Starting phenix.real_space_refine on Mon Dec 30 15:18:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyf_21458/12_2024/6vyf_21458.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyf_21458/12_2024/6vyf_21458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vyf_21458/12_2024/6vyf_21458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyf_21458/12_2024/6vyf_21458.map" model { file = "/net/cci-nas-00/data/ceres_data/6vyf_21458/12_2024/6vyf_21458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyf_21458/12_2024/6vyf_21458.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 92 5.16 5 C 8656 2.51 5 N 2312 2.21 5 O 2564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13624 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3406 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 3 Restraints were copied for chains: C, B, D Time building chain proxies: 7.24, per 1000 atoms: 0.53 Number of scatterers: 13624 At special positions: 0 Unit cell: (126.145, 100.248, 117.791, 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 92 16.00 O 2564 8.00 N 2312 7.00 C 8656 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: 3.24 Conformation dependent library (CDL) restraints added in 1.8 seconds 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 47.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.563A pdb=" N ASN A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 68 removed outlier: 3.885A pdb=" N GLU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 166 removed outlier: 4.279A pdb=" N ALA A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 166 " --> pdb=" O TYR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.885A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.635A pdb=" N THR A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.723A pdb=" N TRP A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.769A pdb=" N ILE A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.617A pdb=" N TRP A 351 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.647A pdb=" N GLY A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.788A pdb=" N LYS A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 421 removed outlier: 3.533A pdb=" N SER A 401 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 removed outlier: 4.035A pdb=" N GLU A 425 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.537A pdb=" N VAL A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 470 through 486 removed outlier: 4.601A pdb=" N ALA A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.563A pdb=" N ASN B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 68 removed outlier: 3.885A pdb=" N GLU B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 removed outlier: 4.278A pdb=" N ALA B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.885A pdb=" N ALA B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 226 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 removed outlier: 3.635A pdb=" N THR B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 303 through 312 removed outlier: 3.722A pdb=" N TRP B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.769A pdb=" N ILE B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.617A pdb=" N TRP B 351 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.647A pdb=" N GLY B 361 " --> pdb=" O ASN B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.788A pdb=" N LYS B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 421 removed outlier: 3.533A pdb=" N SER B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 4.035A pdb=" N GLU B 425 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.538A pdb=" N VAL B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 470 through 486 removed outlier: 4.601A pdb=" N ALA B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.563A pdb=" N ASN C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 68 removed outlier: 3.885A pdb=" N GLU C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 166 removed outlier: 4.279A pdb=" N ALA C 157 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 166 " --> pdb=" O TYR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 229 removed outlier: 3.885A pdb=" N ALA C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE C 226 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 227 " --> pdb=" O ASN C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.635A pdb=" N THR C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 303 through 312 