Starting phenix.real_space_refine on Tue Aug 26 19:40:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1d_35919/08_2025/8j1d_35919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1d_35919/08_2025/8j1d_35919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1d_35919/08_2025/8j1d_35919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1d_35919/08_2025/8j1d_35919.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1d_35919/08_2025/8j1d_35919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1d_35919/08_2025/8j1d_35919.cif" } resolution = 3.59 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= 0.002 sd= 0.026 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 S 104 5.16 5 C 13132 2.51 5 N 3340 2.21 5 O 3620 1.98 5 H 20492 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 40688 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10172 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Chain: "B" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10172 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Chain: "C" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10172 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Chain: "D" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10172 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Time building chain proxies: 6.97, per 1000 atoms: 0.17 Number of scatterers: 40688 At special positions: 0 Unit cell: (157.17, 157.17, 126.48, 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) S 104 16.00 O 3620 8.00 N 3340 7.00 C 13132 6.00 H 20492 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.85 Conformation dependent library (CDL) restraints added in 978.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 63.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.911A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.445A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.541A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 removed outlier: 4.024A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.700A pdb=" N GLN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.586A pdb=" N ASN A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 549 through 570 Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.740A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.579A pdb=" N MET A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 637 removed outlier: 3.840A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 681 removed outlier: 3.777A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 725 Processing helix chain 'A' and resid 726 through 748 removed outlier: 3.670A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.561A pdb=" N GLY A 765 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.939A pdb=" N PHE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.453A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.510A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 260 removed outlier: 4.024A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.700A pdb=" N GLN B 274 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 336 through 357 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.584A pdb=" N ASN B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 451 Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'B' and resid 468 through 491 Processing helix chain 'B' and resid 504 through 534 Processing helix chain 'B' and resid 549 through 570 Processing helix chain 'B' and resid 575 through 592 removed outlier: 3.701A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 589 " --> pdb=" O GLY B 585 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 removed outlier: 3.593A pdb=" N MET B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 637 removed outlier: 3.844A pdb=" N ARG B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 681 removed outlier: 3.778A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 725 Processing helix chain 'B' and resid 726 through 748 removed outlier: 3.671A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.564A pdb=" N GLY B 765 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.938A pdb=" N PHE C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.448A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.537A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 removed outlier: 4.023A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.698A pdb=" N GLN C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 336 through 357 Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 432 through 440 removed outlier: 3.585A pdb=" N ASN C 440 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 453 through 464 Processing helix chain 'C' and resid 468 through 491 Processing helix chain 'C' and resid 504 through 534 Processing helix chain 'C' and resid 549 through 570 Processing helix chain 'C' and resid 575 through 592 removed outlier: 3.734A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 