Starting phenix.real_space_refine on Sun Aug 24 16:32:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yig_33858/08_2025/7yig_33858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yig_33858/08_2025/7yig_33858.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/7yig_33858/08_2025/7yig_33858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yig_33858/08_2025/7yig_33858.map" model { file = "/net/cci-nas-00/data/ceres_data/7yig_33858/08_2025/7yig_33858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yig_33858/08_2025/7yig_33858.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21320 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.26 Number of scatterers: 21320 At special positions: 0 Unit cell: (157.065, 157.065, 130.746, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 128 16.00 O 3848 8.00 N 3544 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 974.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 50.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 15 through 22 removed outlier: 3.739A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.540A pdb=" N SER A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 145 through 156 removed outlier: 4.006A pdb=" N PHE A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.509A pdb=" N ARG A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.880A pdb=" N HIS A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.812A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 238 removed outlier: 3.640A pdb=" N TRP A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 247 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.672A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 329 through 337 removed outlier: 4.022A pdb=" N LYS A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 374 removed outlier: 3.515A pdb=" N VAL A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 419 through 431 removed outlier: 3.827A pdb=" N PHE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 476 removed outlier: 3.720A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 removed outlier: 3.959A pdb=" N ARG A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.737A pdb=" N ALA A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.730A pdb=" N PHE A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 546' Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.952A pdb=" N ALA A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 651 Processing helix chain 'A' and resid 655 through 664 removed outlier: 4.277A pdb=" N SER A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 692 Processing helix chain 'B' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.540A pdb=" N SER B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 145 through 156 removed outlier: 4.006A pdb=" N PHE B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.509A pdb=" N ARG B 160 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 173 through 178 removed outlier: 3.880A pdb=" N HIS B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.812A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 238 removed outlier: 3.640A pdb=" N TRP B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.672A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 329 through 337 removed outlier: 4.023A pdb=" N LYS B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 374 removed outlier: 3.518A pdb=" N VAL B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 358 " --> pdb=" O CYS B 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 419 through 431 removed outlier: 3.827A pdb=" N PHE B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 476 removed outlier: 3.721A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 495 removed outlier: 3.955A pdb=" N ARG B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 Processing helix chain 'B' and resid 520 through 527 Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.737A pdb=" N ALA B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.730A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 546' Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.952A pdb=" N ALA B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 655 through 664 removed outlier: 4.277A pdb=" N SER B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 692 Processing helix chain 'C' and resid 15 through 22 removed outlier: 3.738A pdb=" N VAL C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.540A pdb=" N SER C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 145 through 156 removed outlier: 4.006A pdb=" N PHE C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.509A pdb=" N ARG C 160 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 161' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.880A pdb=" N HIS C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.812A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 