Starting phenix.real_space_refine on Wed May 21 01:06:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1o_39732/05_2025/8z1o_39732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1o_39732/05_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_39732/05_2025/8z1o_39732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1o_39732/05_2025/8z1o_39732.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1o_39732/05_2025/8z1o_39732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1o_39732/05_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-5687/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: 11.68, per 1000 atoms: 0.56 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: 4.63 Conformation dependent library (CDL) restraints added in 2.6 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: 2.36 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: 6.64 Time building geometry restraints manager: 5.45 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: 0.03 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: 0.850 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.680 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.010 ------------------------------------------------------------------------------- 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 : 2.150 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: 0.2580 time to fit residues: 69.8357 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 : 2.094 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.134228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101351 restraints weight = 31119.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101353 restraints weight = 31640.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102514 restraints weight = 30455.771| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 2.309 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: 0.8059 (ptt) cc_final: 0.7757 (ptm) REVERT: B 78 LYS cc_start: 0.7636 (tptt) cc_final: 0.7391 (tptm) REVERT: B 110 MET cc_start: 0.8580 (ppp) cc_final: 0.8251 (ptt) REVERT: B 371 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.8145 (t60) REVERT: C 343 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: C 390 MET cc_start: 0.7191 (mmm) cc_final: 0.6978 (tpt) REVERT: D 70 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: D 279 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: E 131 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8603 (tpp80) REVERT: E 371 TRP cc_start: 0.8778 (OUTLIER) cc_final: 0.8103 (t60) REVERT: F 272 LEU cc_start: 0.8124 (mt) cc_final: 0.7309 (tt) outliers start: 91 outliers final: 56 residues processed: 234 average time/residue: 0.2983 time to fit residues: 112.7110 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 : 2.421 ------------------------------------------------------------------------------- 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: 1.9990 chunk 140 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 225 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.138755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106001 restraints weight = 30876.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106010 restraints weight = 30900.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107019 restraints weight = 32185.545| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1753 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= 0.108 Angle : 0.510 9.806 28710 Z= 0.262 Chirality : 0.040 0.137 3090 Planarity : 0.003 0.046 3804 Dihedral : 3.681 20.105 2929 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.50 % Favored : 98.28 % Rotamer: Outliers : 3.00 % Allowed : 18.64 % 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: 1.30 (0.16), residues: 2736 helix: 2.09 (0.14), residues: 1368 sheet: 1.02 (0.33), residues: 252 loop : -0.77 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 53 HIS 0.003 0.001 HIS C 309 PHE 0.015 0.001 PHE F 101 TYR 0.011 0.001 TYR A 203 ARG 0.006 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 1179) hydrogen bonds : angle 4.16441 ( 3459) covalent geometry : bond 0.00242 (21228) covalent geometry : angle 0.51048 (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 232 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 2.347 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: A 158 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 390 MET cc_start: 0.6897 (tmm) cc_final: 0.6577 (tpp) REVERT: B 110 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8160 (ptp) REVERT: B 371 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.8027 (t60) REVERT: C 390 MET cc_start: 0.7272 (mmm) cc_final: 0.7046 (tpt) REVERT: D 70 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: E 108 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8501 (pt) REVERT: E 131 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8567 (tpp80) REVERT: E 282 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7386 (tp-100) REVERT: F 272 LEU cc_start: 0.7932 (mt) cc_final: 0.7427 (tt) REVERT: F 275 GLN cc_start: 0.7983 (pp30) cc_final: 0.7749 (pp30) REVERT: F 279 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: F 333 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9012 (mm) REVERT: F 456 GLN cc_start: 0.8852 (mt0) cc_final: 0.8509 (mt0) outliers start: 64 outliers final: 44 residues processed: 218 average time/residue: 0.2636 time to fit residues: 96.1868 Evaluate side-chains 198 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 2.933 ------------------------------------------------------------------------------- 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 158 THR 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 371 TRP 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 108 LEU 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: 2.9990 chunk 93 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.135058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102543 restraints weight = 31434.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102275 restraints weight = 35461.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103454 restraints weight = 31673.822| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21228 Z= 0.192 Angle : 0.544 8.179 28710 Z= 0.283 Chirality : 0.042 0.132 3090 Planarity : 0.004 0.044 3804 Dihedral : 3.803 26.838 2929 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.16 % Favored : 97.62 % Rotamer: Outliers : 4.27 % Allowed : 17.98 % Favored : 77.75 % 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: 1.18 (0.16), residues: 2736 helix: 2.04 (0.14), residues: 1368 sheet: 0.72 (0.33), residues: 252 loop : -0.83 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 176 HIS 0.003 0.001 HIS C 309 PHE 0.016 0.002 PHE A 119 TYR 0.029 0.001 TYR A 235 ARG 0.003 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 1179) hydrogen bonds : angle 4.19248 ( 3459) covalent geometry : bond 0.00452 (21228) covalent geometry : angle 0.54447 (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 236 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 145 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8257 (ptp) REVERT: B 371 TRP cc_start: 0.8778 (OUTLIER) cc_final: 0.8040 (t60) REVERT: C 176 TRP cc_start: 0.4043 (OUTLIER) cc_final: 0.3245 (m100) REVERT: C 343 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: C 390 MET cc_start: 0.7441 (mmm) cc_final: 0.7188 (tpt) REVERT: D 70 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: E 131 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8586 (tpp80) REVERT: E 259 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8603 (mm) REVERT: E 371 TRP cc_start: 0.8703 (OUTLIER) cc_final: 0.7995 (t60) REVERT: F 272 LEU cc_start: 0.8090 (mt) cc_final: 0.7421 (tt) REVERT: F 333 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9024 (mm) REVERT: F 409 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8257 (ttmm) outliers start: 91 outliers final: 64 residues processed: 222 average time/residue: 0.2769 time to fit residues: 101.2518 Evaluate side-chains 207 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 133 time to evaluate : 2.374 ------------------------------------------------------------------------------- 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 A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 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 238 LEU 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 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 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 399 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 283 LEU Chi-restraints excluded: chain E residue 371 TRP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 222 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 152 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS E 282 GLN E 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099358 restraints weight = 32096.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101250 restraints weight = 24451.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102099 restraints weight = 24036.225| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2188 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= 0.106 Angle : 0.488 8.920 28710 Z= 0.250 Chirality : 0.040 0.133 3090 Planarity : 0.003 0.041 3804 Dihedral : 3.511 20.914 2929 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.54 % Favored : 98.25 % Rotamer: Outliers : 3.43 % Allowed : 18.73 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2736 helix: 2.26 (0.14), residues: 1368 sheet: 1.13 (0.32), residues: 288 loop : -0.71 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 176 HIS 0.003 0.000 HIS C 309 PHE 0.012 0.001 PHE A 119 TYR 0.010 0.001 TYR A 203 ARG 0.003 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1179) hydrogen bonds : angle 3.95959 ( 3459) covalent geometry : bond 0.00242 (21228) covalent geometry : angle 0.48829 (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 232 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 159 