589 " --> pdb=" O GLY C 585 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.577A pdb=" N MET C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 637 removed outlier: 3.844A pdb=" N ARG C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 681 removed outlier: 3.777A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 725 Processing helix chain 'C' and resid 726 through 748 removed outlier: 3.670A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.562A pdb=" N GLY C 765 " --> pdb=" O VAL C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 168 through 176 removed outlier: 3.927A pdb=" N PHE D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.448A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.537A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 removed outlier: 4.022A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.698A pdb=" N GLN D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 336 through 357 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 432 through 440 removed outlier: 3.585A pdb=" N ASN D 440 " --> pdb=" O ILE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 453 through 464 Processing helix chain 'D' and resid 468 through 491 Processing helix chain 'D' and resid 504 through 534 Processing helix chain 'D' and resid 549 through 570 Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.748A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 589 " --> pdb=" O GLY D 585 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 610 removed outlier: 3.579A pdb=" N MET D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 637 removed outlier: 3.845A pdb=" N ARG D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 681 removed outlier: 3.777A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 725 Processing helix chain 'D' and resid 726 through 748 removed outlier: 3.671A pdb=" N LYS D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 766 removed outlier: 3.562A pdb=" N GLY D 765 " --> pdb=" O VAL D 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.056A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.062A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.057A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.056A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3156 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: 8.77 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 20452 1.03 - 1.22: 40 1.22 - 1.42: 8654 1.42 - 1.61: 11838 1.61 - 1.81: 168 Bond restraints: 41152 Sorted by residual: bond pdb=" N VAL A 148 " pdb=" CA VAL A 148 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.24e+00 bond pdb=" N VAL C 148 " pdb=" H VAL C 148 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" CA VAL B 654 " pdb=" CB VAL B 654 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.22e+00 bond pdb=" N VAL B 148 " pdb=" H VAL B 148 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" N VAL A 148 " pdb=" H VAL A 148 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 41147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 71480 1.35 - 2.71: 2683 2.71 - 4.06: 173 4.06 - 5.41: 47 5.41 - 6.77: 5 Bond angle restraints: 74388 Sorted by residual: angle pdb=" C SER A 650 " pdb=" N ASN A 651 " pdb=" CA ASN A 651 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.70e+00 angle pdb=" C SER D 650 " pdb=" N ASN D 651 " pdb=" CA ASN D 651 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.66e+00 angle pdb=" C SER C 650 " pdb=" N ASN C 651 " pdb=" CA ASN C 651 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.60e+00 angle pdb=" C SER B 650 " pdb=" N ASN B 651 " pdb=" CA ASN B 651 " ideal model delta sigma weight residual 121.54 126.80 -5.26 1.91e+00 2.74e-01 7.58e+00 angle pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 112.00 108.76 3.24 1.40e+00 5.10e-01 5.37e+00 ... (remaining 74383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 17012 16.42 - 32.83: 1649 32.83 - 49.25: 494 49.25 - 65.66: 157 65.66 - 82.08: 28 Dihedral angle restraints: 19340 sinusoidal: 10400 harmonic: 8940 Sorted by residual: dihedral pdb=" CG ARG B 404 " pdb=" CD ARG B 404 " pdb=" NE ARG B 404 " pdb=" CZ ARG B 404 " ideal model delta sinusoidal sigma weight residual -180.00 -137.63 -42.37 2 1.50e+01 4.44e-03 9.69e+00 dihedral pdb=" CG ARG C 404 " pdb=" CD ARG C 404 " pdb=" NE ARG C 404 " pdb=" CZ ARG C 404 " ideal model delta sinusoidal sigma weight residual 180.00 -137.64 -42.36 2 1.50e+01 4.44e-03 9.69e+00 dihedral pdb=" CG ARG D 404 " pdb=" CD ARG D 404 " pdb=" NE ARG D 404 " pdb=" CZ ARG D 404 " ideal model delta sinusoidal sigma weight residual -180.00 -137.65 -42.35 2 1.50e+01 4.44e-03 9.68e+00 ... (remaining 19337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2189 0.033 - 0.065: 802 0.065 - 0.098: 190 0.098 - 0.130: 38 0.130 - 0.163: 5 Chirality restraints: 3224 Sorted by residual: chirality pdb=" CB THR D 701 " pdb=" CA THR D 701 " pdb=" OG1 