238 removed outlier: 3.640A pdb=" N TRP C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 247 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.672A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 329 through 337 removed outlier: 4.023A pdb=" N LYS C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 374 removed outlier: 3.518A pdb=" N VAL C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 358 " --> pdb=" O CYS C 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 419 through 431 removed outlier: 3.827A pdb=" N PHE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 476 removed outlier: 3.721A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 457 " --> pdb=" O MET C 453 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 495 removed outlier: 3.954A pdb=" N ARG C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 514 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 529 through 541 removed outlier: 3.737A pdb=" N ALA C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.730A pdb=" N PHE C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 546' Processing helix chain 'C' and resid 548 through 552 Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.952A pdb=" N ALA C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 651 Processing helix chain 'C' and resid 655 through 664 removed outlier: 4.277A pdb=" N SER C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 692 Processing helix chain 'D' and resid 15 through 22 removed outlier: 3.739A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG D 22 " --> pdb=" O ASN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.540A pdb=" N SER D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 145 through 156 removed outlier: 4.006A pdb=" N PHE D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.509A pdb=" N ARG D 160 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER D 161 " --> pdb=" O ASN D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 161' Processing helix chain 'D' and resid 173 through 178 removed outlier: 3.880A pdb=" N HIS D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 3.812A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 238 removed outlier: 3.640A pdb=" N TRP D 217 " --> pdb=" O PHE D 213 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 247 through 265 Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.672A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS D 300 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 329 through 337 removed outlier: 4.022A pdb=" N LYS D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 374 removed outlier: 3.518A pdb=" N VAL D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE D 356 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 358 " --> pdb=" O CYS D 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS D 361 " --> pdb=" O GLY D 357 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 395 Processing helix chain 'D' and resid 419 through 431 removed outlier: 3.827A pdb=" N PHE D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 476 removed outlier: 3.720A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET D 454 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 457 " --> pdb=" O MET D 453 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 495 removed outlier: 3.953A pdb=" N ARG D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 514 Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 529 through 541 removed outlier: 3.737A pdb=" N ALA D 534 " --> pdb=" O LYS D 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.730A pdb=" N PHE D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 546' Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 563 removed outlier: 3.952A pdb=" N ALA D 561 " --> pdb=" O GLY D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 655 through 664 removed outlier: 4.277A pdb=" N SER D 659 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.585A pdb=" N LEU A 123 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR A 127 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 570 removed outlier: 6.441A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 614 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 578 removed outlier: 6.778A pdb=" N VAL A 630 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 605 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.585A pdb=" N LEU B 123 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR B 127 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 97 Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 377 Processing sheet with id=AA9, first strand: chain 'B' and resid 569 through 570 removed outlier: 6.441A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 614 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 576 through 578 removed outlier: 6.778A