Starting phenix.real_space_refine on Sat Sep 12 08:22:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wb8_21586/09_2026/6wb8_21586.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb8_21586/09_2026/6wb8_21586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wb8_21586/09_2026/6wb8_21586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb8_21586/09_2026/6wb8_21586.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wb8_21586/09_2026/6wb8_21586.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wb8_21586/09_2026/6wb8_21586.cif" model { file = "/net/cci-nas-00/data/ceres_data/6wb8_21586/09_2026/6wb8_21586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb8_21586/09_2026/6wb8_21586.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 9864 2.51 5 N 2360 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14888 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3680 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 5, 'PTRANS': 10, 'TRANS': 447} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 10, 'ASP:plan': 10, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 3.77, per 1000 atoms: 0.25 Number of scatterers: 14888 At special positions: 0 Unit cell: (112.35, 112.35, 101.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2596 8.00 N 2360 7.00 C 9864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG A 803 " - " ASN A 375 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG B 803 " - " ASN B 375 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG C 803 " - " ASN C 375 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG D 803 " - " ASN D 375 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 583.0 milliseconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 62.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 216 through 242 Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.721A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'A' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 579 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 619 removed outlier: 4.362A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 653 removed outlier: 4.102A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 670 through 693 removed outlier: 4.008A pdb=" N ASN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.549A pdb=" N ASP B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 541 Processing helix chain 'B' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN B 578 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 619 removed outlier: 4.362A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 670 through 693 removed outlier: 4.007A pdb=" N ASN B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 484 " --> pdb=" O PHE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 532 through 541 Processing helix chain 'C' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN C 578 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 579 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 619 removed outlier: 4.361A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 668 Processing helix chain 'C' and resid 670 through 693 removed outlier: 4.008A pdb=" N ASN C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 532 through 541 Processing helix chain 'D' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN D 578 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 579 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 619 removed outlier: 4.360A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 668 Processing helix chain 'D' and resid 670 through 693 removed outlier: 4.007A pdb=" N ASN D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.355A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 945 hydrogen bonds defined for protein. 