THR D 701 " pdb=" CG2 THR D 701 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB THR A 701 " pdb=" CA THR A 701 " pdb=" OG1 THR A 701 " pdb=" CG2 THR A 701 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB THR C 701 " pdb=" CA THR C 701 " pdb=" OG1 THR C 701 " pdb=" CG2 THR C 701 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 3221 not shown) Planarity restraints: 5912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 583 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C VAL B 583 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL B 583 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 584 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 498 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 499 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 498 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 499 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.030 5.00e-02 4.00e+02 ... (remaining 5909 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 3408 2.20 - 2.80: 85239 2.80 - 3.40: 113717 3.40 - 4.00: 140040 4.00 - 4.60: 218975 Nonbonded interactions: 561379 Sorted by model distance: nonbonded pdb=" O ILE C 744 " pdb=" HG SER C 747 " model vdw 1.599 2.450 nonbonded pdb=" O ILE D 744 " pdb=" HG SER D 747 " model vdw 1.600 2.450 nonbonded pdb=" O ILE A 744 " pdb=" HG SER A 747 " model vdw 1.601 2.450 nonbonded pdb=" O ILE B 744 " pdb=" HG SER B 747 " model vdw 1.601 2.450 nonbonded pdb=" O SER A 726 " pdb=" H SER A 729 " model vdw 1.608 2.450 ... (remaining 561374 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.680 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: 0.260 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.000 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 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 0.070 20660 Z= 0.130 Angle : 0.594 6.768 28020 Z= 0.322 Chirality : 0.035 0.163 3224 Planarity : 0.004 0.054 3500 Dihedral : 14.255 80.426 7532 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.36 % Favored : 89.72 % Rotamer: Outliers : 0.09 % Allowed : 11.13 % Favored : 88.78 % 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: -1.13 (0.17), residues: 2500 helix: 0.34 (0.14), residues: 1464 sheet: 0.06 (0.70), residues: 56 loop : -2.54 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 775 TYR 0.010 0.001 TYR B 556 PHE 0.016 0.001 PHE B 707 TRP 0.013 0.002 TRP D 409 HIS 0.006 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00280 (20660) covalent geometry : angle 0.59390 (28020) hydrogen bonds : bond 0.14384 ( 1092) hydrogen bonds : angle 5.85255 ( 3156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 151 average time/residue: 0.3465 time to fit residues: 82.5867 Evaluate side-chains 147 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN C 445 ASN D 445 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.155114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.129868 restraints weight = 124010.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.131741 restraints weight = 99527.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.133166 restraints weight = 78231.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.133895 restraints weight = 52775.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.134769 restraints weight = 48461.657| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 20660 Z= 0.404 Angle : 0.773 8.575 28020 Z= 0.425 Chirality : 0.044 0.161 3224 Planarity : 0.007 0.060 3500 Dihedral : 5.192 41.872 2770 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 1.12 % Allowed : 14.36 % Favored : 84.52 % Rotamer: Outliers : 1.80 % Allowed : 12.43 % Favored : 85.77 % 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: 2500 helix: -0.36 (0.13), residues: 1500 sheet: -0.28 (0.69), residues: 56 loop : -3.00 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 757 TYR 0.020 0.003 TYR D 556 PHE 0.027 0.002 PHE D 341 TRP 0.012 0.002 TRP B 409 HIS 0.009 0.002 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00905 (20660) covalent geometry : angle 0.77333 (28020) hydrogen bonds : bond 0.05515 ( 1092) hydrogen bonds : angle 5.34018 ( 3156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.6400 (tpt) cc_final: 0.6162 (tpt) REVERT: A 628 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5688 (m-10) REVERT: B 578 MET cc_start: 0.6373 (tpt) cc_final: 0.6124 (tpt) REVERT: B 628 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5671 (m-10) REVERT: C 578 MET cc_start: 0.6400 (tpt) cc_final: 0.6171 (tpt) REVERT: C 628 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.5732 (m-10) REVERT: D 578 MET cc_start: 0.6418 (tpt) cc_final: 0.6171 (tpt) REVERT: D 628 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5577 (m-10) outliers start: 40 outliers final: 26 residues processed: 170 average time/residue: 0.3314 time to fit residues: 89.8510 Evaluate side-chains 170 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.149776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.122045 restraints weight = 127574.