pdb=" N VAL B 630 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.585A pdb=" N LEU C 123 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR C 127 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 97 Processing sheet with id=AB4, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AB5, first strand: chain 'C' and resid 569 through 570 removed outlier: 6.441A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 614 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 576 through 578 removed outlier: 6.778A pdb=" N VAL C 630 " --> pdb=" O ILE C 577 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 605 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.585A pdb=" N LEU D 123 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR D 127 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 94 through 97 Processing sheet with id=AB9, first strand: chain 'D' and resid 376 through 377 Processing sheet with id=AC1, first strand: chain 'D' and resid 569 through 570 removed outlier: 6.441A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 614 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 576 through 578 removed outlier: 6.778A pdb=" N VAL D 630 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 605 " --> pdb=" O VAL D 597 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2532 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: 3.92 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6704 1.34 - 1.46: 5196 1.46 - 1.58: 9712 1.58 - 1.70: 0 1.70 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" CB ARG B 330 " pdb=" CG ARG B 330 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CB ARG D 330 " pdb=" CG ARG D 330 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CB ARG C 330 " pdb=" CG ARG C 330 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CB ARG A 330 " pdb=" CG ARG A 330 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CA ASP C 601 " pdb=" CB ASP C 601 " ideal model delta sigma weight residual 1.529 1.541 -0.012 1.58e-02 4.01e+03 6.23e-01 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 28631 1.39 - 2.77: 800 2.77 - 4.16: 101 4.16 - 5.54: 28 5.54 - 6.93: 24 Bond angle restraints: 29584 Sorted by residual: angle pdb=" C THR C 441 " pdb=" N THR C 442 " pdb=" CA THR C 442 " ideal model delta sigma weight residual 121.54 114.63 6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C THR A 441 " pdb=" N THR A 442 " pdb=" CA THR A 442 " ideal model delta sigma weight residual 121.54 114.63 6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C THR D 441 " pdb=" N THR D 442 " pdb=" CA THR D 442 " ideal model delta sigma weight residual 121.54 114.63 6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C THR B 441 " pdb=" N THR B 442 " pdb=" CA THR B 442 " ideal model delta sigma weight residual 121.54 114.63 6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N TRP A 292 " pdb=" CA TRP A 292 " pdb=" C TRP A 292 " ideal model delta sigma weight residual 110.44 113.80 -3.36 1.20e+00 6.94e-01 7.86e+00 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11707 17.97 - 35.95: 967 35.95 - 53.92: 206 53.92 - 71.89: 29 71.89 - 89.86: 23 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA THR B 291 " pdb=" C THR B 291 " pdb=" N TRP B 292 " pdb=" CA TRP B 292 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA THR C 291 " pdb=" C THR C 291 " pdb=" N TRP C 292 " pdb=" CA TRP C 292 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA THR A 291 " pdb=" C THR A 291 " pdb=" N TRP A 292 " pdb=" CA TRP A 292 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1853 0.029 - 0.058: 1081 0.058 - 0.087: 301 0.087 - 0.116: 137 0.116 - 0.144: 32 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA ILE D 438 " pdb=" N ILE D 438 " pdb=" C ILE D 438 " pdb=" CB ILE D 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE A 438 " pdb=" N ILE A 438 " pdb=" C ILE A 438 " pdb=" CB ILE A 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE C 438 " pdb=" N ILE C 438 " pdb=" C ILE C 438 " pdb=" CB ILE C 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 13 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C ASN B 13 " 0.025 2.00e-02 2.50e+03 pdb=" O ASN B 13 " -0.009 2.00e-02 2.50e+03 pdb=" N THR B 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 13 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C ASN C 13 " 0.025 2.00e-02 2.50e+03 pdb=" O ASN C 13 " -0.009 2.00e-02 2.50e+03 pdb=" N THR C 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 13 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.03e+00 pdb=" C ASN D 13 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN D 13 " 0.009 2.00e-02 2.50e+03 pdb=" N THR D 14 " 0.008 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 2268 2.75 - 3.35: 24023 3.35 - 3.94: 37664 3.94 - 4.54: 51378 4.54 - 5.14: 80844 Nonbonded interactions: 196177 Sorted by model