2655 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: 2.71 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 2020 1.24 - 1.38: 4381 1.38 - 1.52: 7660 1.52 - 1.66: 1111 1.66 - 1.81: 104 Bond restraints: 15276 Sorted by residual: bond pdb=" C ALA D 356 " pdb=" N PRO D 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.01e+02 bond pdb=" C ALA A 356 " pdb=" N PRO A 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.01e+02 bond pdb=" C ALA C 356 " pdb=" N PRO C 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.00e+02 bond pdb=" C ALA B 356 " pdb=" N PRO B 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.00e+02 bond pdb=" CA ILE B 341 " pdb=" C ILE B 341 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.27e-02 6.20e+03 7.55e+00 ... (remaining 15271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 20316 2.53 - 5.06: 407 5.06 - 7.60: 61 7.60 - 10.13: 12 10.13 - 12.66: 4 Bond angle restraints: 20800 Sorted by residual: angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 111.36 118.20 -6.84 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA C 303 " pdb=" CA ALA C 303 " pdb=" C ALA C 303 " ideal model delta sigma weight residual 111.36 118.19 -6.83 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA A 303 " pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 111.36 118.19 -6.83 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA D 303 " pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 111.36 118.16 -6.80 1.09e+00 8.42e-01 3.89e+01 angle pdb=" CA ILE C 341 " pdb=" C ILE C 341 " pdb=" N LYS C 342 " ideal model delta sigma weight residual 116.60 124.56 -7.96 1.45e+00 4.76e-01 3.01e+01 ... (remaining 20795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 8412 16.09 - 32.19: 172 32.19 - 48.28: 44 48.28 - 64.37: 0 64.37 - 80.47: 12 Dihedral angle restraints: 8640 sinusoidal: 3156 harmonic: 5484 Sorted by residual: dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASN C 432 " pdb=" C ASN C 432 " pdb=" N ILE C 433 " pdb=" CA ILE C 433 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ASN B 432 " pdb=" C ASN B 432 " pdb=" N ILE B 433 " pdb=" CA ILE B 433 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 8637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2345 0.102 - 0.204: 79 0.204 - 0.306: 0 0.306 - 0.409: 0 0.409 - 0.511: 4 Chirality restraints: 2428 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" C1 NAG C 801 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C 801 " pdb=" O5 NAG C 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C1 NAG D 801 " pdb=" ND2 ASN D 328 " pdb=" C2 NAG D 801 " pdb=" O5 NAG D 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 2425 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 458 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 459 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 458 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO B 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 459 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 458 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO C 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 459 " -0.029 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 413 2.68 - 3.23: 16979 3.23 - 3.79: 25543 3.79 - 4.34: 32429 4.34 - 4.90: 52321 Nonbonded interactions: 127685 Sorted by model distance: nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.124 3.040 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.124 3.040 nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.125 3.040 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.125 3.040 nonbonded pdb=" O PRO A 334 " pdb=" NH1 ARG A 338 " model vdw 2.203 3.120 ... (remaining 127680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.011 0.235 15288 Z= 0.496 Angle : 0.954 13.820 20836 Z= 0.514 Chirality : 0.051 0.511 2428 Planarity : 0.005 0.054 2556 Dihedral : 8.791 80.467 5088 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.91 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -3.70 (0.16), residues: 1828 helix: -3.19 (0.11), residues: 996 sheet: 0.97 (0.33), residues: 184 loop : -1.92 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 420 TYR 0.014 0.002 TYR C 386 PHE 0.018 0.002 PHE A 310 TRP 0.033 0.004 TRP C 380 HIS 0.004 0.002 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.01061 / 0.50 (15276) covalent geometry : angle 0.90504 / 0.50 (20800) hydrogen bonds : bond 0.25586 / 16.73 ( 937) hydrogen bonds : angle 8.52790 / 6.07 ( 2655) link_NAG-ASN : bond 0.00806 / 0.54 ( 12) link_NAG-ASN : angle 7.32915 / 6.