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.123293 restraints weight = 87493.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.125271 restraints weight = 64337.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.125366 restraints weight = 47935.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.125800 restraints weight = 47096.718| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20660 Z= 0.134 Angle : 0.568 5.814 28020 Z= 0.301 Chirality : 0.035 0.119 3224 Planarity : 0.005 0.058 3500 Dihedral : 4.533 43.410 2770 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.88 % Favored : 90.16 % Rotamer: Outliers : 1.17 % Allowed : 13.11 % Favored : 85.73 % 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: -1.07 (0.17), residues: 2500 helix: 0.44 (0.13), residues: 1492 sheet: -0.37 (0.62), residues: 56 loop : -2.67 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 757 TYR 0.009 0.001 TYR A 702 PHE 0.022 0.001 PHE A 466 TRP 0.010 0.001 TRP D 409 HIS 0.003 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00298 (20660) covalent geometry : angle 0.56810 (28020) hydrogen bonds : bond 0.04108 ( 1092) hydrogen bonds : angle 4.69655 ( 3156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8263 (pt) REVERT: A 578 MET cc_start: 0.6276 (tpt) cc_final: 0.6009 (tpt) REVERT: A 628 TYR cc_start: 0.6054 (OUTLIER) cc_final: 0.5523 (m-10) REVERT: B 331 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8259 (pt) REVERT: B 578 MET cc_start: 0.6279 (tpt) cc_final: 0.6042 (tpt) REVERT: B 628 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5502 (m-10) REVERT: C 331 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8256 (pt) REVERT: C 578 MET cc_start: 0.6329 (tpt) cc_final: 0.6068 (tpt) REVERT: D 331 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8259 (pt) REVERT: D 578 MET cc_start: 0.6251 (tpt) cc_final: 0.5997 (tpt) outliers start: 26 outliers final: 16 residues processed: 170 average time/residue: 0.3458 time to fit residues: 94.0905 Evaluate side-chains 164 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 54 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 12 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 115 optimal weight: 0.1980 chunk 216 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.150748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.123967 restraints weight = 127024.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.123331 restraints weight = 94904.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.125946 restraints weight = 75424.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.125941 restraints weight = 56436.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.126373 restraints weight = 54227.666| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20660 Z= 0.128 Angle : 0.543 6.287 28020 Z= 0.286 Chirality : 0.034 0.125 3224 Planarity : 0.005 0.059 3500 Dihedral : 4.287 45.166 2770 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.96 % Allowed : 11.24 % Favored : 87.80 % Rotamer: Outliers : 1.12 % Allowed : 13.33 % Favored : 85.55 % 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: -0.65 (0.17), residues: 2500 helix: 0.78 (0.13), residues: 1500 sheet: -0.23 (0.61), residues: 64 loop : -2.55 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 757 TYR 0.009 0.001 TYR B 253 PHE 0.016 0.001 PHE D 756 TRP 0.009 0.001 TRP C 586 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00292 (20660) covalent geometry : angle 0.54303 (28020) hydrogen bonds : bond 0.03623 ( 1092) hydrogen bonds : angle 4.42632 ( 3156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 TYR cc_start: 0.5912 (OUTLIER) cc_final: 0.5462 (m-10) REVERT: B 628 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.5437 (m-10) REVERT: C 341 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8495 (p90) REVERT: D 341 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8500 (p90) outliers start: 25 outliers final: 21 residues processed: 168 average time/residue: 0.3447 time to fit residues: 92.6288 Evaluate side-chains 169 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 126 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 159 optimal weight: 50.0000 chunk 214 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 100 optimal weight: 40.0000 chunk 128 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.148598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.121894 restraints weight = 127392.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.122219 restraints weight = 94359.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.124065 restraints weight = 80189.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.124287 restraints weight = 55329.