time to evaluate : 2.411 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: 0.3658 (OUTLIER) cc_final: 0.2511 (m100) REVERT: B 208 MET cc_start: 0.8349 (ttp) cc_final: 0.7982 (ttp) REVERT: C 176 TRP cc_start: 0.4014 (OUTLIER) cc_final: 0.3167 (m100) REVERT: C 343 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: C 390 MET cc_start: 0.7466 (mmm) cc_final: 0.7212 (tpt) REVERT: E 131 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8615 (tpp80) REVERT: E 208 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8181 (ttp) REVERT: E 259 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8466 (mm) REVERT: F 271 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7764 (tp30) REVERT: F 272 LEU cc_start: 0.8371 (mt) cc_final: 0.7751 (tt) REVERT: F 275 GLN cc_start: 0.7956 (pp30) cc_final: 0.7704 (pp30) REVERT: F 279 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: F 297 LYS cc_start: 0.7300 (tppt) cc_final: 0.7006 (tppp) REVERT: F 333 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8987 (mm) REVERT: F 409 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8212 (ttmm) REVERT: F 456 GLN cc_start: 0.8856 (mt0) cc_final: 0.8514 (mt0) outliers start: 73 outliers final: 54 residues processed: 219 average time/residue: 0.2861 time to fit residues: 102.6565 Evaluate side-chains 212 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 149 time to evaluate : 2.125 ------------------------------------------------------------------------------- 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 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 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 180 LEU 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 105 LEU 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 232 VAL 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 D residue 438 VAL 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 208 MET Chi-restraints excluded: chain E residue 259 ILE 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 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 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: 0.8980 chunk 138 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 230 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 237 optimal weight: 0.2980 chunk 152 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN B 211 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101403 restraints weight = 31790.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100424 restraints weight = 28760.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102410 restraints weight = 23344.356| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21228 Z= 0.094 Angle : 0.473 8.917 28710 Z= 0.239 Chirality : 0.040 0.129 3090 Planarity : 0.003 0.039 3804 Dihedral : 3.314 20.951 2929 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.64 % Favored : 98.14 % Rotamer: Outliers : 3.38 % Allowed : 18.78 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.17), residues: 2736 helix: 2.46 (0.14), residues: 1368 sheet: 0.57 (0.30), residues: 348 loop : -0.50 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 176 HIS 0.002 0.000 HIS F 309 PHE 0.010 0.001 PHE B 132 TYR 0.011 0.001 TYR A 203 ARG 0.002 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 1179) hydrogen bonds : angle 3.80922 ( 3459) covalent geometry : bond 0.00211 (21228) covalent geometry : angle 0.47349 (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 240 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 168 time to evaluate : 2.400 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: A 390 MET cc_start: 0.7103 (tmm) cc_final: 0.6712 (tpp) REVERT: B 176 TRP cc_start: 0.3383 (OUTLIER) cc_final: 0.2301 (m100) REVERT: B 208 MET cc_start: 0.8264 (ttp) cc_final: 0.7842 (ttp) REVERT: B 259 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7844 (mm) REVERT: C 176 TRP cc_start: 0.3471 (OUTLIER) cc_final: 0.3099 (m100) REVERT: C 343 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: C 390 MET cc_start: 0.7498 (mmm) cc_final: 0.7249 (tpt) REVERT: D 238 LEU cc_start: 0.9279 (tp) cc_final: 0.9066 (tp) REVERT: D 390 MET cc_start: 0.7198 (tpt) cc_final: 0.6995 (tpp) REVERT: E 131 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8622 (tpp80) REVERT: E 208 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8076 (ttp) REVERT: E 259 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8389 (mm) REVERT: F 271 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7685 (tm-30) REVERT: F 272 LEU cc_start: 0.8323 (mt) cc_final: 0.7344 (tt) REVERT: F 275 GLN cc_start: 0.7983 (pp30) cc_final: 0.7774 (pp30) REVERT: F 279 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: F 297 LYS cc_start: 0.7283 (tppt) cc_final: 0.7020 (tppp) REVERT: F 333 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8951 (mm) REVERT: F 409 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8232 (ttmm) REVERT: F 456 GLN cc_start: 0.8820 (mt0) cc_final: 0.8467 (mt0) outliers start: 72 outliers final: 54 residues processed: 226 average