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 675 MET cc_start: 0.8569 (tpt) cc_final: 0.7933 (tpt) REVERT: D 675 MET cc_start: 0.8600 (tpt) cc_final: 0.7693 (tpt) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.1234 time to fit residues: 70.1746 Evaluate side-chains 221 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN A 379 HIS A 458 GLN A 543 ASN A 550 HIS A 636 GLN B 323 GLN B 379 HIS B 458 GLN B 543 ASN B 550 HIS B 636 GLN C 323 GLN C 379 HIS C 458 GLN C 543 ASN C 550 HIS C 636 GLN D 323 GLN D 379 HIS D 458 GLN D 543 ASN D 550 HIS D 636 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.092393 restraints weight = 22073.566| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.39 r_work: 0.2898 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15288 Z= 0.176 Angle : 0.687 12.038 20836 Z= 0.370 Chirality : 0.047 0.432 2428 Planarity : 0.005 0.047 2556 Dihedral : 5.165 32.958 2016 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.72 % Favored : 96.06 % Rotamer: Outliers : 1.71 % Allowed : 8.68 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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 are not related in a simple way. whole: 0.14 (0.18), residues: 1828 helix: 0.83 (0.15), residues: 1040 sheet: 1.08 (0.34), residues: 184 loop : -1.50 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 581 TYR 0.019 0.002 TYR A 527 PHE 0.019 0.002 PHE A 676 TRP 0.019 0.002 TRP A 293 HIS 0.002 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (15276) covalent geometry : angle 0.65688 / 0.36 (20800) hydrogen bonds : bond 0.05623 / 3.69 ( 937) hydrogen bonds : angle 4.71843 / 3.31 ( 2655) link_NAG-ASN : bond 0.00884 / 0.59 ( 12) link_NAG-ASN : angle 4.86789 / 4.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 ASP cc_start: 0.8672 (m-30) cc_final: 0.8265 (m-30) REVERT: A 595 LYS cc_start: 0.8892 (tptt) cc_final: 0.8565 (ttmt) REVERT: A 603 MET cc_start: 0.8755 (ttp) cc_final: 0.8517 (ttp) REVERT: A 675 MET cc_start: 0.8879 (tpt) cc_final: 0.7885 (tpt) REVERT: B 511 ASP cc_start: 0.8680 (m-30) cc_final: 0.8225 (m-30) REVERT: B 595 LYS cc_start: 0.8898 (tptt) cc_final: 0.8573 (ttmt) REVERT: B 603 MET cc_start: 0.8797 (ttp) cc_final: 0.8564 (ttp) REVERT: B 675 MET cc_start: 0.8896 (tpt) cc_final: 0.7892 (tpt) REVERT: C 511 ASP cc_start: 0.8698 (m-30) cc_final: 0.8290 (m-30) REVERT: C 595 LYS cc_start: 0.8886 (tptt) cc_final: 0.8566 (ttmt) REVERT: C 603 MET cc_start: 0.8774 (ttp) cc_final: 0.8539 (ttp) REVERT: D 511 ASP cc_start: 0.8663 (m-30) cc_final: 0.8234 (m-30) REVERT: D 595 LYS cc_start: 0.8889 (tptt) cc_final: 0.8562 (ttmt) REVERT: D 603 MET cc_start: 0.8793 (ttp) cc_final: 0.8549 (ttp) outliers start: 26 outliers final: 12 residues processed: 277 average time/residue: 0.1326 time to fit residues: 53.5412 Evaluate side-chains 213 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 236 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 ASN C 313 ASN D 313 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098659 restraints weight = 22635.832| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.55 r_work: 0.3068 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15288 Z= 0.147 Angle : 0.599 10.634 20836 Z= 0.322 Chirality : 0.043 0.391 2428 Planarity : 0.004 0.043 2556 Dihedral : 4.702 27.768 2016 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.61 % Favored : 96.01 % Rotamer: Outliers : 1.38 % Allowed : 13.49 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 1.04 (0.19), residues: 1828 helix: 1.80 (0.16), residues: 1044 sheet: 0.93 (0.34), residues: 184 loop : -1.44 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.015 0.002 TYR C 527 PHE 0.014 0.001 PHE A 600 TRP 0.018 0.002 TRP B 293 HIS 0.002 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (15276) covalent geometry : angle 0.57346 / 0.32 (20800) hydrogen bonds : bond 0.04590 / 3.02 ( 937) hydrogen bonds : angle 4.30890 / 3.02 ( 2655) link_NAG-ASN : bond 0.00798 / 0.53 ( 12) link_NAG-ASN : angle 4.18374 / 3.63 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8923 (mtmm) REVERT: A 469 PHE cc_start: 0.7492 (t80) cc_final: 0.7249 (t80) REVERT: A 485 PHE cc_start: 0.8903 (t80) cc_final: 0.8686 (t80) REVERT: A 511 ASP cc_start: 0.8759 (m-30) cc_final: 0.8301 (m-30) REVERT: A 595 LYS cc_start: 0.8835 (tptt) cc_final: 0.8519 (ttmt) REVERT: A 603 MET cc_start: 0.8703 (ttp) cc_final: 0.8457 (ttp) REVERT: A 675 MET cc_start: 0.8832 (tpt) cc_final: 0.8019 (tpt) REVERT: A 688 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7727 (mmmm) REVERT: B 281 LYS cc_start: 0.9169 (mtmt) cc_final: 0.8940 (mtmm) REVERT: B 469 PHE cc_start: 0.7561 (t80) cc_final: 0.7313 (t80) REVERT: B 485 PHE cc_start: 0.8904 (t80) cc_final: 0.8684 (t80) REVERT: B 511 ASP cc_start: 0.8792 (m-30) cc_final: 