 Z= 0.105 Angle : 0.492 8.858 28710 Z= 0.252 Chirality : 0.040 0.133 3090 Planarity : 0.003 0.042 3804 Dihedral : 3.531 20.022 2929 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.54 % Favored : 98.25 % Rotamer: Outliers : 3.33 % Allowed : 19.20 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.16), residues: 2736 helix: 2.23 (0.14), residues: 1368 sheet: 1.10 (0.32), residues: 288 loop : -0.73 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 176 HIS 0.003 0.001 HIS C 309 PHE 0.012 0.001 PHE A 119 TYR 0.028 0.001 TYR A 235 ARG 0.003 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 1179) hydrogen bonds : angle 3.97681 ( 3459) covalent geometry : bond 0.00237 (21228) covalent geometry : angle 0.49188 (28710) *********************** 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 235 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 164 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 TRP cc_start: 0.3654 (OUTLIER) cc_final: 0.2585 (m100) REVERT: B 208 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7800 (ttp) REVERT: B 259 ILE cc_start: 0.8292 (tp) cc_final: 0.8054 (mm) REVERT: C 176 TRP cc_start: 0.4111 (OUTLIER) cc_final: 0.3270 (m100) REVERT: C 343 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: C 390 MET cc_start: 0.7461 (mmm) cc_final: 0.7223 (tpt) REVERT: E 131 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8538 (tpp80) REVERT: E 208 MET cc_start: 0.8428 (ttp) cc_final: 0.7950 (ttp) REVERT: E 259 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8569 (mm) REVERT: E 282 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7427 (tp-100) REVERT: E 390 MET cc_start: 0.7485 (mmm) cc_final: 0.7206 (tpt) REVERT: F 272 LEU cc_start: 0.8350 (mt) cc_final: 0.7840 (tt) REVERT: F 275 GLN cc_start: 0.7964 (pp30) cc_final: 0.7727 (pp30) REVERT: F 279 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: F 297 LYS cc_start: 0.7314 (tppt) cc_final: 0.7028 (tppp) REVERT: F 333 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8996 (mm) REVERT: F 409 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8215 (ttmm) REVERT: F 456 GLN cc_start: 0.8859 (mt0) cc_final: 0.8516 (mt0) outliers start: 71 outliers final: 47 residues processed: 222 average time/residue: 0.2981 time to fit residues: 108.7759 Evaluate side-chains 209 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 2.446 ------------------------------------------------------------------------------- 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 176 TRP Chi-restraints excluded: chain A residue 232 VAL 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 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 438 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 D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 155 ILE 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 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain E residue 40 VAL 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 282 GLN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 16 GLU 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 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 279 GLU 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 217 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 268 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 152 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 346 ASN E 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100405 restraints weight = 31801.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.101118 restraints weight = 23200.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102611 restraints weight = 19199.197| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21228 Z= 0.100 Angle : 0.484 9.388 28710 Z= 0.245 Chirality : 0.040 0.130 3090 Planarity : 0.003 0.039 3804 Dihedral : 3.387 21.621 2929 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.75 % Favored : 98.03 % Rotamer: Outliers : 3.15 % Allowed : 19.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.16), residues: 2736 helix: 2.37 (0.14), residues: 1368 sheet: 0.51 (0.30), residues: 348 loop : -0.51 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 176 HIS 0.002 0.000 HIS F 309 PHE 0.011 0.001 PHE B 132 TYR 0.012 0.001 TYR A 203 ARG 0.002 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1179) hydrogen bonds : angle 3.87060 ( 3459) covalent geometry : bond 0.00227 (21228) covalent geometry : angle 0.48366 (28710) *********************** 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 232 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 165 time to evaluate : 2.278 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: 0.3850 (OUTLIER) cc_final: 0.2731 (m100) REVERT: B 208 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7851 (ttp) REVERT: B 259 ILE cc_start: 0.8155 (tp) cc_final: 0.7911 (mm) REVERT: B 282 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7964 (tp40) REVERT: B 412 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8605 (mmm) REVERT: C 129 ILE cc_start: 0.9039 (pt) cc_final: 0.8533 (mt) REVERT: C 176 TRP cc_start: 0.3381 (OUTLIER) cc_final: 0.2955 (m100) REVERT: C 275 GLN cc_start: 0.7695 (pp30) cc_final: 0.7393 (pp30) REVERT: C 390 MET cc_start: 0.7524 (mmm) cc_final: 0.7250 (tpt) REVERT: D 238 LEU cc_start: 0.9324 (tp) cc_final: 0.9110 (tp) REVERT: D 390 MET cc_start: 0.7290 (tpp) cc_final: 0.6679 (tpt) REVERT: E 131 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8558 (tpp80) REVERT: E 208 MET cc_start: 0.8453 (ttp) cc_final: 0.8149 (ttp) REVERT: E 259 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8441 (mm) REVERT: E 390 MET cc_start: 0.7513 (mmm) cc_final: 0.7310 (tpt) REVERT: F 271 