Starting phenix.real_space_refine on Wed Mar 4 16:01:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb8_21586/03_2026/6wb8_21586.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb8_21586/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wb8_21586/03_2026/6wb8_21586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb8_21586/03_2026/6wb8_21586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wb8_21586/03_2026/6wb8_21586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb8_21586/03_2026/6wb8_21586.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 3.28, per 1000 atoms: 0.22 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: 1.44 Conformation dependent library (CDL) restraints added in 558.8 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: 0.49 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: 2.45 Time building geometry restraints manager: 1.88 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: 8640 16.09 - 32.19: 184 32.19 - 48.28: 56 48.28 - 64.37: 0 64.37 - 80.47: 12 Dihedral angle restraints: 8892 sinusoidal: 3408 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 8889 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: 0.670 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.350 Find NCS groups from input model: 0.100 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 8.890 80.467 5340 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 covalent geometry : bond 0.01061 (15276) covalent geometry : angle 0.90504 (20800) hydrogen bonds : bond 0.25586 ( 937) hydrogen bonds : angle 8.52790 ( 2655) link_NAG-ASN : bond 0.00806 ( 12) link_NAG-ASN : angle 7.32915 ( 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 : 0.592 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: 0.1305 time to fit residues: 73.4894 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 : 0.552 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3543 r_free = 0.3543 target = 0.127752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.092517 restraints weight = 22102.516| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.40 r_work: 0.2907 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15288 Z= 0.177 Angle : 0.683 12.163 20836 Z= 0.369 Chirality : 0.047 0.442 2428 Planarity : 0.005 0.047 2556 Dihedral : 5.224 33.034 2268 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.72 % Favored : 96.06 % Rotamer: Outliers : 1.78 % Allowed : 8.36 % Favored : 89.87 % 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: 0.16 (0.18), residues: 1828 helix: 0.84 (0.15), residues: 1040 sheet: 1.11 (0.34), residues: 184 loop : -1.48 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 581 TYR 0.020 0.002 TYR C 527 PHE 0.018 0.002 PHE A 676 TRP 0.019 0.002 TRP C 293 HIS 0.002 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00370 (15276) covalent geometry : angle 0.65239 (20800) hydrogen bonds : bond 0.05481 ( 937) hydrogen bonds : angle 4.70174 ( 2655) link_NAG-ASN : bond 0.00893 ( 12) link_NAG-ASN : angle 4.87103 ( 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 298 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 ASP cc_start: 0.8647 (m-30) cc_final: 0.8215 (m-30) REVERT: A 595 LYS cc_start: 0.8890 (tptt) cc_final: 0.8564 (ttmt) REVERT: A 603 MET cc_start: 0.8755 (ttp) cc_final: 0.8525 (ttp) REVERT: A 675 MET cc_start: 0.8891 (tpt) cc_final: 0.7879 (tpt) REVERT: B 511 ASP cc_start: 0.8693 (m-30) cc_final: 0.8247 (m-30) REVERT: B 595 LYS cc_start: 0.8895 (tptt) cc_final: 0.8571 (ttmt) REVERT: B 603 MET cc_start: 0.8790 (ttp) cc_final: 0.8567 (ttp) REVERT: B 675 MET cc_start: 0.8904 (tpt) cc_final: 0.7845 (tpt) REVERT: C 511 ASP