0.8209 (m-30) REVERT: B 595 LYS cc_start: 0.8825 (tptt) cc_final: 0.8505 (ttmt) REVERT: B 603 MET cc_start: 0.8709 (ttp) cc_final: 0.8455 (ttp) REVERT: B 675 MET cc_start: 0.8843 (tpt) cc_final: 0.7978 (tpt) REVERT: C 281 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8938 (mtmm) REVERT: C 469 PHE cc_start: 0.7592 (t80) cc_final: 0.7379 (t80) REVERT: C 485 PHE cc_start: 0.8908 (t80) cc_final: 0.8691 (t80) REVERT: C 511 ASP cc_start: 0.8760 (m-30) cc_final: 0.8281 (m-30) REVERT: C 595 LYS cc_start: 0.8806 (tptt) cc_final: 0.8505 (ttmt) REVERT: C 603 MET cc_start: 0.8704 (ttp) cc_final: 0.8453 (ttp) REVERT: C 688 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7745 (mmmm) REVERT: D 281 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8942 (mtmm) REVERT: D 469 PHE cc_start: 0.7592 (t80) cc_final: 0.7384 (t80) REVERT: D 511 ASP cc_start: 0.8757 (m-30) cc_final: 0.8296 (m-30) REVERT: D 595 LYS cc_start: 0.8817 (tptt) cc_final: 0.8524 (ttmt) REVERT: D 603 MET cc_start: 0.8689 (ttp) cc_final: 0.8447 (ttp) REVERT: D 688 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7763 (mmmm) outliers start: 21 outliers final: 10 residues processed: 260 average time/residue: 0.1255 time to fit residues: 48.1583 Evaluate side-chains 213 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.095291 restraints weight = 22458.713| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.53 r_work: 0.3018 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15288 Z= 0.171 Angle : 0.596 9.900 20836 Z= 0.322 Chirality : 0.044 0.371 2428 Planarity : 0.004 0.043 2556 Dihedral : 4.592 22.730 2016 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.94 % Favored : 95.84 % Rotamer: Outliers : 1.58 % Allowed : 13.09 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 1.18 (0.20), residues: 1828 helix: 1.94 (0.16), residues: 1032 sheet: 0.69 (0.34), residues: 192 loop : -1.29 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.021 0.002 TYR B 239 PHE 0.017 0.001 PHE B 600 TRP 0.009 0.001 TRP A 414 HIS 0.002 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (15276) covalent geometry : angle 0.57507 / 0.32 (20800) hydrogen bonds : bond 0.04555 / 3.03 ( 937) hydrogen bonds : angle 4.21148 / 2.95 ( 2655) link_NAG-ASN : bond 0.00782 / 0.52 ( 12) link_NAG-ASN : angle 3.84364 / 3.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.9168 (mtmt) cc_final: 0.8962 (mtmm) REVERT: A 469 PHE cc_start: 0.7490 (t80) cc_final: 0.7164 (t80) REVERT: A 511 ASP cc_start: 0.8857 (m-30) cc_final: 0.8339 (m-30) REVERT: A 595 LYS cc_start: 0.8819 (tptt) cc_final: 0.8511 (ttmt) REVERT: A 603 MET cc_start: 0.8650 (ttp) cc_final: 0.8355 (ttp) REVERT: A 688 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7741 (mmmm) REVERT: B 281 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8958 (mtmm) REVERT: B 469 PHE cc_start: 0.7420 (t80) cc_final: 0.7067 (t80) REVERT: B 507 TRP cc_start: 0.8510 (m100) cc_final: 0.8304 (m100) REVERT: B 511 ASP cc_start: 0.8861 (m-30) cc_final: 0.8442 (m-30) REVERT: B 595 LYS cc_start: 0.8831 (tptt) cc_final: 0.8516 (ttmt) REVERT: B 603 MET cc_start: 0.8658 (ttp) cc_final: 0.8370 (ttp) REVERT: C 281 LYS cc_start: 0.9168 (mtmt) cc_final: 0.8962 (mtmm) REVERT: C 469 PHE cc_start: 0.7577 (t80) cc_final: 0.7286 (t80) REVERT: C 511 ASP cc_start: 0.8857 (m-30) cc_final: 0.8339 (m-30) REVERT: C 595 LYS cc_start: 0.8834 (tptt) cc_final: 0.8526 (ttmt) REVERT: C 688 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7753 (mmmm) REVERT: D 281 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8970 (mtmm) REVERT: D 469 PHE cc_start: 0.7585 (t80) cc_final: 0.7298 (t80) REVERT: D 511 ASP cc_start: 0.8866 (m-30) cc_final: 0.8337 (m-30) REVERT: D 595 LYS cc_start: 0.8839 (tptt) cc_final: 0.8525 (ttmt) REVERT: D 603 MET cc_start: 0.8644 (ttp) cc_final: 0.8407 (ttp) REVERT: D 688 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7782 (mmmm) outliers start: 24 outliers final: 15 residues processed: 226 average time/residue: 0.1134 time to fit residues: 38.6943 Evaluate side-chains 214 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 143 optimal weight: 0.0970 chunk 136 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 434 ASN B 434 ASN C 434 ASN D 434 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.096575 restraints weight = 22398.571| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.56 