distance: nonbonded pdb=" OH TYR A 195 " pdb=" OE2 GLU B 596 " model vdw 2.152 3.040 nonbonded pdb=" OE2 GLU A 596 " pdb=" OH TYR D 195 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR B 195 " pdb=" OE2 GLU C 596 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR C 195 " pdb=" OE2 GLU D 596 " model vdw 2.152 3.040 nonbonded pdb=" O LEU D 418 " pdb=" OG SER D 422 " model vdw 2.257 3.040 ... (remaining 196172 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' and resid 11 through 692) 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 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: 4.650 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.900 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.003 0.026 21804 Z= 0.126 Angle : 0.575 6.931 29584 Z= 0.315 Chirality : 0.041 0.144 3404 Planarity : 0.003 0.030 3668 Dihedral : 14.209 89.864 7884 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.80 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.16), residues: 2616 helix: 0.32 (0.16), residues: 1200 sheet: -3.52 (0.36), residues: 192 loop : -2.74 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 677 TYR 0.018 0.001 TYR D 460 PHE 0.019 0.002 PHE B 293 TRP 0.008 0.001 TRP D 388 HIS 0.003 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00272 (21804) covalent geometry : angle 0.57458 (29584) hydrogen bonds : bond 0.19039 ( 876) hydrogen bonds : angle 6.02776 ( 2532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.864 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1434 time to fit residues: 78.2931 Evaluate side-chains 284 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN A 479 ASN A 579 HIS B 83 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN B 479 ASN B 579 HIS C 83 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN C 479 ASN C 579 HIS D 83 GLN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 479 ASN D 579 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.202819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.172791 restraints weight = 25450.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174850 restraints weight = 57906.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.175552 restraints weight = 28787.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.176263 restraints weight = 18490.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176659 restraints weight = 16165.776| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21804 Z= 0.200 Angle : 0.614 8.482 29584 Z= 0.328 Chirality : 0.045 0.189 3404 Planarity : 0.004 0.029 3668 Dihedral : 4.727 24.785 2864 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.56 % Favored : 91.13 % Rotamer: Outliers : 0.67 % Allowed : 8.61 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.16), residues: 2616 helix: 0.11 (0.15), residues: 1248 sheet: -3.35 (0.36), residues: 212 loop : -2.89 (0.15), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 21 TYR 0.013 0.002 TYR D 460 PHE 0.015 0.002 PHE D 28 TRP 0.011 0.001 TRP A 388 HIS 0.003 0.001 HIS C 539 Details of bonding type rmsd covalent geometry : bond 0.00489 (21804) covalent geometry : angle 0.61360 (29584) hydrogen bonds : bond 0.05155 ( 876) hydrogen bonds : angle 4.94775 ( 2532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 296 time to evaluate : 0.823 Fit side-chains REVERT: A 107 PHE cc_start: 0.7842 (m-80) cc_final: 0.7622 (m-80) REVERT: A 453 MET cc_start: 0.8888 (mtt) cc_final: 0.8552 (mtt) REVERT: A 601 ASP cc_start: 0.7628 (t0) cc_final: 0.7370 (t0) REVERT: B 107 PHE cc_start: 0.7831 (m-80) cc_final: 0.7617 (m-80) REVERT: B 453 MET cc_start: 0.8886 (mtt) cc_final: 0.8575 (mtt) REVERT: B 601 ASP cc_start: 0.7603 (t0) cc_final: 0.7350 (t0) REVERT: C 107 PHE cc_start: 0.7834 (m-80) cc_final: 0.7616 (m-80) REVERT: C 453 MET cc_start: 0.8892 (mtt) cc_final: 0.8576 (mtt) REVERT: C 601 ASP cc_start: 0.7601 (t0) cc_final: 0.7352 (t0) REVERT: D 107 PHE cc_start: 0.7845 (m-80) cc_final: 0.7629 (m-80) REVERT: D 453 MET cc_start: 0.8893 (mtt) cc_final: 0.8558 (mtt) REVERT: D 601 ASP cc_start: 0.7600 (t0) cc_final: 0.7347 (t0) outliers start: 16 outliers final: 16 residues processed: 304 average time/residue: 0.1412 time to fit residues: 69.7398 Evaluate side-chains 284 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 268 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 675 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 675 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 119 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 190 optimal weight: 0.3980 chunk 237 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.208701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.176835 restraints weight = 25320.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.177612 restraints weight = 48975.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178631 restraints weight = 36999.