time/residue: 0.2781 time to fit residues: 102.8690 Evaluate side-chains 219 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 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 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 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 259 ILE 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 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 208 MET Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 283 LEU 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 279 GLU 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: 0.4980 chunk 19 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.138128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100928 restraints weight = 31657.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099893 restraints weight = 28745.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102060 restraints weight = 22950.607| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21228 Z= 0.100 Angle : 0.477 8.596 28710 Z= 0.241 Chirality : 0.040 0.130 3090 Planarity : 0.003 0.038 3804 Dihedral : 3.289 21.089 2929 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.32 % Favored : 98.46 % Rotamer: Outliers : 3.19 % Allowed : 19.20 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.16), residues: 2736 helix: 2.48 (0.14), residues: 1368 sheet: 0.61 (0.30), residues: 348 loop : -0.49 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 176 HIS 0.005 0.000 HIS F 309 PHE 0.011 0.001 PHE B 132 TYR 0.013 0.001 TYR A 203 ARG 0.005 0.000 ARG B 160 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 1179) hydrogen bonds : angle 3.78877 ( 3459) covalent geometry : bond 0.00227 (21228) covalent geometry : angle 0.47686 (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 233 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 2.326 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: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.7098 (tmm) cc_final: 0.6718 (tpp) REVERT: B 129 ILE cc_start: 0.8567 (pt) cc_final: 0.8338 (tt) REVERT: B 176 TRP cc_start: 0.3375 (OUTLIER) cc_final: 0.2243 (m100) REVERT: B 208 MET cc_start: 0.8301 (ttp) cc_final: 0.7719 (ttp) REVERT: B 259 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7865 (mm) REVERT: C 176 TRP cc_start: 0.3309 (OUTLIER) cc_final: 0.3060 (m100) REVERT: C 343 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: C 390 MET cc_start: 0.7518 (mmm) cc_final: 0.7257 (tpt) REVERT: D 238 LEU cc_start: 0.9273 (tp) cc_final: 0.9056 (tp) REVERT: D 390 MET cc_start: 0.7222 (tpt) cc_final: 0.7014 (tpp) REVERT: E 131 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8618 (tpp80) REVERT: E 208 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8063 (ttp) REVERT: E 259 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8391 (mm) REVERT: F 271 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7695 (tm-30) REVERT: F 272 LEU cc_start: 0.8340 (mt) cc_final: 0.7332 (tt) REVERT: F 279 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: F 297 LYS cc_start: 0.7282 (tppt) cc_final: 0.7019 (tppp) REVERT: F 333 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8959 (mm) REVERT: F 409 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8221 (ttmm) REVERT: F 456 GLN cc_start: 0.8850 (mt0) cc_final: 0.8463 (mt0) outliers start: 68 outliers final: 53 residues processed: 222 average time/residue: 0.2814 time to fit residues: 101.6056 Evaluate side-chains 221 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 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 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 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain 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 180 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 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 208 MET Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 283 LEU 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 279 GLU 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: 0.6980 chunk 179 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096926 restraints weight = 31930.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098487 restraints weight = 23242.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099907 restraints weight = 18115.542| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2472 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= 0.157 Angle : 0.522 9.230 28710 Z= 0.267 Chirality : 0.041 0.141 3090 Planarity : 0.003 0.040 3804 Dihedral : 3.507 25.266 2929 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.08 % Favored : 97.70 % Rotamer: Outliers : 3.66 % Allowed : 18.73 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.16), residues: 2736 helix: 2.34 (0.14), residues: 1374 sheet: 1.18 (0.32), residues: 288 loop : -0.79 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 176 HIS 0.004 0.001 HIS F 309 PHE 0.016 0.001 PHE A 119 TYR 0.015 0.001 TYR A 203 ARG 0.003 0.000 ARG B 160 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1179) hydrogen