cc_start: 0.8672 (m-30) cc_final: 0.8264 (m-30) REVERT: C 595 LYS cc_start: 0.8882 (tptt) cc_final: 0.8564 (ttmt) REVERT: C 603 MET cc_start: 0.8776 (ttp) cc_final: 0.8549 (ttp) REVERT: D 511 ASP cc_start: 0.8677 (m-30) cc_final: 0.8253 (m-30) REVERT: D 595 LYS cc_start: 0.8886 (tptt) cc_final: 0.8559 (ttmt) REVERT: D 603 MET cc_start: 0.8793 (ttp) cc_final: 0.8550 (ttp) outliers start: 27 outliers final: 12 residues processed: 279 average time/residue: 0.1337 time to fit residues: 53.8960 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 : 0.538 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN B 313 ASN C 313 ASN D 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096773 restraints weight = 22684.158| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.52 r_work: 0.3033 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3679 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= 0.167 Angle : 0.611 10.616 20836 Z= 0.329 Chirality : 0.044 0.399 2428 Planarity : 0.004 0.044 2556 Dihedral : 4.679 28.500 2268 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.88 % Favored : 95.68 % Rotamer: Outliers : 1.38 % Allowed : 13.62 % Favored : 85.00 % 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: 0.98 (0.19), residues: 1828 helix: 1.78 (0.16), residues: 1040 sheet: 0.94 (0.34), residues: 184 loop : -1.51 (0.24), residues: 604 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 0.016 0.001 PHE A 600 TRP 0.015 0.002 TRP A 293 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00362 (15276) covalent geometry : angle 0.58596 (20800) hydrogen bonds : bond 0.04828 ( 937) hydrogen bonds : angle 4.33717 ( 2655) link_NAG-ASN : bond 0.00818 ( 12) link_NAG-ASN : angle 4.20262 ( 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 261 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 PHE cc_start: 0.7565 (t80) cc_final: 0.7355 (t80) REVERT: A 485 PHE cc_start: 0.8911 (t80) cc_final: 0.8697 (t80) REVERT: A 511 ASP cc_start: 0.8766 (m-30) cc_final: 0.8279 (m-30) REVERT: A 595 LYS cc_start: 0.8889 (tptt) cc_final: 0.8581 (ttmt) REVERT: A 688 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7778 (ttmt) REVERT: B 469 PHE cc_start: 0.7618 (t80) cc_final: 0.7406 (t80) REVERT: B 485 PHE cc_start: 0.8920 (t80) cc_final: 0.8687 (t80) REVERT: B 511 ASP cc_start: 0.8785 (m-30) cc_final: 0.8233 (m-30) REVERT: B 572 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8553 (tttp) REVERT: B 595 LYS cc_start: 0.8898 (tptt) cc_final: 0.8585 (ttmt) REVERT: C 469 PHE cc_start: 0.7575 (t80) cc_final: 0.7359 (t80) REVERT: C 485 PHE cc_start: 0.8915 (t80) cc_final: 0.8700 (t80) REVERT: C 511 ASP cc_start: 0.8764 (m-30) cc_final: 0.8558 (m-30) REVERT: C 595 LYS cc_start: 0.8832 (tptt) cc_final: 0.8514 (ttmt) REVERT: C 603 MET cc_start: 0.8744 (ttp) cc_final: 0.8503 (ttp) REVERT: C 688 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7763 (mmmm) REVERT: D 469 PHE cc_start: 0.7578 (t80) cc_final: 0.7365 (t80) REVERT: D 511 ASP cc_start: 0.8753 (m-30) cc_final: 0.8175 (m-30) REVERT: D 595 LYS cc_start: 0.8838 (tptt) cc_final: 0.8522 (ttmt) REVERT: D 603 MET cc_start: 0.8734 (ttp) cc_final: 0.8532 (ttp) outliers start: 21 outliers final: 8 residues processed: 248 average time/residue: 0.1276 time to fit residues: 46.1240 Evaluate side-chains 212 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095026 restraints weight = 22474.720| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.55 r_work: 0.3011 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15288 Z= 0.172 Angle : 0.597 9.789 20836 Z= 0.322 Chirality : 0.044 0.375 2428 Planarity : 0.004 0.043 2556 Dihedral : 