r_work: 0.3038 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15288 Z= 0.140 Angle : 0.563 9.556 20836 Z= 0.302 Chirality : 0.042 0.357 2428 Planarity : 0.003 0.042 2556 Dihedral : 4.403 20.869 2016 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.10 % Favored : 95.68 % Rotamer: Outliers : 1.84 % Allowed : 14.93 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 1.28 (0.20), residues: 1828 helix: 2.02 (0.16), residues: 1028 sheet: 0.74 (0.35), residues: 184 loop : -1.19 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 581 TYR 0.021 0.001 TYR B 486 PHE 0.018 0.001 PHE D 480 TRP 0.008 0.001 TRP B 293 HIS 0.002 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (15276) covalent geometry : angle 0.54220 / 0.30 (20800) hydrogen bonds : bond 0.04165 / 2.76 ( 937) hydrogen bonds : angle 4.12054 / 2.88 ( 2655) link_NAG-ASN : bond 0.00789 / 0.53 ( 12) link_NAG-ASN : angle 3.65224 / 3.18 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 PHE cc_start: 0.7459 (t80) cc_final: 0.7089 (t80) REVERT: A 511 ASP cc_start: 0.8877 (m-30) cc_final: 0.8368 (m-30) REVERT: A 595 LYS cc_start: 0.8809 (tptt) cc_final: 0.8505 (ttmt) REVERT: A 603 MET cc_start: 0.8622 (ttp) cc_final: 0.8411 (ttp) REVERT: A 688 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7723 (mmmm) REVERT: B 469 PHE cc_start: 0.7459 (t80) cc_final: 0.7063 (t80) REVERT: B 507 TRP cc_start: 0.8545 (m100) cc_final: 0.8338 (m100) REVERT: B 511 ASP cc_start: 0.8900 (m-30) cc_final: 0.8436 (m-30) REVERT: B 595 LYS cc_start: 0.8796 (tptt) cc_final: 0.8494 (ttmt) REVERT: B 603 MET cc_start: 0.8642 (ttp) cc_final: 0.8431 (ttp) REVERT: C 469 PHE cc_start: 0.7544 (t80) cc_final: 0.7232 (t80) REVERT: C 511 ASP cc_start: 0.8884 (m-30) cc_final: 0.8381 (m-30) REVERT: C 595 LYS cc_start: 0.8811 (tptt) cc_final: 0.8506 (ttmt) REVERT: C 688 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7729 (mmmm) REVERT: D 469 PHE cc_start: 0.7538 (t80) cc_final: 0.7225 (t80) REVERT: D 511 ASP cc_start: 0.8888 (m-30) cc_final: 0.8376 (m-30) REVERT: D 595 LYS cc_start: 0.8799 (tptt) cc_final: 0.8493 (ttmt) REVERT: D 603 MET cc_start: 0.8668 (ttp) cc_final: 0.8426 (ttp) REVERT: D 675 MET cc_start: 0.8729 (mmm) cc_final: 0.8224 (tpt) REVERT: D 688 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7751 (mmmm) outliers start: 28 outliers final: 16 residues processed: 240 average time/residue: 0.1258 time to fit residues: 44.3046 Evaluate side-chains 218 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 49 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 150 optimal weight: 0.3980 chunk 109 optimal weight: 0.1980 chunk 147 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 681 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099464 restraints weight = 22512.335| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.55 r_work: 0.3070 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15288 Z= 0.119 Angle : 0.527 9.255 20836 Z= 0.285 Chirality : 0.041 0.344 2428 Planarity : 0.003 0.040 2556 Dihedral : 4.250 20.184 2016 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.61 % Favored : 96.17 % Rotamer: Outliers : 1.64 % Allowed : 14.21 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 1.33 (0.20), residues: 1828 helix: 2.05 (0.16), residues: 1032 sheet: 0.67 (0.34), residues: 192 loop : -1.15 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 581 TYR 0.018 0.001 TYR A 486 PHE 0.015 0.001 PHE D 480 TRP 0.007 0.001 TRP B 293 HIS 0.002 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (15276) covalent geometry : angle 0.50775 / 0.28 (20800) hydrogen bonds : bond 0.03798 / 2.53 ( 937) hydrogen bonds : angle 4.11487 / 2.87 ( 2655) link_NAG-ASN : bond 0.00793 / 0.53 ( 12) link_NAG-ASN : angle 3.47312 / 3.03 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 469 PHE cc_start: 0.7454 (t80) cc_final: 0.7057 (t80) REVERT: A 511 ASP cc_start: 0.8862 (m-30) cc_final: 0.8397 (m-30) REVERT: A 595 LYS cc_start: 0.8777 (tptt) cc_final: 0.8511 (ttmt) REVERT: A 597 LEU cc_start: 0.8250 (mt) cc_final: 0.7610 (mt) REVERT: B 306 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.7306 (ptp-170) REVERT: B 469 PHE cc_start: 0.7458 (t80) cc_final: 0.7110 (t80) REVERT: B 511 ASP cc_start: 0.8968 (m-30) cc_final: 0.8445 (m-30) REVERT: B 595 LYS cc_start: 0.8710 (tptt) cc_final: 0.8461 (ttmt) REVERT: B 597 LEU cc_start: 0.8269 (mt) cc_final: 0.7633 (mt) REVERT: B 688 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7703 (mmmm) REVERT: C 469 PHE cc_start: 0.7507 (t80) cc_final: 0.7180 (t80) REVERT: C 511 ASP cc_start: 0.8872 (m-30) cc_final: 0.8400 (m-30) REVERT: C 595 LYS cc_start: 0.8730 (tptt) cc_final: 0.8481 (ttmt) REVERT: C 597 LEU cc_start: 0.8297 (mt) cc_final: 0.7663 (mt) REVERT: C 688 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7678 (mmmm) REVERT: D 469 PHE cc_start: 0.7500 (t80) cc_final: 0.7176 (t80) REVERT: D 511 ASP cc_start: 0.8880 (m-30) cc_final: 0.8408 (m-30) REVERT: D 595 LYS cc_start: 0.8755 (tptt) cc_final: 0.8502 (ttmt) REVERT: D 597 LEU cc_start: 0.8284 (mt) cc_final: 0.7664 (mt) REVERT: D 688 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7704 (mmmm) outliers start: 25 outliers final: 19 residues processed: 232 average time/residue: 0.1168 time to fit residues: 40.8701 Evaluate side-chains 232 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 77 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 681 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.094131 restraints weight = 22352.508| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.51 r_work: 0.3000 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15288 Z= 0.183 Angle : 0.578 9.138 20836 Z= 0.310 Chirality : 0.043 0.338 2428 Planarity : 0.004 0.045 2556 Dihedral : 4.374 19.456 2016 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 2.24 % Allowed : 15.26 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 1.05 (0.20), residues: 1828 helix: 1.82 (0.16), residues: 1036 sheet: 0.31 (0.33), residues: 192 loop : -1.19 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 581 TYR 0.022 0.002 TYR C 239 PHE 0.018 0.001 PHE A 600 TRP 0.009 0.001 TRP B 507 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (15276) covalent geometry : angle 0.56041 / 0.31 (20800) hydrogen bonds : bond 0.04359 / 2.90 ( 937) hydrogen bonds : angle 4.19066 / 2.93 ( 2655) link_NAG-ASN : bond 0.00738 / 0.49 ( 12) link_NAG-ASN : angle 3.42895 / 2.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7532 (t80) REVERT: A 511 ASP cc_start: 0.8797 (m-30) cc_final: 0.8444 (m-30) REVERT: A 595 LYS cc_start: 0.8900 (tptt) cc_final: 0.8578 (ttmt) REVERT: B 245 ASN cc_start: 0.7715 (m-40) cc_final: 0.6876 (p0) REVERT: B 483 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7532 (t80) REVERT: B 511 ASP cc_start: 0.8828 (m-30) cc_final: 0.8425 (m-30) REVERT: B 595 LYS cc_start: 0.8882 (tptt) cc_final: 0.8562 (ttmt) REVERT: B 688 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7737 (mmmm) REVERT: C 469 PHE cc_start: 0.7485 (t80) cc_final: 0.7071 (t80) REVERT: C 483 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7530 (t80) REVERT: C 511 ASP cc_start: 0.8797 (m-30) cc_final: 0.8431 (m-30) REVERT: C 595 LYS cc_start: 0.8815 (tptt) cc_final: 0.8536 (ttmt) REVERT: C 688 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7717 (mmmm) REVERT: D 469 PHE cc_start: 0.7473 (t80) cc_final: 0.7068 (t80) REVERT: D 483 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7562 (t80) REVERT: D 511 ASP cc_start: 0.8816 (m-30) cc_final: 0.8454 (m-30) REVERT: D 595 LYS cc_start: 0.8820 (tptt) cc_final: 0.8507 (ttmt) REVERT: D 688 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7748 (mmmm) outliers start: 34 outliers final: 24 residues processed: 234 average time/residue: 0.1257 time to fit residues: 43.6238 Evaluate side-chains 242 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 411 LYS Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 323 GLN C 323 GLN C 681 ASN D 323 GLN ** D 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094561 restraints weight = 22705.502| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.53 r_work: 0.2998 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15288 Z= 0.166 Angle : 0.560 9.134 20836 Z= 0.301 Chirality : 0.042 0.338 2428 Planarity : 0.004 0.043 2556 Dihedral : 4.344 19.621 2016 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.94 % Favored : 95.84 % Rotamer: Outliers : 2.37 % Allowed : 15.53 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 1.02 (0.20), residues: 1828 helix: 1.82 (0.16), residues: 1032 sheet: 0.20 (0.32), residues: 192 loop : -1.20 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 581 TYR 0.016 0.001 TYR C 486 PHE 0.017 0.001 PHE A 600 TRP 0.008 0.001 TRP B 293 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (15276) covalent geometry : angle 0.54159 / 0.30 (20800) hydrogen bonds : bond 0.04203 / 2.80 ( 937) hydrogen bonds : angle 4.16574 / 2.91 ( 2655) link_NAG-ASN : bond 0.00766 / 0.51 ( 12) link_NAG-ASN : angle 3.43427 / 2.