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.124747 restraints weight = 53421.808| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20660 Z= 0.192 Angle : 0.571 6.821 28020 Z= 0.306 Chirality : 0.035 0.127 3224 Planarity : 0.005 0.060 3500 Dihedral : 4.430 46.677 2770 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.96 % Allowed : 11.08 % Favored : 87.96 % Rotamer: Outliers : 1.97 % Allowed : 13.87 % 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: -0.76 (0.17), residues: 2500 helix: 0.72 (0.13), residues: 1500 sheet: -0.29 (0.64), residues: 64 loop : -2.65 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 404 TYR 0.010 0.001 TYR D 556 PHE 0.023 0.002 PHE A 466 TRP 0.007 0.001 TRP A 586 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00436 (20660) covalent geometry : angle 0.57149 (28020) hydrogen bonds : bond 0.03850 ( 1092) hydrogen bonds : angle 4.46504 ( 3156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8435 (pt) REVERT: A 628 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5611 (m-10) REVERT: B 331 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8428 (pt) REVERT: B 628 TYR cc_start: 0.6073 (OUTLIER) cc_final: 0.5564 (m-10) REVERT: C 331 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8353 (pt) REVERT: D 331 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8418 (pt) outliers start: 44 outliers final: 36 residues processed: 171 average time/residue: 0.3369 time to fit residues: 91.8907 Evaluate side-chains 181 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 97 optimal weight: 50.0000 chunk 76 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 185 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 447 HIS ** 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 = 0.4498 r_free = 0.4498 target = 0.151053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.125189 restraints weight = 124908.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.124652 restraints weight = 93109.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.126574 restraints weight = 80206.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.127422 restraints weight = 55715.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.128142 restraints weight = 52758.705| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20660 Z= 0.185 Angle : 0.570 6.785 28020 Z= 0.303 Chirality : 0.035 0.128 3224 Planarity : 0.005 0.060 3500 Dihedral : 4.454 47.790 2770 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.96 % Allowed : 12.20 % Favored : 86.84 % Rotamer: Outliers : 2.20 % Allowed : 14.23 % Favored : 83.57 % 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: -0.84 (0.17), residues: 2500 helix: 0.68 (0.13), residues: 1516 sheet: -0.11 (0.69), residues: 56 loop : -2.76 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 404 TYR 0.010 0.001 TYR D 556 PHE 0.017 0.001 PHE D 341 TRP 0.007 0.002 TRP A 409 HIS 0.006 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00421 (20660) covalent geometry : angle 0.56996 (28020) hydrogen bonds : bond 0.03748 ( 1092) hydrogen bonds : angle 4.43036 ( 3156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8448 (pt) REVERT: A 628 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.5433 (m-10) REVERT: B 331 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8381 (pt) REVERT: B 628 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.5492 (m-10) REVERT: C 331 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8437 (pt) REVERT: D 331 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8436 (pt) REVERT: D 574 TYR cc_start: 0.4527 (m-10) cc_final: 0.4148 (m-80) outliers start: 49 outliers final: 37 residues processed: 176 average time/residue: 0.3367 time to fit residues: 95.5551 Evaluate side-chains 183 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 61 optimal weight: 0.6980 chunk 157 optimal weight: 0.2980 chunk 100 optimal weight: 50.0000 chunk 182 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 162 optimal weight: 40.0000 chunk 126 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** 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 = 0.4671 r_free = 0.4671 target = 0.160297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.136790 restraints weight = 120519.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.140552 restraints weight = 93416.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.141595 restraints weight = 59194.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.141996 restraints weight = 43252.