4.507 23.311 2268 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.16 % Favored : 95.62 % 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: 1.16 (0.19), residues: 1828 helix: 1.96 (0.16), residues: 1028 sheet: 0.71 (0.35), residues: 192 loop : -1.37 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 581 TYR 0.021 0.002 TYR A 486 PHE 0.017 0.001 PHE B 600 TRP 0.012 0.001 TRP B 293 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00384 (15276) covalent geometry : angle 0.57601 (20800) hydrogen bonds : bond 0.04543 ( 937) hydrogen bonds : angle 4.19789 ( 2655) link_NAG-ASN : bond 0.00774 ( 12) link_NAG-ASN : angle 3.81526 ( 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 247 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 PHE cc_start: 0.7592 (t80) cc_final: 0.7308 (t80) REVERT: A 511 ASP cc_start: 0.8882 (m-30) cc_final: 0.8353 (m-30) REVERT: A 595 LYS cc_start: 0.8830 (tptt) cc_final: 0.8511 (ttmt) REVERT: A 603 MET cc_start: 0.8980 (ttp) cc_final: 0.8711 (ttp) REVERT: A 688 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7733 (mmmm) REVERT: B 469 PHE cc_start: 0.7511 (t80) cc_final: 0.7196 (t80) REVERT: B 507 TRP cc_start: 0.8542 (m100) cc_final: 0.8321 (m100) REVERT: B 511 ASP cc_start: 0.8875 (m-30) cc_final: 0.8430 (m-30) REVERT: B 595 LYS cc_start: 0.8902 (tptt) cc_final: 0.8590 (ttmt) REVERT: C 469 PHE cc_start: 0.7589 (t80) cc_final: 0.7304 (t80) REVERT: C 511 ASP cc_start: 0.8890 (m-30) cc_final: 0.8345 (m-30) REVERT: C 595 LYS cc_start: 0.8884 (tptt) cc_final: 0.8571 (ttmt) REVERT: C 675 MET cc_start: 0.8735 (tpt) cc_final: 0.8458 (tpp) REVERT: C 688 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7788 (mmmm) REVERT: D 469 PHE cc_start: 0.7598 (t80) cc_final: 0.7313 (t80) REVERT: D 511 ASP cc_start: 0.8788 (m-30) cc_final: 0.8454 (m-30) REVERT: D 595 LYS cc_start: 0.8890 (tptt) cc_final: 0.8573 (ttmt) REVERT: D 603 MET cc_start: 0.8650 (ttp) cc_final: 0.8384 (ttp) REVERT: D 688 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7798 (mmmm) outliers start: 21 outliers final: 12 residues processed: 234 average time/residue: 0.1412 time to fit residues: 48.0861 Evaluate side-chains 204 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU 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: 5.9990 chunk 151 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3691 r_free = 0.3691 target = 0.131833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096182 restraints weight = 22345.186| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.53 r_work: 0.3030 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4328 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= 0.138 Angle : 0.558 9.372 20836 Z= 0.300 Chirality : 0.042 0.357 2428 Planarity : 0.004 0.042 2556 Dihedral : 4.267 20.925 2268 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 1.71 % Allowed : 14.61 % Favored : 83.68 % 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: 2.03 (0.16), residues: 1028 sheet: 0.72 (0.34), residues: 184 loop : -1.20 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 581 TYR 0.022 0.001 TYR C 239 PHE 0.019 0.001 PHE D 480 TRP 0.009 0.001 TRP B 293 HIS 0.002 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00292 (15276) covalent geometry : angle 0.53800 (20800) hydrogen bonds : bond 0.04120 ( 937) hydrogen bonds : angle 4.10593 ( 2655) link_NAG-ASN : bond 0.00784 ( 12) link_NAG-ASN : angle 3.57101 ( 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 259 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.7597 (m-40) cc_final: 0.7356 (t0) REVERT: A 469 PHE cc_start: 0.7552 (t80) cc_final: 0.7246 (t80) REVERT: A 511 