removed outlier: 3.723A pdb=" N TRP C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.768A pdb=" N ILE C 325 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 342 Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.617A pdb=" N TRP C 351 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.647A pdb=" N GLY C 361 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 removed outlier: 3.787A pdb=" N LYS C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 421 removed outlier: 3.533A pdb=" N SER C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 removed outlier: 4.036A pdb=" N GLU C 425 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.537A pdb=" N VAL C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 470 through 486 removed outlier: 4.601A pdb=" N ALA C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.562A pdb=" N ASN D 38 " --> pdb=" O ASN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 68 removed outlier: 3.885A pdb=" N GLU D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 166 removed outlier: 4.278A pdb=" N ALA D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 229 removed outlier: 3.884A pdb=" N ALA D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE D 226 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 227 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 252 removed outlier: 3.635A pdb=" N THR D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'D' and resid 303 through 312 removed outlier: 3.723A pdb=" N TRP D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS D 312 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.769A pdb=" N ILE D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 342 Processing helix chain 'D' and resid 348 through 352 removed outlier: 3.617A pdb=" N TRP D 351 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.647A pdb=" N GLY D 361 " --> pdb=" O ASN D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.787A pdb=" N LYS D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 421 removed outlier: 3.533A pdb=" N SER D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 414 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 426 removed outlier: 4.036A pdb=" N GLU D 425 " --> pdb=" O LYS D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 456 removed outlier: 3.538A pdb=" N VAL D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 470 through 486 removed outlier: 4.600A pdb=" N ALA D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.968A pdb=" N GLY A 272 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR A 261 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS A 260 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY A 432 " --> pdb=" O CYS A 260 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 262 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASP A 434 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE A 264 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 429 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.968A pdb=" N GLY B 272 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR B 261 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 260 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY B 432 " --> pdb=" O CYS B 260 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 262 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASP B 434 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 264 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE B 429 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.967A pdb=" N GLY C 272 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR C 261 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS C 260 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY C 432 " --> pdb=" O CYS C 260 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 262 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASP C 434 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE C 264 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE C 429 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 101 Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 178 Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.968A pdb=" N GLY D 272 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR D 261 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS D 260 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY D 432 " --> pdb=" O CYS D 260 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE D 262 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASP D 434 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE D 264 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE D 429 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 101 Processing sheet with id=AB3, first strand: chain 'D' and resid 177 through 178 536 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 3.73 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: 4424 1.34 - 1.46: 3140 1.46 - 1.58: 6204 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 13896 Sorted by residual: bond pdb=" C HIS A 68 " pdb=" N PRO A 69 " ideal model delta sigma weight residual 1.334 1.321 0.012 8.40e-03 1.42e+04 2.11e+00 bond pdb=" C HIS C 68 " pdb=" N PRO C 69 " ideal model delta sigma weight residual 1.334 1.322 0.012 8.40e-03 1.42e+04 1.93e+00 bond pdb=" C HIS B 68 " pdb=" N PRO B 69 " ideal model delta sigma weight residual 1.334 1.322 0.012 8.40e-03 1.42e+04 1.90e+00 bond pdb=" C HIS D 68 " pdb=" N PRO D 69 " ideal model delta sigma weight residual 1.334 1.322 0.011 8.40e-03 1.42e+04 1.86e+00 bond pdb=" CA GLN B 319 " pdb=" C GLN B 319 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.17e-02 7.31e+03 1.29e+00 ... (remaining 13891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 18424 2.10 - 4.20: 296 4.20 - 6.30: 20 6.30 - 8.40: 0 8.40 - 10.50: 4 Bond angle restraints: 18744 Sorted by residual: angle pdb=" CB MET B 222 " pdb=" CG MET B 222 " pdb=" SD MET B 222 " ideal model delta sigma weight residual 112.70 123.20 -10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET C 222 " pdb=" CG MET C 222 " pdb=" SD MET C 222 " ideal model delta sigma weight residual 112.70 123.17 -10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET A 222 " pdb=" CG MET A 222 " pdb=" SD MET A 222 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET D 222 " pdb=" CG MET D 222 " pdb=" SD MET D 222 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N ASN C 315 " pdb=" CA ASN C 315 " pdb=" C ASN C 315 " ideal model delta sigma weight residual 110.61 106.52 4.09 1.25e+00 6.40e-01 1.07e+01 ... (remaining 18739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.77: 7116 13.77 - 27.53: 900 27.53 - 41.30: 288 41.30 - 55.06: 52 55.06 - 68.83: 20 Dihedral angle restraints: 8376 sinusoidal: 3352 harmonic: 5024 Sorted by residual: dihedral pdb=" CA PHE B 108 " pdb=" C PHE B 108 " pdb=" N ARG B 109 " pdb=" CA ARG B 109 " ideal model delta harmonic sigma weight residual 180.00 -146.55 -33.45 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA PHE C 108 " pdb=" C PHE C 108 " pdb=" N ARG C 109 " pdb=" CA ARG C 109 " ideal model delta harmonic sigma weight residual 180.00 -146.55 -33.45 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA PHE A 108 " pdb=" C PHE A 108 " pdb=" N ARG A 109 " pdb=" CA ARG A 109 " ideal model delta harmonic sigma weight residual 180.00 -146.58 -33.42 0 5.00e+00 4.00e-02 4.47e+01 ... (remaining 8373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1282 0.035 - 0.070: 563 0.070 - 0.105: 144 0.105 - 0.141: 67 0.141 - 0.176: 4 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA ILE B 291 " pdb=" N ILE B 291 " pdb=" C ILE B 291 " pdb=" CB ILE B 291 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE C 291 " pdb=" N ILE C 291 " pdb=" C ILE C 291 " pdb=" CB ILE C 291 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE D 291 " pdb=" N ILE D 291 " pdb=" C ILE D 291 " pdb=" CB ILE D 291 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 2057 not shown) Planarity restraints: 2396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 184 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO C 185 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 185 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 185 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 184 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO A 185 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 184 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO D 185 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 185 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 185 " 0.022 5.00e-02 4.00e+02 ... (remaining 2393 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2386 2.76 - 3.29: 12880 3.29 - 3.83: 20541 3.83 - 4.36: 25628 4.36 - 4.90: 43787 Nonbonded interactions: 105222 Sorted by model distance: nonbonded pdb=" O GLU A 322 " pdb=" OG SER A 326 " model vdw 2.223 3.040 nonbonded pdb=" O GLU