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.179373 restraints weight = 20935.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.181769 restraints weight = 17714.560| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21804 Z= 0.116 Angle : 0.523 8.139 29584 Z= 0.276 Chirality : 0.041 0.173 3404 Planarity : 0.003 0.029 3668 Dihedral : 4.481 24.298 2864 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.87 % Favored : 91.97 % Rotamer: Outliers : 0.67 % Allowed : 11.22 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.16), residues: 2616 helix: 0.35 (0.15), residues: 1256 sheet: -3.26 (0.38), residues: 192 loop : -2.95 (0.15), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 21 TYR 0.009 0.001 TYR D 460 PHE 0.012 0.001 PHE A 28 TRP 0.012 0.001 TRP A 388 HIS 0.002 0.001 HIS C 539 Details of bonding type rmsd covalent geometry : bond 0.00275 (21804) covalent geometry : angle 0.52267 (29584) hydrogen bonds : bond 0.04080 ( 876) hydrogen bonds : angle 4.53609 ( 2532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 319 time to evaluate : 0.834 Fit side-chains REVERT: A 65 CYS cc_start: 0.6158 (t) cc_final: 0.5919 (t) REVERT: A 453 MET cc_start: 0.8841 (mtt) cc_final: 0.8609 (mtt) REVERT: A 601 ASP cc_start: 0.7553 (t0) cc_final: 0.7169 (t0) REVERT: B 65 CYS cc_start: 0.6157 (t) cc_final: 0.5923 (t) REVERT: B 453 MET cc_start: 0.8838 (mtt) cc_final: 0.8612 (mtt) REVERT: B 596 GLU cc_start: 0.7360 (tt0) cc_final: 0.7080 (tt0) REVERT: B 601 ASP cc_start: 0.7556 (t0) cc_final: 0.7197 (t0) REVERT: C 65 CYS cc_start: 0.6145 (t) cc_final: 0.5911 (t) REVERT: C 453 MET cc_start: 0.8849 (mtt) cc_final: 0.8622 (mtt) REVERT: C 596 GLU cc_start: 0.7288 (tt0) cc_final: 0.7031 (tt0) REVERT: C 601 ASP cc_start: 0.7537 (t0) cc_final: 0.7181 (t0) REVERT: D 65 CYS cc_start: 0.6159 (t) cc_final: 0.5926 (t) REVERT: D 195 TYR cc_start: 0.8274 (t80) cc_final: 0.7957 (t80) REVERT: D 453 MET cc_start: 0.8849 (mtt) cc_final: 0.8620 (mtt) REVERT: D 596 GLU cc_start: 0.7318 (tt0) cc_final: 0.7060 (tt0) REVERT: D 601 ASP cc_start: 0.7554 (t0) cc_final: 0.7199 (t0) outliers start: 16 outliers final: 12 residues processed: 327 average time/residue: 0.1409 time to fit residues: 75.1516 Evaluate side-chains 304 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 292 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 45 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 214 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 251 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.206849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174562 restraints weight = 25392.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.175268 restraints weight = 50067.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.176410 restraints weight = 37028.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.177176 restraints weight = 20973.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.179149 restraints weight = 17523.746| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21804 Z= 0.135 Angle : 0.526 8.000 29584 Z= 0.278 Chirality : 0.042 0.170 3404 Planarity : 0.003 0.028 3668 Dihedral : 4.458 23.004 2864 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.95 % Favored : 91.90 % Rotamer: Outliers : 1.43 % Allowed : 12.73 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.16), residues: 2616 helix: 0.38 (0.15), residues: 1256 sheet: -3.16 (0.39), residues: 188 loop : -2.88 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 21 TYR 0.009 0.001 TYR D 508 PHE 0.012 0.001 PHE C 258 TRP 0.011 0.001 TRP A 388 HIS 0.002 0.001 HIS C 539 Details of bonding type rmsd covalent geometry : bond 0.00324 (21804) covalent geometry : angle 0.52624 (29584) hydrogen bonds : bond 0.04220 ( 876) hydrogen bonds : angle 4.50984 ( 2532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 0.685 Fit side-chains REVERT: A 65 CYS cc_start: 0.6201 (t) cc_final: 0.5904 (t) REVERT: A 453 MET cc_start: 0.8911 (mtt) cc_final: 0.8690 (mtt) REVERT: A 601 ASP cc_start: 0.7630 (t0) cc_final: 0.7230 (t0) REVERT: B 65 CYS cc_start: 0.6189 (t) cc_final: 0.5889 (t) REVERT: B 453 MET cc_start: 0.8911 (mtt) cc_final: 0.8695 (mtt) REVERT: B 601 ASP cc_start: 0.7629 (t0) cc_final: 0.7235 (t0) REVERT: C 65 CYS cc_start: 0.6196 (t) cc_final: 0.5897 (t) REVERT: C 453 MET cc_start: 0.8916 (mtt) cc_final: 0.8699 (mtt) REVERT: C 601 ASP cc_start: 0.7637 (t0) cc_final: 0.7244 (t0) REVERT: D 65 CYS cc_start: 0.6192 (t) cc_final: 0.5896 (t) REVERT: D 453 MET cc_start: 0.8924 (mtt) cc_final: 0.8704 (mtt) REVERT: D 601 ASP cc_start: 0.7632 (t0) cc_final: 0.7239 (t0) outliers start: 34 outliers final: 16 residues processed: 329 average time/residue: 0.1306 time to fit residues: 70.1965 Evaluate side-chains 297 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 281 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 111 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 212 optimal weight: 20.0000 chunk 4 optimal weight: 0.0470 chunk 23 optimal weight: 0.0570 chunk 159 optimal weight: 4.9990 chunk 246 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.211062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.176438 restraints weight = 25317.