ASP cc_start: 0.8863 (m-30) cc_final: 0.8354 (m-30) REVERT: A 595 LYS cc_start: 0.8799 (tptt) cc_final: 0.8494 (ttmt) REVERT: A 688 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7688 (mmmm) REVERT: B 362 ASN cc_start: 0.7580 (m-40) cc_final: 0.7349 (t0) REVERT: B 469 PHE cc_start: 0.7540 (t80) cc_final: 0.7219 (t80) REVERT: B 511 ASP cc_start: 0.8906 (m-30) cc_final: 0.8420 (m-30) REVERT: B 595 LYS cc_start: 0.8824 (tptt) cc_final: 0.8530 (ttmt) REVERT: C 362 ASN cc_start: 0.7585 (m-40) cc_final: 0.7353 (t0) REVERT: C 469 PHE cc_start: 0.7582 (t80) cc_final: 0.7246 (t80) REVERT: C 511 ASP cc_start: 0.8858 (m-30) cc_final: 0.8402 (m-30) REVERT: C 595 LYS cc_start: 0.8807 (tptt) cc_final: 0.8502 (ttmt) REVERT: C 688 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7700 (mmmm) REVERT: D 362 ASN cc_start: 0.7623 (m-40) cc_final: 0.7390 (t0) REVERT: D 469 PHE cc_start: 0.7587 (t80) cc_final: 0.7258 (t80) REVERT: D 511 ASP cc_start: 0.8815 (m-30) cc_final: 0.8434 (m-30) REVERT: D 595 LYS cc_start: 0.8806 (tptt) cc_final: 0.8495 (ttmt) REVERT: D 603 MET cc_start: 0.8666 (ttp) cc_final: 0.8380 (ttp) REVERT: D 688 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7716 (mmmm) outliers start: 26 outliers final: 11 residues processed: 254 average time/residue: 0.1286 time to fit residues: 47.7347 Evaluate side-chains 214 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU 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 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU 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: 0.7980 chunk 130 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 681 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.095648 restraints weight = 22449.693| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.53 r_work: 0.3021 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15288 Z= 0.141 Angle : 0.548 9.142 20836 Z= 0.296 Chirality : 0.042 0.346 2428 Planarity : 0.003 0.044 2556 Dihedral : 4.191 19.999 2268 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.50 % Favored : 96.28 % Rotamer: Outliers : 1.38 % Allowed : 15.39 % 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: 1.19 (0.20), residues: 1828 helix: 1.95 (0.16), residues: 1036 sheet: 0.44 (0.33), residues: 192 loop : -1.19 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 581 TYR 0.016 0.001 TYR D 486 PHE 0.016 0.001 PHE C 600 TRP 0.009 0.001 TRP B 507 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00302 (15276) covalent geometry : angle 0.52908 (20800) hydrogen bonds : bond 0.04109 ( 937) hydrogen bonds : angle 4.14716 ( 2655) link_NAG-ASN : bond 0.00759 ( 12) link_NAG-ASN : angle 3.44054 ( 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 238 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.7592 (t0) cc_final: 0.7334 (t0) REVERT: A 469 PHE cc_start: 0.7531 (t80) cc_final: 0.7222 (t80) REVERT: A 511 ASP cc_start: 0.8927 (m-30) cc_final: 0.8453 (m-30) REVERT: A 595 LYS cc_start: 0.8822 (tptt) cc_final: 0.8540 (ttmt) REVERT: A 688 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7744 (mmmm) REVERT: B 362 ASN cc_start: 0.7589 (t0) cc_final: 0.7331 (t0) REVERT: B 469 PHE cc_start: 0.7532 (t80) cc_final: 0.7185 (t80) REVERT: B 511 ASP cc_start: 0.8960 (m-30) cc_final: 0.8409 (m-30) REVERT: B 595 LYS cc_start: 0.8833 (tptt) cc_final: 0.8549 (ttmt) REVERT: C 362 ASN cc_start: 0.7574 (t0) cc_final: 0.7324 (t0) REVERT: C 469 PHE cc_start: 0.7552 (t80) cc_final: 0.7191 (t80) REVERT: C 511 ASP cc_start: 0.8894 (m-30) cc_final: 0.8347 (m-30) REVERT: C 595 LYS cc_start: 0.8815 (tptt) cc_final: 0.8532 (ttmt) REVERT: C 688 