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7605 (t80) REVERT: A 511 ASP cc_start: 0.8862 (m-30) cc_final: 0.8468 (m-30) REVERT: A 583 MET cc_start: 0.8340 (mmm) cc_final: 0.7738 (mmm) REVERT: A 595 LYS cc_start: 0.8921 (tptt) cc_final: 0.8596 (ttmt) REVERT: B 245 ASN cc_start: 0.7709 (m-40) cc_final: 0.6972 (p0) REVERT: B 483 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7564 (t80) REVERT: B 511 ASP cc_start: 0.8874 (m-30) cc_final: 0.8431 (m-30) REVERT: B 595 LYS cc_start: 0.8898 (tptt) cc_final: 0.8577 (ttmt) REVERT: B 688 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7727 (mmmm) REVERT: C 483 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7571 (t80) REVERT: C 511 ASP cc_start: 0.8874 (m-30) cc_final: 0.8484 (m-30) REVERT: C 595 LYS cc_start: 0.8829 (tptt) cc_final: 0.8519 (ttmt) REVERT: C 688 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7717 (mmmm) REVERT: D 483 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7613 (t80) REVERT: D 511 ASP cc_start: 0.8870 (m-30) cc_final: 0.8467 (m-30) REVERT: D 595 LYS cc_start: 0.8832 (tptt) cc_final: 0.8517 (ttmt) REVERT: D 688 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7763 (mmmm) outliers start: 36 outliers final: 26 residues processed: 241 average time/residue: 0.1257 time to fit residues: 45.3183 Evaluate side-chains 244 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 411 LYS Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN C 323 GLN C 681 ASN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096475 restraints weight = 22848.070| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.56 r_work: 0.3028 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15288 Z= 0.132 Angle : 0.544 8.994 20836 Z= 0.292 Chirality : 0.042 0.332 2428 Planarity : 0.003 0.042 2556 Dihedral : 4.245 19.885 2016 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.16 % Favored : 95.62 % Rotamer: Outliers : 2.04 % Allowed : 16.45 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 1.12 (0.20), residues: 1828 helix: 1.85 (0.16), residues: 1044 sheet: 0.32 (0.33), residues: 192 loop : -1.15 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 581 TYR 0.016 0.001 TYR A 486 PHE 0.028 0.001 PHE B 469 TRP 0.009 0.001 TRP B 507 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (15276) covalent geometry : angle 0.52636 / 0.29 (20800) hydrogen bonds : bond 0.03975 / 2.65 ( 937) hydrogen bonds : angle 4.14818 / 2.90 ( 2655) link_NAG-ASN : bond 0.00778 / 0.52 ( 12) link_NAG-ASN : angle 3.36969 / 2.93 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 483 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7606 (t80) REVERT: A 511 ASP cc_start: 0.8844 (m-30) cc_final: 0.8432 (m-30) REVERT: A 595 LYS cc_start: 0.8833 (tptt) cc_final: 0.8502 (ttmt) REVERT: B 245 ASN cc_start: 0.7707 (m-40) cc_final: 0.6930 (p0) REVERT: B 483 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7587 (t80) REVERT: B 511 ASP cc_start: 0.8858 (m-30) cc_final: 0.8402 (m-30) REVERT: B 583 MET cc_start: 0.8098 (mmm) cc_final: 0.7729 (mtm) REVERT: B 595 LYS cc_start: 0.8847 (tptt) cc_final: 0.8530 (ttmt) REVERT: B 688 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7705 (mmmm) REVERT: C 469 PHE cc_start: 0.7468 (t80) cc_final: 0.7160 (t80) REVERT: C 483 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7581 (t80) REVERT: C 511 ASP cc_start: 0.8844 (m-30) cc_final: 0.8435 (m-30) REVERT: C 595 LYS cc_start: 0.8803 (tptt) cc_final: 0.8523 (ttmt) REVERT: C 688 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7685 (mmmm) REVERT: D 469 PHE cc_start: 0.7460 (t80) cc_final: 0.7157 (t80) REVERT: D 483 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7631 (t80) REVERT: D 511 ASP cc_start: 0.8862 (m-30) cc_final: 0.8464 (m-30) REVERT: D 595 LYS cc_start: 0.8823 (tptt) cc_final: 0.8523 (ttmt) REVERT: D 688 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7726 (mmmm) outliers start: 31 outliers final: 18 residues processed: 239 average time/residue: 0.1102 time to fit residues: 39.9226 Evaluate side-chains 237 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093903 