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177046 restraints weight = 37008.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178753 restraints weight = 27098.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.178956 restraints weight = 15595.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.180784 restraints weight = 13937.544| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21804 Z= 0.090 Angle : 0.489 8.095 29584 Z= 0.255 Chirality : 0.040 0.187 3404 Planarity : 0.003 0.029 3668 Dihedral : 4.303 23.579 2864 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.34 % Favored : 92.51 % Rotamer: Outliers : 1.01 % Allowed : 13.70 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.16), residues: 2616 helix: 0.67 (0.15), residues: 1260 sheet: -3.14 (0.39), residues: 188 loop : -2.77 (0.15), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 677 TYR 0.007 0.001 TYR D 508 PHE 0.013 0.001 PHE C 93 TRP 0.010 0.001 TRP A 388 HIS 0.002 0.000 HIS C 539 Details of bonding type rmsd covalent geometry : bond 0.00205 (21804) covalent geometry : angle 0.48920 (29584) hydrogen bonds : bond 0.03337 ( 876) hydrogen bonds : angle 4.21892 ( 2532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 315 time to evaluate : 0.836 Fit side-chains REVERT: A 601 ASP cc_start: 0.7603 (t0) cc_final: 0.7178 (t0) REVERT: B 601 ASP cc_start: 0.7618 (t0) cc_final: 0.7163 (t0) REVERT: C 601 ASP cc_start: 0.7633 (t0) cc_final: 0.7172 (t0) REVERT: D 601 ASP cc_start: 0.7626 (t0) cc_final: 0.7169 (t0) outliers start: 24 outliers final: 19 residues processed: 327 average time/residue: 0.1158 time to fit residues: 62.0801 Evaluate side-chains 314 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 295 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 118 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 200 optimal weight: 0.0170 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.202949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.170076 restraints weight = 25258.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171673 restraints weight = 51406.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172567 restraints weight = 33937.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173210 restraints weight = 19988.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175763 restraints weight = 16742.186| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21804 Z= 0.215 Angle : 0.601 8.038 29584 Z= 0.319 Chirality : 0.046 0.203 3404 Planarity : 0.003 0.026 3668 Dihedral : 4.612 22.607 2864 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.25 % Favored : 90.60 % Rotamer: Outliers : 1.89 % Allowed : 13.91 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.16), residues: 2616 helix: 0.35 (0.15), residues: 1256 sheet: -3.21 (0.39), residues: 188 loop : -2.83 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.012 0.002 TYR A 419 PHE 0.014 0.002 PHE B 258 TRP 0.012 0.001 TRP A 513 HIS 0.003 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00528 (21804) covalent geometry : angle 0.60053 (29584) hydrogen bonds : bond 0.05008 ( 876) hydrogen bonds : angle 4.68120 ( 2532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 298 time to evaluate : 0.739 Fit side-chains REVERT: A 331 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8446 (mt) REVERT: A 601 ASP cc_start: 0.7729 (t0) cc_final: 0.7241 (t0) REVERT: B 601 ASP cc_start: 0.7720 (t0) cc_final: 0.7252 (t0) REVERT: C 601 ASP cc_start: 0.7719 (t0) cc_final: 0.7251 (t0) REVERT: D 331 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8441 (mt) REVERT: D 601 ASP cc_start: 0.7726 (t0) cc_final: 0.7251 (t0) outliers start: 45 outliers final: 28 residues processed: 321 average time/residue: 0.1352 time to fit residues: 71.3386 Evaluate side-chains 312 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 179 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 230 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.209831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.181963 restraints weight = 25540.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.182527 restraints weight = 44639.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182441 restraints weight = 35096.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.183168 restraints weight = 18510.