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.142421 restraints weight = 41044.512| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20660 Z= 0.139 Angle : 0.543 6.199 28020 Z= 0.286 Chirality : 0.034 0.142 3224 Planarity : 0.004 0.051 3500 Dihedral : 4.333 48.454 2770 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.68 % Favored : 88.36 % Rotamer: Outliers : 1.97 % Allowed : 14.36 % Favored : 83.66 % 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: -0.62 (0.17), residues: 2500 helix: 0.85 (0.13), residues: 1516 sheet: -0.28 (0.62), residues: 64 loop : -2.66 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 404 TYR 0.008 0.001 TYR A 628 PHE 0.015 0.001 PHE B 756 TRP 0.008 0.001 TRP D 409 HIS 0.004 0.001 HIS D 388 Details of bonding type rmsd covalent geometry : bond 0.00318 (20660) covalent geometry : angle 0.54285 (28020) hydrogen bonds : bond 0.03500 ( 1092) hydrogen bonds : angle 4.31732 ( 3156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8337 (pt) REVERT: A 628 TYR cc_start: 0.5804 (OUTLIER) cc_final: 0.5262 (m-10) REVERT: B 331 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8336 (pt) REVERT: B 628 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.5270 (m-10) REVERT: C 331 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8332 (pt) REVERT: D 331 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8330 (pt) REVERT: D 574 TYR cc_start: 0.4414 (m-10) cc_final: 0.4051 (m-80) outliers start: 44 outliers final: 38 residues processed: 176 average time/residue: 0.3310 time to fit residues: 93.3676 Evaluate side-chains 184 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 155 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 241 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** 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 = 0.4649 r_free = 0.4649 target = 0.158690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.134287 restraints weight = 120649.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.135437 restraints weight = 96284.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.136747 restraints weight = 81283.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.137548 restraints weight = 50936.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.137855 restraints weight = 47168.839| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20660 Z= 0.183 Angle : 0.568 6.790 28020 Z= 0.301 Chirality : 0.035 0.136 3224 Planarity : 0.005 0.056 3500 Dihedral : 4.412 49.278 2770 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.96 % Allowed : 12.12 % Favored : 86.92 % Rotamer: Outliers : 2.24 % Allowed : 14.32 % Favored : 83.44 % 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: -0.72 (0.17), residues: 2500 helix: 0.75 (0.13), residues: 1520 sheet: -0.13 (0.68), residues: 56 loop : -2.69 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 404 TYR 0.012 0.001 TYR C 556 PHE 0.021 0.001 PHE D 466 TRP 0.006 0.002 TRP C 409 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00417 (20660) covalent geometry : angle 0.56816 (28020) hydrogen bonds : bond 0.03633 ( 1092) hydrogen bonds : angle 4.37574 ( 3156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8394 (pt) REVERT: A 574 TYR cc_start: 0.4495 (m-10) cc_final: 0.4114 (m-80) REVERT: A 628 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.5244 (m-10) REVERT: A 702 TYR cc_start: 0.7942 (t80) cc_final: 0.7716 (t80) REVERT: B 331 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8392 (pt) REVERT: B 628 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5382 (m-10) REVERT: C 331 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8387 (pt) REVERT: C 574 TYR cc_start: 0.4483 (m-10) cc_final: 0.4109 (m-80) REVERT: D 331 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8384 (pt) REVERT: D 574 TYR cc_start: 0.4466 (m-10) cc_final: 0.4095 (m-80) outliers start: 50 outliers final: 39 residues processed: 185 average time/residue: 0.3190 time to fit residues: 94.4463 Evaluate side-chains 190 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** 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 = 0.4672 r_free = 0.4672 target = 0.160163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.136816 restraints weight = 120752.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.140823 restraints weight = 92416.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.141781 restraints weight = 56685.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.142069 restraints weight = 42279.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.142362 restraints weight = 40618.303| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20660 Z= 0.140 Angle : 0.543 6.147 28020 Z= 0.285 Chirality : 0.034 0.141 3224 Planarity : 0.004 0.055 3500 Dihedral : 4.324 49.643 2770 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.96 % Favored : 88.08 % Rotamer: Outliers : 2.02 % Allowed : 14.95 % Favored : 83.03 % 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: -0.53 (0.18), residues: 2500 helix: 0.90 (0.13), residues: 1520 sheet: -0.26 (0.62), residues: 64 loop : -2.59 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 404 TYR 0.009 0.001 TYR A 556 PHE 0.018 0.001 PHE D 466 TRP 0.008 0.001 TRP C 409 HIS 0.004 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00320 (20660) covalent geometry : angle 0.54270 (28020) hydrogen bonds : bond 0.03414 ( 1092) hydrogen bonds : angle 4.26772 ( 