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7750 (tm-30) REVERT: F 272 LEU cc_start: 0.8379 (mt) cc_final: 0.7442 (tt) REVERT: F 275 GLN cc_start: 0.8001 (pp30) cc_final: 0.7718 (pp30) REVERT: F 297 LYS cc_start: 0.7273 (tppt) cc_final: 0.6995 (tppp) REVERT: F 333 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8949 (mm) REVERT: F 409 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8247 (ttmm) REVERT: F 456 GLN cc_start: 0.8840 (mt0) cc_final: 0.8485 (mt0) outliers start: 67 outliers final: 53 residues processed: 221 average time/residue: 0.2985 time to fit residues: 107.5286 Evaluate side-chains 214 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 2.286 ------------------------------------------------------------------------------- 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 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 282 GLN Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 412 MET 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 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 283 LEU Chi-restraints excluded: chain D residue 346 ASN 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 176 TRP Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 438 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 175 GLN B 360 HIS D 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097540 restraints weight = 31826.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098623 restraints weight = 23913.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100164 restraints weight = 19238.248| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21228 Z= 0.156 Angle : 0.517 8.996 28710 Z= 0.265 Chirality : 0.041 0.131 3090 Planarity : 0.003 0.040 3804 Dihedral : 3.539 24.707 2929 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.97 % Favored : 97.81 % Rotamer: Outliers : 3.76 % Allowed : 19.34 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.16), residues: 2736 helix: 2.29 (0.14), residues: 1368 sheet: 1.06 (0.32), residues: 288 loop : -0.73 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 176 HIS 0.003 0.001 HIS F 309 PHE 0.016 0.002 PHE A 119 TYR 0.020 0.001 TYR A 235 ARG 0.002 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1179) hydrogen bonds : angle 3.94481 ( 3459) covalent geometry : bond 0.00366 (21228) covalent geometry : angle 0.51716 (28710) *********************** 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 225 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 145 time to evaluate : 2.093 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: 0.4208 (OUTLIER) cc_final: 0.3095 (m100) REVERT: B 259 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7923 (mm) REVERT: B 412 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8553 (mmm) REVERT: C 129 ILE cc_start: 0.9138 (pt) cc_final: 0.8588 (mt) REVERT: C 176 TRP cc_start: 0.3481 (OUTLIER) cc_final: 0.2890 (m100) REVERT: C 343 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: C 390 MET cc_start: 0.7512 (mmm) cc_final: 0.7252 (tpt) REVERT: D 70 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: D 390 MET cc_start: 0.7020 (tpp) cc_final: 0.6438 (tpt) REVERT: E 131 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8615 (tpp80) REVERT: E 208 MET cc_start: 0.8428 (ttp) cc_final: 0.8170 (ttp) REVERT: E 259 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (mm) REVERT: E 272 LEU cc_start: 0.8958 (mt) cc_final: 0.8384 (tt) REVERT: F 176 TRP cc_start: 0.4723 (OUTLIER) cc_final: 0.3143 (m100) REVERT: F 271 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7788 (tm-30) REVERT: F 272 LEU cc_start: 0.8403 (mt) cc_final: 0.7393 (tt) REVERT: F 275 GLN cc_start: 0.8019 (pp30) cc_final: 0.7613 (pp30) REVERT: F 297 LYS cc_start: 0.7274 (tppt) cc_final: 0.7022 (tppp) REVERT: F 333 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8984 (mm) REVERT: F 409 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8227 (ttmm) outliers start: 80 outliers final: 58 residues processed: 210 average time/residue: 0.2755 time to fit residues: 94.6609 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 : 2.130 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain A residue 346 ASN 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 412 MET 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 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 315 VAL Chi-restraints excluded: chain D residue 346 ASN 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 282 GLN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 438 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 30 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 225 optimal weight: 0.2980 chunk 227 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 282 GLN B 360 HIS D 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097303 restraints weight = 31952.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098221 restraints weight = 23669.