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.183708 restraints weight = 15369.288| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21804 Z= 0.114 Angle : 0.524 8.532 29584 Z= 0.274 Chirality : 0.041 0.173 3404 Planarity : 0.003 0.028 3668 Dihedral : 4.434 23.950 2864 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.80 % Favored : 92.05 % Rotamer: Outliers : 1.05 % Allowed : 14.54 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.16), residues: 2616 helix: 0.52 (0.15), residues: 1272 sheet: -3.18 (0.39), residues: 188 loop : -2.78 (0.15), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 21 TYR 0.008 0.001 TYR D 508 PHE 0.013 0.001 PHE A 258 TRP 0.011 0.001 TRP B 388 HIS 0.003 0.000 HIS D 539 Details of bonding type rmsd covalent geometry : bond 0.00271 (21804) covalent geometry : angle 0.52404 (29584) hydrogen bonds : bond 0.03808 ( 876) hydrogen bonds : angle 4.34483 ( 2532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 301 time to evaluate : 0.804 Fit side-chains REVERT: A 65 CYS cc_start: 0.6249 (t) cc_final: 0.5811 (t) REVERT: A 601 ASP cc_start: 0.7741 (t0) cc_final: 0.7280 (t0) REVERT: B 65 CYS cc_start: 0.6237 (t) cc_final: 0.5810 (t) REVERT: B 601 ASP cc_start: 0.7740 (t0) cc_final: 0.7281 (t0) REVERT: C 65 CYS cc_start: 0.6226 (t) cc_final: 0.5793 (t) REVERT: C 601 ASP cc_start: 0.7747 (t0) cc_final: 0.7283 (t0) REVERT: D 65 CYS cc_start: 0.6231 (t) cc_final: 0.5793 (t) REVERT: D 601 ASP cc_start: 0.7752 (t0) cc_final: 0.7281 (t0) outliers start: 25 outliers final: 24 residues processed: 305 average time/residue: 0.1280 time to fit residues: 63.7253 Evaluate side-chains 319 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 295 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 28 optimal weight: 0.1980 chunk 219 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.204654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174257 restraints weight = 25837.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.176265 restraints weight = 53090.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176813 restraints weight = 32266.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.177229 restraints weight = 21126.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177901 restraints weight = 17942.855| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21804 Z= 0.145 Angle : 0.551 8.315 29584 Z= 0.288 Chirality : 0.043 0.174 3404 Planarity : 0.003 0.027 3668 Dihedral : 4.447 23.194 2864 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.72 % Favored : 91.13 % Rotamer: Outliers : 1.68 % Allowed : 14.16 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.16), residues: 2616 helix: 0.44 (0.15), residues: 1280 sheet: -3.18 (0.39), residues: 188 loop : -2.84 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.010 0.001 TYR D 508 PHE 0.018 0.002 PHE B 93 TRP 0.011 0.001 TRP B 388 HIS 0.003 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00353 (21804) covalent geometry : angle 0.55133 (29584) hydrogen bonds : bond 0.04217 ( 876) hydrogen bonds : angle 4.43541 ( 2532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 0.767 Fit side-chains REVERT: A 65 CYS cc_start: 0.6319 (t) cc_final: 0.5868 (t) REVERT: A 410 GLU cc_start: 0.7236 (tt0) cc_final: 0.7030 (mt-10) REVERT: A 601 ASP cc_start: 0.7782 (t0) cc_final: 0.7334 (t0) REVERT: B 65 CYS cc_start: 0.6309 (t) cc_final: 0.5868 (t) REVERT: B 601 ASP cc_start: 0.7781 (t0) cc_final: 0.7341 (t0) REVERT: C 65 CYS cc_start: 0.6299 (t) cc_final: 0.5857 (t) REVERT: C 601 ASP cc_start: 0.7808 (t0) cc_final: 0.7333 (t0) REVERT: D 65 CYS cc_start: 0.6305 (t) cc_final: 0.5857 (t) REVERT: D 601 ASP cc_start: 0.7794 (t0) cc_final: 0.7317 (t0) outliers start: 40 outliers final: 37 residues processed: 319 average time/residue: 0.1217 time to fit residues: 63.9663 Evaluate side-chains 322 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 100 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.203116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171188 restraints weight = 25353.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.172607 restraints weight = 53134.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.173359 restraints weight = 35525.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173976 restraints weight = 21607.