C 322 " pdb=" OG SER C 326 " model vdw 2.223 3.040 nonbonded pdb=" O GLU D 322 " pdb=" OG SER D 326 " model vdw 2.224 3.040 nonbonded pdb=" O GLU B 322 " pdb=" OG SER B 326 " model vdw 2.224 3.040 nonbonded pdb=" O PRO B 74 " pdb=" ND1 HIS B 75 " model vdw 2.226 3.120 ... (remaining 105217 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.170 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.005 0.033 13896 Z= 0.353 Angle : 0.678 10.495 18744 Z= 0.404 Chirality : 0.044 0.176 2060 Planarity : 0.004 0.040 2396 Dihedral : 13.956 68.828 5128 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.27 % Allowed : 7.46 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.53 (0.18), residues: 1696 helix: -2.08 (0.16), residues: 728 sheet: -0.89 (0.33), residues: 228 loop : -3.04 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 311 HIS 0.006 0.002 HIS A 75 PHE 0.016 0.001 PHE B 108 TYR 0.016 0.002 TYR D 162 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 1.655 Fit side-chains REVERT: A 124 ASP cc_start: 0.7549 (p0) cc_final: 0.7334 (p0) REVERT: A 180 PHE cc_start: 0.8068 (t80) cc_final: 0.7790 (t80) REVERT: A 222 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7177 (tpp) REVERT: A 318 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7821 (mtp85) REVERT: B 25 ILE cc_start: 0.7692 (mm) cc_final: 0.7469 (mm) REVERT: B 180 PHE cc_start: 0.8103 (t80) cc_final: 0.7757 (t80) REVERT: B 222 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6976 (tpp) REVERT: B 310 ASP cc_start: 0.8513 (t70) cc_final: 0.8177 (t0) REVERT: C 180 PHE cc_start: 0.8109 (t80) cc_final: 0.7861 (t80) REVERT: C 222 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7189 (tpp) REVERT: D 180 PHE cc_start: 0.8111 (t80) cc_final: 0.7777 (t80) REVERT: D 222 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7182 (tpp) REVERT: D 318 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7780 (mtp85) outliers start: 4 outliers final: 0 residues processed: 193 average time/residue: 0.3272 time to fit residues: 87.1575 Evaluate side-chains 143 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 222 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 366 ASN A 449 GLN A 485 GLN B 340 ASN B 366 ASN B 485 GLN C 366 ASN C 449 GLN C 485 GLN D 340 ASN D 366 ASN D 449 GLN D 485 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13896 Z= 0.199 Angle : 0.528 6.203 18744 Z= 0.288 Chirality : 0.043 0.149 2060 Planarity : 0.004 0.036 2396 Dihedral : 5.604 46.815 1864 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.55 % Allowed : 12.30 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.19), residues: 1696 helix: -0.38 (0.20), residues: 728 sheet: -0.48 (0.34), residues: 228 loop : -2.85 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 311 HIS 0.006 0.002 HIS C 75 PHE 0.015 0.001 PHE B 108 TYR 0.012 0.001 TYR B 162 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.583 Fit side-chains REVERT: A 180 PHE cc_start: 0.8000 (t80) cc_final: 0.7779 (t80) REVERT: B 25 ILE cc_start: 0.7752 (mm) cc_final: 0.7517 (mm) REVERT: B 180 PHE cc_start: 0.8105 (t80) cc_final: 0.7771 (t80) REVERT: B 221 LEU cc_start: 0.7375 (mt) cc_final: 0.7159 (mt) REVERT: C 124 ASP cc_start: 0.7692 (p0) cc_final: 0.7488 (p0) REVERT: C 180 PHE cc_start: 0.8036 (t80) cc_final: 0.7825 (t80) REVERT: D 124 ASP cc_start: 0.7470 (p0) cc_final: 0.7258 (p0) REVERT: D 180 PHE cc_start: 0.8061 (t80) cc_final: 0.7765 (t80) outliers start: 23 outliers final: 18 residues processed: 171 average time/residue: 0.3055 time to fit residues: 73.0229 Evaluate side-chains 156 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 434 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 0.0980 chunk 43 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN C 340 ASN D 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13896 Z= 0.197 Angle : 0.503 5.644 18744 Z= 0.272 Chirality : 0.042 0.147 2060 Planarity : 0.003 0.031 2396 Dihedral : 4.889 29.154 1852 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.49 % Allowed : 13.84 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1696 helix: 0.21 (0.20), residues: 748 sheet: -0.29 (0.34), residues: 228 loop : -2.65 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 311 HIS 0.009 0.002 HIS B 75 PHE 0.014 0.001 PHE C 108 TYR 0.012 0.001 TYR C 162 ARG 0.002 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.593 Fit side-chains REVERT: A 75 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.7344 (p-80) REVERT: A 180 PHE cc_start: 0.7996 (t80) cc_final: 0.7787 (t80) REVERT: B 25 ILE cc_start: 0.7747 (mm) cc_final: 0.7513 (mm) REVERT: B 75 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7168 (p-80) REVERT: B 180 PHE cc_start: 0.8091 (t80) cc_final: 0.7752 (t80) REVERT: C 75 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7328 (p-80) REVERT: C 109 ARG cc_start: 0.7358 (ptt90) cc_final: 0.6883 (ptt90) REVERT: C 180 PHE cc_start: 0.8043 (t80) cc_final: 0.7816 (t80) REVERT: D 75 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7361 (p-80) REVERT: D 180 PHE cc_start: 0.8010 (t80) cc_final: 0.7758 (t80) outliers start: 37 outliers final: 23 residues processed: 178 average time/residue: 0.2873 time to fit residues: 73.2321 Evaluate side-chains 165 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 434 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 449 GLN C 449 GLN D 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13896 Z= 0.342 Angle : 0.579 5.864 18744 Z= 0.312 Chirality : 0.045 0.164 2060 Planarity : 0.004 0.030 2396 Dihedral : 5.290 31.747 1852 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.90 % Allowed : 14.05 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1696 helix: 0.14 (0.20), residues: 748 sheet: -0.31 (0.34), residues: 228 loop : -2.55 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 351 HIS 0.010 0.002 HIS C 75 PHE 0.016 0.002 PHE B 108 TYR 0.014 0.002 TYR C 162 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 1.668 Fit side-chains REVERT: A 75 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7188 (p-80) REVERT: A 180 PHE cc_start: 0.8046 (t80) cc_final: 0.7803 (t80) REVERT: B 25 ILE cc_start: 0.7703 (mm) cc_final: 0.7442 (mm) REVERT: B 75 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7198 (p-80) REVERT: B 180 PHE cc_start: 0.8111 (t80) cc_final: 0.7844 (t80) REVERT: B 318 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7738 (mtp85) REVERT: B 338 MET cc_start: 0.8909 (mmm) cc_final: 0.8548 (mmp) REVERT: B 434 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7526 (t0) REVERT: C 75 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7235 (p-80) REVERT: C 109 ARG cc_start: 0.7427 (ptt90) cc_final: 0.6998 (ptt90) REVERT: C 180 PHE cc_start: 0.8081 (t80) cc_final: 0.7765 (t80) REVERT: C 434 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7546 (t0) REVERT: D 75 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7228 (p-80) REVERT: D 180 PHE cc_start: 0.8065 (t80) cc_final: 0.7761 (t80) REVERT: D 318 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7783 (mtp85) outliers start: 58 outliers final: 42 residues processed: 182 average time/residue: 0.2712 time to fit residues: 71.3815 Evaluate side-chains 186 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13896 Z= 0.281 Angle : 0.541 5.434 18744 Z= 0.294 Chirality : 0.044 0.184 2060 Planarity : 0.003 0.030 2396 Dihedral : 5.168 31.224 1852 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.43 % Allowed : 15.39 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.48 (0.20), residues: 1696 helix: 0.29 (0.20), residues: 748 sheet: -0.29 (0.37), residues: 192 loop : -2.56 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 311 HIS 0.009 0.002 HIS B 75 PHE 0.015 0.001 PHE D 108 TYR 0.014 0.002 TYR C 162 ARG 0.004 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 1.510 Fit side-chains REVERT: A 75 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7189 (p-80) REVERT: A 180 PHE cc_start: 0.8025 (t80) cc_final: 0.7756 (t80) REVERT: B 25 ILE cc_start: 0.7730 (mm) cc_final: 0.7486 (mm) REVERT: B 75 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7168 (p-80) REVERT: B 180 PHE cc_start: 0.8087 (t80) cc_final: 0.7781 (t80) REVERT: B 318 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7762 (mtp85) REVERT: B 338 MET cc_start: 0.8905 (mmm) cc_final: 0.8373 (mmt) REVERT: B 434 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7491 (t70) REVERT: C 75 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7189 (p-80) REVERT: C 109 ARG cc_start: 0.7408 (ptt90) cc_final: 0.6944 (ptt90) REVERT: C 180 PHE cc_start: 0.8060 (t80) cc_final: 0.7797 (t80) REVERT: C 434 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7420 (t0) REVERT: D 75 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7208 (p-80) REVERT: D 180 PHE cc_start: 0.8038 (t80) cc_final: 0.7770 (t80) REVERT: D 434 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7425 (t0) outliers start: 51 outliers final: 41 residues processed: 179 average time/residue: 0.2752 time to fit residues: 71.7036 Evaluate side-chains 188 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 0.0570 chunk 32 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN D 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13896 Z= 0.133 Angle : 0.465 5.259 18744 Z= 0.256 Chirality : 0.041 0.176 2060 Planarity : 0.003 0.029 2396 Dihedral : 4.568 26.419 1852 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.29 % Allowed : 15.99 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.20), residues: 1696 helix: 0.85 (0.20), residues: 728 sheet: -0.08 (0.38), residues: 188 loop : -2.58 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 311 HIS 0.007 0.002 HIS A 75 PHE 0.014 0.001 PHE D 108 TYR 0.011 0.001 TYR B 251 ARG 0.004 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 1.249 Fit side-chains REVERT: A 43 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8774 (m) REVERT: A 180 PHE cc_start: 0.7988 (t80) cc_final: 0.7770 (t80) REVERT: B 43 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8805 (m) REVERT: B 180 PHE cc_start: 0.8075 (t80) cc_final: 0.7722 (t80) REVERT: B 434 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7371 (t70) REVERT: C 43 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8754 (m) REVERT: C 180 PHE cc_start: 0.8031 (t80) cc_final: 0.7789 (t80) REVERT: C 434 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7378 (t70) REVERT: D 43 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8769 (m) REVERT: D 180 PHE cc_start: 0.7983 (t80) cc_final: 0.7777 (t80) REVERT: D 434 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7405 (t70) outliers start: 49 outliers final: 24 residues processed: 182 average time/residue: 0.3324 time to fit residues: 86.2715 Evaluate side-chains 167 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 101 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13896 Z= 0.245 Angle : 0.522 5.938 18744 Z= 0.283 Chirality : 0.044 0.187 2060 Planarity : 0.003 0.028 2396 Dihedral : 4.840 28.148 1852 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.10 % Allowed : 15.26 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.20), residues: 1696 helix: 0.68 (0.20), residues: 748 sheet: -0.15 (0.38), residues: 192 loop : -2.50 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 311 HIS 0.010 0.002 HIS A 75 PHE 0.014 0.001 PHE A 108 TYR 0.012 0.002 TYR C 162 ARG 0.004 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 1.554 Fit side-chains REVERT: A 180 PHE cc_start: 0.8015 (t80) cc_final: 0.7782 (t80) REVERT: B 180 PHE cc_start: 0.8044 (t80) cc_final: 0.7729 (t80) REVERT: B 434 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7293 (t70) REVERT: C 75 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7275 (p-80) REVERT: C 180 PHE cc_start: 0.8007 (t80) cc_final: 0.7774 (t80) REVERT: C 222 MET cc_start: 0.7179 (tpp) cc_final: 0.6973 (tmm) REVERT: C 338 MET cc_start: 0.8946 (mmm) cc_final: 0.8439 (mmp) REVERT: C 434 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7292 (t70) REVERT: D 180 PHE cc_start: 0.8020 (t80) cc_final: 0.7744 (t80) REVERT: D 338 MET cc_start: 0.8948 (mmm) cc_final: 0.8448 (mmp) REVERT: D 434 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7303 (t70) outliers start: 61 outliers final: 44 residues processed: 184 average time/residue: 0.2763 time to fit residues: 73.6501 Evaluate side-chains 181 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13896 Z= 0.266 Angle : 0.534 5.286 18744 Z= 0.290 Chirality : 0.044 0.187 2060 Planarity : 0.003 0.029 2396 Dihedral : 4.965 29.507 1852 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.63 % Allowed : 16.06 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1696 helix: 0.59 (0.20), residues: 748 sheet: -0.12 (0.38), residues: 192 loop : -2.47 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 351 HIS 0.011 0.002 HIS B 75 PHE 0.015 0.001 PHE B 108 TYR 0.013 0.002 TYR D 162 ARG 0.005 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 1.618 Fit side-chains REVERT: A 180 PHE cc_start: 0.8024 (t80) cc_final: 0.7790 (t80) REVERT: B 180 PHE cc_start: 0.8068 (t80) cc_final: 0.7732 (t80) REVERT: B 318 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7797 (mtp85) REVERT: C 75 HIS cc_start: 0.7880 (OUTLIER) cc_final: 0.7162 (p-80) REVERT: C 180 PHE cc_start: 0.8028 (t80) cc_final: 0.7747 (t80) REVERT: C 222 