bonds : angle 3.90142 ( 3459) covalent geometry : bond 0.00369 (21228) covalent geometry : angle 0.52182 (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 227 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 149 time to evaluate : 2.353 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: symmetry clash REVERT: B 129 ILE cc_start: 0.8588 (pt) cc_final: 0.8305 (mt) REVERT: B 176 TRP cc_start: 0.3925 (OUTLIER) cc_final: 0.2851 (m100) REVERT: B 208 MET cc_start: 0.8458 (ttp) cc_final: 0.8231 (ttp) REVERT: B 259 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7893 (mm) REVERT: B 282 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7842 (tp40) REVERT: C 78 LYS cc_start: 0.7299 (tttt) cc_final: 0.6787 (mttp) REVERT: C 176 TRP cc_start: 0.3515 (OUTLIER) cc_final: 0.2931 (m100) REVERT: C 343 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: E 131 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8647 (tpp80) REVERT: E 208 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (ttp) REVERT: E 259 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8419 (mm) REVERT: E 272 LEU cc_start: 0.8933 (mt) cc_final: 0.8234 (tt) REVERT: F 271 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7755 (tm-30) REVERT: F 272 LEU cc_start: 0.8293 (mt) cc_final: 0.7637 (tt) REVERT: F 279 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: F 297 LYS cc_start: 0.7373 (tppt) cc_final: 0.7135 (tppp) REVERT: F 333 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8991 (mm) REVERT: F 409 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8214 (ttmm) outliers start: 78 outliers final: 59 residues processed: 212 average time/residue: 0.2767 time to fit residues: 96.2399 Evaluate side-chains 213 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 143 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 282 GLN Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 110 MET 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 259 ILE Chi-restraints excluded: chain E residue 283 LEU 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 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 390 MET Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 244 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 255 optimal weight: 0.0070 chunk 219 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100164 restraints weight = 31754.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099386 restraints weight = 30072.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101513 restraints weight = 23746.277| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21228 Z= 0.104 Angle : 0.491 9.174 28710 Z= 0.249 Chirality : 0.040 0.131 3090 Planarity : 0.003 0.039 3804 Dihedral : 3.357 21.251 2929 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.57 % Favored : 98.25 % Rotamer: Outliers : 3.52 % Allowed : 18.92 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.68 (0.16), residues: 2736 helix: 2.42 (0.14), residues: 1374 sheet: 0.65 (0.30), residues: 348 loop : -0.57 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 176 HIS 0.005 0.000 HIS F 309 PHE 0.012 0.001 PHE B 132 TYR 0.014 0.001 TYR A 203 ARG 0.003 0.000 ARG B 160 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 1179) hydrogen bonds : angle 3.80284 ( 3459) covalent geometry : bond 0.00236 (21228) covalent geometry : angle 0.49147 (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 233 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 158 time to evaluate : 2.432 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: symmetry clash REVERT: A 226 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8310 (pt) REVERT: B 176 TRP cc_start: 0.3712 (OUTLIER) cc_final: 0.2903 (m100) REVERT: B 208 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7718 (ttp) REVERT: B 259 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7860 (mm) REVERT: C 129 ILE cc_start: 0.9051 (pt) cc_final: 0.8577 (mt) REVERT: C 176 TRP cc_start: 0.3424 (OUTLIER) cc_final: 0.3185 (m100) REVERT: C 343 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: C 390 MET cc_start: 0.7633 (tpt) cc_final: 0.7353 (tpt) REVERT: D 238 LEU cc_start: 0.9304 (tp) cc_final: 0.9080 (tp) REVERT: E 131 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8620 (tpp80) REVERT: E 208 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (ttp) REVERT: E 272 LEU cc_start: 0.8930 (mt) cc_final: 0.8315 (tt) REVERT: F 78 LYS cc_start: 0.7436 (tttt) cc_final: 0.7030 (mttp) REVERT: F 259 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7789 (mm) REVERT: F 271 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7751 (tm-30) REVERT: F 272 LEU cc_start: 0.8293 (mt) cc_final: 0.7740 (tt) REVERT: F 279 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: F 409 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8223 (ttmm) REVERT: F 456 GLN cc_start: 0.8871 (mt0) cc_final: 0.8480 (mt0) outliers start: 75 outliers final: 55 residues processed: 219 average time/residue: 0.2777 time to fit residues: 99.7755 