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099644 restraints weight = 19303.246| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21228 Z= 0.151 Angle : 0.518 9.000 28710 Z= 0.265 Chirality : 0.041 0.133 3090 Planarity : 0.003 0.041 3804 Dihedral : 3.551 23.997 2929 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.94 % Favored : 97.84 % Rotamer: Outliers : 3.76 % Allowed : 19.06 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.16), residues: 2736 helix: 2.26 (0.14), residues: 1368 sheet: 1.08 (0.31), residues: 288 loop : -0.74 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 176 HIS 0.003 0.001 HIS F 309 PHE 0.015 0.001 PHE A 119 TYR 0.013 0.001 TYR A 203 ARG 0.002 0.000 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 1179) hydrogen bonds : angle 3.94342 ( 3459) covalent geometry : bond 0.00356 (21228) covalent geometry : angle 0.51771 (28710) *********************** 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 224 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 144 time to evaluate : 2.195 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: 0.4286 (OUTLIER) cc_final: 0.3186 (m100) REVERT: B 259 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7975 (mm) REVERT: B 371 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.8004 (t60) REVERT: B 412 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8559 (mmm) REVERT: C 78 LYS cc_start: 0.7202 (tttt) cc_final: 0.6855 (mttp) REVERT: C 129 ILE cc_start: 0.9120 (pt) cc_final: 0.8599 (mt) REVERT: C 176 TRP cc_start: 0.3525 (OUTLIER) cc_final: 0.2930 (m100) REVERT: C 343 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: D 70 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: D 386 SER cc_start: 0.8112 (m) cc_final: 0.7810 (p) REVERT: D 390 MET cc_start: 0.7013 (tpp) cc_final: 0.6453 (tpt) REVERT: E 131 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8632 (tpp80) REVERT: E 208 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8176 (ttp) REVERT: E 272 LEU cc_start: 0.8964 (mt) cc_final: 0.8360 (tt) REVERT: E 329 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8726 (mp0) REVERT: F 176 TRP cc_start: 0.4437 (OUTLIER) cc_final: 0.3270 (m100) REVERT: F 243 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8528 (tt) REVERT: F 259 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8144 (mm) REVERT: F 271 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7883 (tp30) REVERT: F 272 LEU cc_start: 0.8435 (mt) cc_final: 0.7638 (tt) REVERT: F 275 GLN cc_start: 0.7989 (pp30) cc_final: 0.7770 (pp30) REVERT: F 297 LYS cc_start: 0.7305 (tppt) cc_final: 0.7081 (tppp) REVERT: F 333 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8979 (mm) REVERT: F 409 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8230 (ttmm) outliers start: 80 outliers final: 58 residues processed: 211 average time/residue: 0.2812 time to fit residues: 96.8750 Evaluate side-chains 215 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 142 time to evaluate : 2.270 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain A residue 346 ASN 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 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 371 TRP Chi-restraints excluded: chain B residue 412 MET 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 148 THR 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 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 315 VAL 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 208 MET Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 438 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 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 409 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 244 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 360 HIS D 346 ASN E 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098275 restraints weight = 31898.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097838 restraints weight = 27760.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099548 restraints weight = 22827.751| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21228 Z= 0.128 Angle : 0.501 8.651 28710 Z= 0.255 Chirality : 0.041 0.130 3090 Planarity : 0.003 0.040 3804 Dihedral : 3.479 22.774 2929 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.97 % Favored : 97.81 % Rotamer: Outliers : 3.66 % Allowed : 18.92 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.16), residues: 2736 helix: 2.29 (0.14), residues: 1374 sheet: 0.45 (0.27), residues: 378 loop : -0.59 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 176 HIS 0.003 0.001 HIS F 309 PHE 0.013 0.001 PHE A 119 TYR 0.013 0.001 TYR A 235 ARG 0.002 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 1179) hydrogen bonds : angle 3.89611 ( 3459) covalent geometry : bond 0.00299 (21228) covalent geometry : angle 0.50091 (28710) *********************** 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 231 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 153 time to evaluate : 2.361 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: B 176 TRP cc_start: 0.3973 (OUTLIER) cc_final: 0.2975 (m100) REVERT: B 371 TRP cc_start: 0.8633 (OUTLIER) cc_final: 0.7962 (t60) REVERT: B 412 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8561 (mmm) REVERT: C 129 ILE cc_start: 0.9109 (pt) cc_final: 0.8619 (mt) REVERT: C 176 TRP cc_start: 0.3518 (OUTLIER) cc_final: 0.3210 (m100) REVERT: C 343 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: D 70 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: D 161 GLU cc_start: 0.7643 (mp0) cc_final: 0.7440 (mp0) REVERT: D 386 SER cc_start: 0.8165 (m) cc_final: 0.7859 (p) REVERT: D 390 MET cc_start: 0.6949 (tpp) cc_final: 0.6406 (tpt) REVERT: E 131 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8633 (tpp80) REVERT: E 208 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8064 (ttp) REVERT: E 272 LEU cc_start: 0.8955 (mt) cc_final: 0.8369 (tt) REVERT: E 297 LYS cc_start: 0.7293 (tppt) cc_final: 0.6444 (mmmt) REVERT: E 329 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (mp0) REVERT: F 129 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8964 (tt) REVERT: F 176 TRP cc_start: 0.4363 (OUTLIER) cc_final: 0.3220 (m100) REVERT: F 259 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8113 (mm) REVERT: F 271 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7909 (tp30) REVERT: F 272 LEU cc_start: 0.8424 (mt) cc_final: 0.7591 (tt) REVERT: F 297 LYS cc_start: 0.7385 (tppt) cc_final: 0.7184 (tppp) REVERT: F 309 HIS cc_start: 0.7883 (m170) cc_final: 0.7672 (m170) REVERT: F 333 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8993 (mm) REVERT: F 409 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8231 (ttmm) outliers start: 78 outliers final: 55 residues processed: 217 average time/residue: 0.2942 time to fit residues: 104.2222 Evaluate side-chains 214 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 145 time to evaluate : 2.390 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain A residue 346 ASN 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 371 TRP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 412 MET 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 148 THR 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 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 208 MET Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 329 GLU 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 409 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 229 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099189 restraints weight = 31673.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098741 restraints weight = 26291.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099890 restraints weight = 23585.875| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21228 Z= 0.113 Angle : 0.504 9.106 28710 Z= 0.255 Chirality : 0.041 0.138 3090 Planarity : 0.003 0.039 3804 Dihedral : 3.412 22.251 2929 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.01 % Favored : 97.77 % Rotamer: Outliers : 3.24 % Allowed : 19.48 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2736 helix: 2.34 (0.14), residues: 1374 sheet: 0.53 (0.28), residues: 378 loop : -0.59 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 176 HIS 0.003 0.000 HIS F 309 PHE 0.012 0.001 PHE B 132 TYR 0.019 0.001 TYR A 235 ARG 0.002 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 1179) hydrogen bonds : angle 3.86568 ( 3459) covalent geometry : bond 0.00263 (21228) covalent geometry : angle 0.50403 (28710) ********************** 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 223 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 154 time to evaluate : 2.252 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: 0.9038 (mmm) cc_final: 0.8810 (mmt) REVERT: B 176 TRP cc_start: 0.3920 (OUTLIER) cc_final: 0.2933 (m100) REVERT: B 208 MET cc_start: 0.8556 (ttp) cc_final: 0.8282 (ttp) REVERT: B 412 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8583 (mmm) REVERT: C 129 ILE cc_start: 0.9095 (pt) cc_final: 0.8638 (mt) REVERT: C 176 TRP cc_start: 0.3631 (OUTLIER) cc_final: 0.3265 (m100) REVERT: C 343 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: D 238 LEU cc_start: 0.9337 (tp) cc_final: 0.9131 (tp) REVERT: D 386 SER cc_start: 0.8165 (m) cc_final: 0.7842 (p) REVERT: D 390 MET cc_start: 0.6942 (tpp) cc_final: 0.6402 (tpt) REVERT: E 131 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8643 (tpp80) REVERT: E 208 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7965 (ttp) REVERT: E 272 LEU cc_start: 0.8892 (mt) cc_final: 0.8294 (tt) REVERT: E 297 LYS cc_start: 0.7276 (tppt) cc_final: 0.6436 (mmmt) REVERT: F 129 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8961 (tt) REVERT: F 259 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8091 (mm) REVERT: F 271 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7846 (tp30) REVERT: F 272 LEU cc_start: 0.8346 (mt) cc_final: 0.8098 (tt) REVERT: F 333 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9022 (mm) REVERT: F 409 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8244 (ttmm) REVERT: F 456 GLN cc_start: 0.8884 (mt0) cc_final: 0.8512 (mt0) outliers start: 69 outliers final: 54 residues processed: 209 average time/residue: 0.2904 time to fit residues: 98.8313 Evaluate side-chains 206 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 258 ILE 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 412 MET 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 148 THR 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 343 GLU 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 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 208 MET Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 315 VAL 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 409 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 33 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 30.0000 chunk 127 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103461 restraints weight = 31450.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103673 restraints weight = 31704.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104867 restraints weight = 29791.580| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2845 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= 0.132 Angle : 0.522 9.794 28710 Z= 0.264 Chirality : 0.041 0.143 3090 Planarity : 0.003 0.040 3804 Dihedral : 3.459 23.427 2929 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.23 % Favored : 97.59 % Rotamer: Outliers : 2.96 % Allowed : 19.86 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.16), residues: 2736 helix: 2.31 (0.14), residues: 1374 sheet: 0.49 (0.27), residues: 378 loop : -0.61 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 176 HIS 0.007 0.001 HIS F 309 PHE 0.013 0.001 PHE A 119 TYR 0.017 0.001 TYR A 203 ARG 0.003 0.000 ARG D 160 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 1179) hydrogen bonds : angle 3.89485 ( 3459) covalent geometry : bond 0.00310 (21228) covalent geometry : angle 0.52230 (28710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5140.52 seconds wall clock time: 90 minutes 37.84 seconds (5437.84 seconds total)