MET cc_start: 0.7204 (tpp) cc_final: 0.6992 (tmm) REVERT: D 180 PHE cc_start: 0.8028 (t80) cc_final: 0.7749 (t80) outliers start: 54 outliers final: 52 residues processed: 179 average time/residue: 0.2803 time to fit residues: 72.9794 Evaluate side-chains 181 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13896 Z= 0.266 Angle : 0.537 5.358 18744 Z= 0.291 Chirality : 0.044 0.187 2060 Planarity : 0.003 0.029 2396 Dihedral : 4.995 29.844 1852 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.90 % Allowed : 15.86 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.20), residues: 1696 helix: 0.59 (0.20), residues: 748 sheet: -0.09 (0.38), residues: 192 loop : -2.47 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 351 HIS 0.010 0.002 HIS A 75 PHE 0.015 0.001 PHE B 108 TYR 0.013 0.002 TYR D 162 ARG 0.003 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 1.603 Fit side-chains REVERT: A 180 PHE cc_start: 0.8032 (t80) cc_final: 0.7732 (t80) REVERT: B 180 PHE cc_start: 0.8107 (t80) cc_final: 0.7747 (t80) REVERT: C 75 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7158 (p-80) REVERT: C 180 PHE cc_start: 0.8033 (t80) cc_final: 0.7743 (t80) REVERT: C 222 MET cc_start: 0.7178 (tpp) cc_final: 0.6971 (tmm) REVERT: C 338 MET cc_start: 0.8874 (mmm) cc_final: 0.8568 (mmp) REVERT: D 180 PHE cc_start: 0.8037 (t80) cc_final: 0.7750 (t80) REVERT: D 338 MET cc_start: 0.8872 (mmm) cc_final: 0.8572 (mmp) outliers start: 58 outliers final: 56 residues processed: 181 average time/residue: 0.2785 time to fit residues: 75.0413 Evaluate side-chains 186 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 129 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 14 optimal weight: 0.0470 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.0980 chunk 145 optimal weight: 10.0000 overall best weight: 1.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13896 Z= 0.156 Angle : 0.482 5.238 18744 Z= 0.264 Chirality : 0.042 0.181 2060 Planarity : 0.003 0.029 2396 Dihedral : 4.608 27.290 1852 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.63 % Allowed : 16.33 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.20), residues: 1696 helix: 0.97 (0.20), residues: 728 sheet: 0.32 (0.39), residues: 184 loop : -2.47 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 351 HIS 0.009 0.002 HIS A 75 PHE 0.011 0.001 PHE B 108 TYR 0.011 0.001 TYR D 162 ARG 0.004 0.000 ARG C 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 1.568 Fit side-chains REVERT: A 43 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8785 (m) REVERT: A 180 PHE cc_start: 0.8004 (t80) cc_final: 0.7745 (t80) REVERT: B 43 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8794 (m) REVERT: B 180 PHE cc_start: 0.8057 (t80) cc_final: 0.7744 (t80) REVERT: C 43 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8780 (m) REVERT: C 180 PHE cc_start: 0.7968 (t80) cc_final: 0.7732 (t80) REVERT: C 222 MET cc_start: 0.7150 (tpp) cc_final: 0.6942 (tmm) REVERT: C 434 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7320 (t70) REVERT: D 180 PHE cc_start: 0.7978 (t80) cc_final: 0.7743 (t80) REVERT: D 434 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7337 (t70) outliers start: 54 outliers final: 40 residues processed: 176 average time/residue: 0.2750 time to fit residues: 70.0847 Evaluate side-chains 176 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0020 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 140 optimal weight: 0.0020 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.8138 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.151704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111785 restraints weight = 19168.134| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.95 r_work: 0.3060 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13896 Z= 0.181 Angle : 0.497 6.506 18744 Z= 0.268 Chirality : 0.042 0.172 2060 Planarity : 0.003 0.028 2396 Dihedral : 4.609 26.921 1852 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.23 % Allowed : 16.47 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.20), residues: 1696 helix: 1.02 (0.20), residues: 728 sheet: 0.32 (0.39), residues: 184 loop : -2.44 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 199 HIS 0.009 0.002 HIS D 75 PHE 0.012 0.001 PHE B 108 TYR 0.011 0.001 TYR D 162 ARG 0.008 0.000 ARG C 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.48 seconds wall clock time: 50 minutes 31.09 seconds (3031.09 seconds total)