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174616 restraints weight = 18531.141| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21804 Z= 0.189 Angle : 0.590 8.233 29584 Z= 0.312 Chirality : 0.044 0.180 3404 Planarity : 0.003 0.026 3668 Dihedral : 4.663 23.276 2864 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.44 % Favored : 90.41 % Rotamer: Outliers : 1.85 % Allowed : 13.99 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.16), residues: 2616 helix: 0.25 (0.15), residues: 1288 sheet: -3.22 (0.38), residues: 188 loop : -2.87 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 22 TYR 0.011 0.001 TYR D 508 PHE 0.017 0.002 PHE D 93 TRP 0.010 0.001 TRP B 388 HIS 0.003 0.001 HIS D 539 Details of bonding type rmsd covalent geometry : bond 0.00464 (21804) covalent geometry : angle 0.59016 (29584) hydrogen bonds : bond 0.04784 ( 876) hydrogen bonds : angle 4.64864 ( 2532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 0.706 Fit side-chains REVERT: A 65 CYS cc_start: 0.6458 (t) cc_final: 0.5980 (t) REVERT: A 331 LEU cc_start: 0.8740 (tt) cc_final: 0.8417 (mt) REVERT: A 601 ASP cc_start: 0.7842 (t0) cc_final: 0.7381 (t0) REVERT: B 65 CYS cc_start: 0.6449 (t) cc_final: 0.5978 (t) REVERT: B 601 ASP cc_start: 0.7852 (t0) cc_final: 0.7375 (t0) REVERT: C 65 CYS cc_start: 0.6433 (t) cc_final: 0.5966 (t) REVERT: C 601 ASP cc_start: 0.7863 (t0) cc_final: 0.7388 (t0) REVERT: D 65 CYS cc_start: 0.6445 (t) cc_final: 0.5966 (t) REVERT: D 331 LEU cc_start: 0.8749 (tt) cc_final: 0.8428 (mt) REVERT: D 601 ASP cc_start: 0.7851 (t0) cc_final: 0.7381 (t0) outliers start: 44 outliers final: 43 residues processed: 317 average time/residue: 0.1161 time to fit residues: 60.9053 Evaluate side-chains 324 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 39 optimal weight: 0.5980 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 161 optimal weight: 0.0170 chunk 191 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.204957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173368 restraints weight = 25952.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.175014 restraints weight = 52968.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175908 restraints weight = 37017.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.176577 restraints weight = 21313.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.178837 restraints weight = 17274.867| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21804 Z= 0.124 Angle : 0.542 8.461 29584 Z= 0.283 Chirality : 0.042 0.158 3404 Planarity : 0.003 0.027 3668 Dihedral : 4.484 23.708 2864 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.45 % Favored : 91.40 % Rotamer: Outliers : 1.64 % Allowed : 14.92 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.16), residues: 2616 helix: 0.43 (0.15), residues: 1284 sheet: -3.18 (0.39), residues: 188 loop : -2.82 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.010 0.001 TYR D 508 PHE 0.015 0.002 PHE D 93 TRP 0.011 0.001 TRP B 388 HIS 0.003 0.001 HIS D 539 Details of bonding type rmsd covalent geometry : bond 0.00295 (21804) covalent geometry : angle 0.54232 (29584) hydrogen bonds : bond 0.03916 ( 876) hydrogen bonds : angle 4.40125 ( 2532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 0.827 Fit side-chains REVERT: A 427 MET cc_start: 0.8642 (mmt) cc_final: 0.8080 (mmt) REVERT: A 601 ASP cc_start: 0.7710 (t0) cc_final: 0.7303 (t0) REVERT: B 427 MET cc_start: 0.8647 (mmt) cc_final: 0.8077 (mmt) REVERT: B 601 ASP cc_start: 0.7698 (t0) cc_final: 0.7260 (t0) REVERT: C 427 MET cc_start: 0.8630 (mmt) cc_final: 0.8061 (mmt) REVERT: C 601 ASP cc_start: 0.7706 (t0) cc_final: 0.7263 (t0) REVERT: D 427 MET cc_start: 0.8634 (mmt) cc_final: 0.8071 (mmt) REVERT: D 601 ASP cc_start: 0.7699 (t0) cc_final: 0.7258 (t0) outliers start: 39 outliers final: 31 residues processed: 309 average time/residue: 0.1173 time to fit residues: 60.0787 Evaluate side-chains 317 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 74 optimal weight: 5.9990 chunk 155 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 186 optimal weight: 0.0070 chunk 263 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.203795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171697 restraints weight = 25803.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173640 restraints weight = 52612.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.174864 restraints weight = 32580.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.175015 restraints weight = 21531.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.176045 restraints weight = 17923.304| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21804 Z= 0.094 Angle : 0.516 8.552 29584 Z= 0.266 Chirality : 0.040 0.156 3404 Planarity : 0.003 0.027 3668 Dihedral : 4.304 23.696 2864 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.37 % Favored : 91.48 % Rotamer: Outliers : 1.39 % Allowed : 15.38 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.16), residues: 2616 helix: 0.72 (0.15), residues: 1280 sheet: -3.19 (0.39), residues: 188 loop : -2.75 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 22 TYR 0.010 0.001 TYR D 508 PHE 0.014 0.001 PHE A 93 TRP 0.014 0.001 TRP D 513 HIS 0.002 0.000 HIS D 539 Details of bonding type rmsd covalent geometry : bond 0.00213 (21804) covalent geometry : angle 0.51622 (29584) hydrogen bonds : bond 0.03210 ( 876) hydrogen bonds : angle 4.14566 ( 2532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2877.65 seconds wall clock time: 50 minutes 57.58 seconds (3057.58 seconds total)