3156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8336 (pt) REVERT: A 574 TYR cc_start: 0.4384 (m-10) cc_final: 0.4035 (m-80) REVERT: A 628 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.5311 (m-10) REVERT: B 331 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8337 (pt) REVERT: B 628 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.5232 (m-10) REVERT: B 702 TYR cc_start: 0.7832 (t80) cc_final: 0.7632 (t80) REVERT: C 331 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8330 (pt) REVERT: C 574 TYR cc_start: 0.4371 (m-10) cc_final: 0.4010 (m-80) REVERT: C 718 MET cc_start: 0.5527 (ttp) cc_final: 0.5310 (ttp) REVERT: D 331 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8332 (pt) REVERT: D 574 TYR cc_start: 0.4388 (m-10) cc_final: 0.4042 (m-80) outliers start: 45 outliers final: 39 residues processed: 184 average time/residue: 0.3140 time to fit residues: 91.9454 Evaluate side-chains 190 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 9 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** 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 = 0.4571 r_free = 0.4571 target = 0.154744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.129468 restraints weight = 121769.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.130292 restraints weight = 86228.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.131867 restraints weight = 72790.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.132465 restraints weight = 49332.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.133139 restraints weight = 47201.378| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20660 Z= 0.129 Angle : 0.530 6.156 28020 Z= 0.278 Chirality : 0.034 0.152 3224 Planarity : 0.004 0.054 3500 Dihedral : 4.203 50.731 2770 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.96 % Allowed : 11.24 % Favored : 87.80 % Rotamer: Outliers : 1.97 % Allowed : 15.08 % Favored : 82.94 % 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: -0.35 (0.18), residues: 2500 helix: 1.14 (0.14), residues: 1500 sheet: -0.18 (0.62), residues: 64 loop : -2.64 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 404 TYR 0.009 0.001 TYR C 253 PHE 0.017 0.001 PHE A 466 TRP 0.008 0.001 TRP C 409 HIS 0.003 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00299 (20660) covalent geometry : angle 0.53018 (28020) hydrogen bonds : bond 0.03233 ( 1092) hydrogen bonds : angle 4.16572 ( 3156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8334 (pt) REVERT: A 574 TYR cc_start: 0.4502 (m-10) cc_final: 0.4135 (m-80) REVERT: A 628 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.5310 (m-10) REVERT: B 331 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8399 (pt) REVERT: B 628 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.5274 (m-10) REVERT: B 702 TYR cc_start: 0.7939 (t80) cc_final: 0.7734 (t80) REVERT: C 331 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8387 (pt) REVERT: C 574 TYR cc_start: 0.4526 (m-10) cc_final: 0.4151 (m-80) REVERT: D 331 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8383 (pt) REVERT: D 574 TYR cc_start: 0.4422 (m-10) cc_final: 0.4072 (m-80) outliers start: 44 outliers final: 38 residues processed: 180 average time/residue: 0.2924 time to fit residues: 82.9065 Evaluate side-chains 191 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 127 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** 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 = 0.4646 r_free = 0.4646 target = 0.158253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.134627 restraints weight = 121794.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.135754 restraints weight = 104054.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.137019 restraints weight = 88452.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.138597 restraints weight = 55084.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.139105 restraints weight = 47662.823| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20660 Z= 0.226 Angle : 0.603 7.073 28020 Z= 0.322 Chirality : 0.037 0.130 3224 Planarity : 0.005 0.059 3500 Dihedral : 4.498 51.092 2770 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.96 % Allowed : 12.60 % Favored : 86.44 % Rotamer: Outliers : 1.89 % Allowed : 15.35 % Favored : 82.76 % 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: -0.73 (0.17), residues: 2500 helix: 0.80 (0.13), residues: 1504 sheet: -0.05 (0.71), residues: 56 loop : -2.75 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 404 TYR 0.014 0.002 TYR A 556 PHE 0.019 0.002 PHE A 466 TRP 0.007 0.002 TRP C 776 HIS 0.007 0.002 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00517 (20660) covalent geometry : angle 0.60279 (28020) hydrogen bonds : bond 0.03761 ( 1092) hydrogen bonds : angle 4.40095 ( 3156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4896.80 seconds wall clock time: 85 minutes 7.45 seconds (5107.45 seconds total)