Evaluate side-chains 217 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 151 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 283 LEU 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 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 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 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 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 279 GLU Chi-restraints excluded: chain F residue 390 MET Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 92 optimal weight: 0.0020 chunk 43 optimal weight: 0.6980 chunk 262 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 91 optimal weight: 0.0470 chunk 133 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 overall best weight: 0.4286 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.139419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106409 restraints weight = 30950.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106612 restraints weight = 30321.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107490 restraints weight = 32942.057| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21228 Z= 0.094 Angle : 0.487 8.714 28710 Z= 0.247 Chirality : 0.040 0.140 3090 Planarity : 0.003 0.038 3804 Dihedral : 3.260 20.116 2929 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.83 % Favored : 97.99 % Rotamer: Outliers : 3.05 % Allowed : 19.48 % 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: 1.80 (0.16), residues: 2736 helix: 2.52 (0.14), residues: 1374 sheet: 0.77 (0.30), residues: 348 loop : -0.54 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 176 HIS 0.006 0.000 HIS F 309 PHE 0.012 0.001 PHE B 132 TYR 0.016 0.001 TYR A 203 ARG 0.002 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 1179) hydrogen bonds : angle 3.74334 ( 3459) covalent geometry : bond 0.00209 (21228) covalent geometry : angle 0.48736 (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 227 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 2.106 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: symmetry clash REVERT: B 176 TRP cc_start: 0.3674 (OUTLIER) cc_final: 0.2905 (m100) REVERT: B 208 MET cc_start: 0.8054 (ttp) cc_final: 0.7493 (ttp) REVERT: C 129 ILE cc_start: 0.8932 (pt) cc_final: 0.8489 (mt) REVERT: C 176 TRP cc_start: 0.3570 (OUTLIER) cc_final: 0.3240 (m100) REVERT: C 297 LYS cc_start: 0.6786 (tppp) cc_final: 0.6326 (mmmt) REVERT: C 343 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: D 238 LEU cc_start: 0.9307 (tp) cc_final: 0.9078 (tp) REVERT: D 412 MET cc_start: 0.8873 (mmm) cc_final: 0.8634 (mmt) REVERT: E 208 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7807 (ttp) REVERT: E 272 LEU cc_start: 0.8886 (mt) cc_final: 0.8151 (tt) REVERT: E 297 LYS cc_start: 0.7089 (tppt) cc_final: 0.6416 (mmmt) REVERT: F 259 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8132 (mm) REVERT: F 271 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7610 (tp30) REVERT: F 272 LEU cc_start: 0.8189 (mt) cc_final: 0.7950 (tt) REVERT: F 279 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: F 409 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8215 (ttmm) REVERT: F 456 GLN cc_start: 0.8794 (mt0) cc_final: 0.8413 (mt0) outliers start: 65 outliers final: 51 residues processed: 213 average time/residue: 0.2734 time to fit residues: 95.6157 Evaluate side-chains 207 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU 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 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 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 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 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 438 VAL Chi-restraints excluded: chain F residue 40 VAL 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 390 MET Chi-restraints excluded: chain F residue 409 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105716 restraints weight = 31522.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105892 restraints weight = 33933.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107294 restraints weight = 32215.287| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21228 Z= 0.120 Angle : 0.505 8.663 28710 Z= 0.255 Chirality : 0.041 0.143 3090 Planarity : 0.003 0.037 3804 Dihedral : 3.318 22.834 2929 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.90 % Favored : 97.92 % Rotamer: Outliers : 2.96 % Allowed : 19.48 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.16), residues: 2736 helix: 2.49 (0.14), residues: 1374 sheet: 0.73 (0.30), residues: 348 loop : -0.56 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 176 HIS 0.006 0.001 HIS F 309 PHE 0.013 0.001 PHE B 132 TYR 0.020 0.001 TYR A 203 ARG 0.002 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 1179) hydrogen bonds : angle 3.78904 ( 3459) covalent geometry : bond 0.00282 (21228) covalent geometry : angle 0.50479 (28710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.76 seconds wall clock time: 85 minutes 58.11 seconds (5158.11 seconds total)