restraints weight = 22616.454| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.54 r_work: 0.2994 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15288 Z= 0.165 Angle : 0.563 9.013 20836 Z= 0.303 Chirality : 0.042 0.335 2428 Planarity : 0.004 0.043 2556 Dihedral : 4.304 19.768 2016 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.10 % Favored : 95.68 % Rotamer: Outliers : 1.71 % Allowed : 17.37 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 1.01 (0.20), residues: 1828 helix: 1.75 (0.16), residues: 1036 sheet: 0.24 (0.33), residues: 192 loop : -1.12 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 581 TYR 0.016 0.001 TYR A 486 PHE 0.029 0.001 PHE A 469 TRP 0.007 0.001 TRP B 293 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (15276) covalent geometry : angle 0.54531 / 0.30 (20800) hydrogen bonds : bond 0.04193 / 2.80 ( 937) hydrogen bonds : angle 4.16509 / 2.91 ( 2655) link_NAG-ASN : bond 0.00770 / 0.51 ( 12) link_NAG-ASN : angle 3.37698 / 2.94 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASN cc_start: 0.7720 (m-40) cc_final: 0.6938 (p0) REVERT: A 306 ARG cc_start: 0.7709 (ptp-170) cc_final: 0.7439 (ptp-170) REVERT: A 483 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7642 (t80) REVERT: A 511 ASP cc_start: 0.8860 (m-30) cc_final: 0.8464 (m-30) REVERT: A 581 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7854 (ttt90) REVERT: A 595 LYS cc_start: 0.8938 (tptt) cc_final: 0.8608 (ttmt) REVERT: B 245 ASN cc_start: 0.7707 (m-40) cc_final: 0.6972 (p0) REVERT: B 483 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7635 (t80) REVERT: B 511 ASP cc_start: 0.8866 (m-30) cc_final: 0.8411 (m-30) REVERT: B 583 MET cc_start: 0.8277 (mmm) cc_final: 0.7746 (mmm) REVERT: B 595 LYS cc_start: 0.8936 (tptt) cc_final: 0.8602 (ttmt) REVERT: B 607 ILE cc_start: 0.9081 (mt) cc_final: 0.8873 (mt) REVERT: B 688 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7774 (mmmm) REVERT: C 245 ASN cc_start: 0.7786 (m-40) cc_final: 0.6967 (p0) REVERT: C 306 ARG cc_start: 0.7697 (ptp-170) cc_final: 0.7323 (ptp-170) REVERT: C 483 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7616 (t80) REVERT: C 511 ASP cc_start: 0.8871 (m-30) cc_final: 0.8478 (m-30) REVERT: C 595 LYS cc_start: 0.8899 (tptt) cc_final: 0.8612 (ttmt) REVERT: C 688 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7735 (mmmm) REVERT: D 245 ASN cc_start: 0.7777 (m-40) cc_final: 0.6960 (p0) REVERT: D 306 ARG cc_start: 0.7727 (ptp-170) cc_final: 0.7366 (ptp-170) REVERT: D 511 ASP cc_start: 0.8851 (m-30) cc_final: 0.8437 (m-30) REVERT: D 595 LYS cc_start: 0.8905 (tptt) cc_final: 0.8583 (ttmt) REVERT: D 688 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7744 (mmmm) outliers start: 26 outliers final: 19 residues processed: 238 average time/residue: 0.1146 time to fit residues: 40.9443 Evaluate side-chains 243 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 141 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 21 optimal weight: 0.1980 chunk 79 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 323 GLN C 681 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097071 restraints weight = 22477.597| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.54 r_work: 0.3046 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15288 Z= 0.122 Angle : 0.536 9.088 20836 Z= 0.288 Chirality : 0.041 0.342 2428 Planarity : 0.004 0.041 2556 Dihedral : 4.200 20.227 2016 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.72 % Favored : 96.06 % Rotamer: Outliers : 1.58 % Allowed : 17.37 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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 are not related in a simple way. whole: 0.99 (0.20), residues: 1828 helix: 1.71 (0.16), residues: 1068 sheet: 0.42 (0.34), residues: 192 loop : -1.34 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 581 TYR 0.016 0.001 TYR A 486 PHE 0.027 0.001 PHE D 469 TRP 0.007 0.001 TRP B 507 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (15276) covalent geometry : angle 0.51779 / 0.28 (20800) hydrogen bonds : bond 0.03810 / 2.54 ( 937) hydrogen bonds : angle 4.12747 / 2.88 ( 2655) link_NAG-ASN : bond 0.00809 / 0.54 ( 12) link_NAG-ASN : angle 3.37201 / 2.94 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2958.44 seconds wall clock time: 51 minutes 37.92 seconds (3097.92 seconds total)