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7731 (mmmm) REVERT: D 362 ASN cc_start: 0.7606 (t0) cc_final: 0.7348 (t0) REVERT: D 469 PHE cc_start: 0.7544 (t80) cc_final: 0.7185 (t80) REVERT: D 511 ASP cc_start: 0.8887 (m-30) cc_final: 0.8450 (m-30) REVERT: D 595 LYS cc_start: 0.8824 (tptt) cc_final: 0.8542 (ttmt) REVERT: D 603 MET cc_start: 0.8664 (ttp) cc_final: 0.8446 (ttp) REVERT: D 688 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7734 (mmmm) outliers start: 21 outliers final: 11 residues processed: 233 average time/residue: 0.1264 time to fit residues: 43.3961 Evaluate side-chains 224 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU 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 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU 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: 0.8980 chunk 174 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3641 r_free = 0.3641 target = 0.128137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.092611 restraints weight = 22362.706| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.49 r_work: 0.2969 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4560 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= 0.194 Angle : 0.589 9.043 20836 Z= 0.316 Chirality : 0.043 0.339 2428 Planarity : 0.004 0.044 2556 Dihedral : 4.317 19.643 2268 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.88 % Favored : 95.90 % Rotamer: Outliers : 1.78 % Allowed : 15.92 % Favored : 82.30 % 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: 0.93 (0.20), residues: 1828 helix: 1.76 (0.16), residues: 1036 sheet: 0.07 (0.31), residues: 192 loop : -1.25 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 581 TYR 0.022 0.001 TYR A 239 PHE 0.016 0.001 PHE D 600 TRP 0.011 0.001 TRP B 293 HIS 0.002 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00443 (15276) covalent geometry : angle 0.57181 (20800) hydrogen bonds : bond 0.04490 ( 937) hydrogen bonds : angle 4.19844 ( 2655) link_NAG-ASN : bond 0.00732 ( 12) link_NAG-ASN : angle 3.40607 ( 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 241 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ARG cc_start: 0.7800 (ptp-170) cc_final: 0.7384 (ptp-170) REVERT: A 362 ASN cc_start: 0.7624 (t0) cc_final: 0.7356 (t0) REVERT: A 469 PHE cc_start: 0.7528 (t80) cc_final: 0.7125 (t80) REVERT: A 483 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7514 (t80) REVERT: A 511 ASP cc_start: 0.8979 (m-30) cc_final: 0.8495 (m-30) REVERT: A 595 LYS cc_start: 0.8928 (tptt) cc_final: 0.8595 (ttmt) REVERT: A 688 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7739 (mmmm) REVERT: B 245 ASN cc_start: 0.7671 (m-40) cc_final: 0.6880 (p0) REVERT: B 362 ASN cc_start: 0.7606 (t0) cc_final: 0.7347 (t0) REVERT: B 469 PHE cc_start: 0.7523 (t80) cc_final: 0.7142 (t80) REVERT: B 483 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7535 (t80) REVERT: B 511 ASP cc_start: 0.8975 (m-30) cc_final: 0.8483 (m-30) REVERT: B 595 LYS cc_start: 0.8917 (tptt) cc_final: 0.8581 (ttmt) REVERT: C 306 ARG cc_start: 0.7802 (ptp-170) cc_final: 0.7389 (ptp-170) REVERT: C 362 ASN cc_start: 0.7608 (t0) cc_final: 0.7349 (t0) REVERT: C 483 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7496 (t80) REVERT: C 511 ASP cc_start: 0.8981 (m-30) cc_final: 0.8484 (m-30) REVERT: C 590 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8291 (mmp) REVERT: C 595 LYS cc_start: 0.8915 (tptt) cc_final: 0.8581 (ttmt) REVERT: C 688 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7724 (mmmm) REVERT: D 306 ARG cc_start: 0.7796 (ptp-170) cc_final: 0.7384 (ptp-170) REVERT: D 362 ASN cc_start: 0.7610 (t0) cc_final: 0.7353 (t0) REVERT: D 483 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7420 (t80) REVERT: D 511 ASP cc_start: 0.8908 (m-30) cc_final: 0.8396 (m-30) REVERT: D 590 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8250 (mmp) REVERT: D 595 LYS cc_start: 0.8923 (tptt) cc_final: 0.8585 (ttmt) REVERT: D 603 MET cc_start: 0.8729 (ttp) cc_final: 0.8459 (ttp) REVERT: D 688 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7717 (mmmm) outliers start: 27 outliers final: 14 residues processed: 229 average time/residue: 0.1310 time to fit residues: 44.0288 Evaluate side-chains 226 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 483 PHE 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 483 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU 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 C residue 590 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 483 PHE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 590 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 0.0370 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.130300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095101 restraints weight = 22591.110| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.54 r_work: 0.3011 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4716 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= 0.133 Angle : 0.535 8.963 20836 Z= 0.289 Chirality : 0.042 0.338 2428 Planarity : 0.003 0.041 2556 Dihedral : 4.118 20.094 2268 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.67 % Favored : 96.12 % Rotamer: Outliers : 1.25 % Allowed : 17.30 % Favored : 81.45 % 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: 1.13 (0.20), residues: 1828 helix: 1.87 (0.16), residues: 1048 sheet: 0.18 (0.32), residues: 192 loop : -1.11 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 581 TYR 0.024 0.001 TYR B 239 PHE 0.013 0.001 PHE A 676 TRP 0.008 0.001 TRP B 293 HIS 0.001 0.000 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00278 (15276) covalent geometry : angle 0.51744 (20800) hydrogen bonds : bond 0.04019 ( 937) hydrogen bonds : angle 4.13068 ( 2655) link_NAG-ASN : bond 0.00780 ( 12) link_NAG-ASN : angle 3.35190 ( 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 242 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.7616 (t0) cc_final: 0.7355 (t0) REVERT: A 469 PHE cc_start: 0.7523 (t80) cc_final: 0.7140 (t80) REVERT: A 483 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7569 (t80) REVERT: A 511 ASP cc_start: 0.8938 (m-30) cc_final: 0.8500 (m-30) REVERT: A 583 MET cc_start: 0.8274 (mmm) cc_final: 0.7647 (mmm) REVERT: A 595 LYS cc_start: 0.8862 (tptt) cc_final: 0.8564 (ttmt) REVERT: B 245 ASN cc_start: 0.7637 (m-40) cc_final: 0.6870 (p0) REVERT: B 306 ARG cc_start: 0.7972 (ptp-170) cc_final: 0.7437 (mtp-110) REVERT: B 362 ASN cc_start: 0.7598 (t0) cc_final: 0.7343 (t0) REVERT: B 469 PHE cc_start: 0.7540 (t80) cc_final: 0.7149 (t80) REVERT: B 483 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7592 (t80) REVERT: B 511 ASP cc_start: 0.8828 (m-30) cc_final: 0.8517 (m-30) REVERT: B 595 LYS cc_start: 0.8854 (tptt) cc_final: 0.8553 (ttmt) REVERT: C 362 ASN cc_start: 0.7604 (t0) cc_final: 0.7345 (t0) REVERT: C 469 PHE cc_start: 0.7487 (t80) cc_final: 0.7058 (t80) REVERT: C 483 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7569 (t80) REVERT: C 511 ASP cc_start: 0.8954 (m-30) cc_final: 0.8400 (m-30) REVERT: C 595 LYS cc_start: 0.8846 (tptt) cc_final: 0.8545 (ttmt) REVERT: C 688 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7748 (mmmm) REVERT: D 362 ASN cc_start: 0.7608 (t0) cc_final: 0.7352 (t0) REVERT: D 469 PHE cc_start: 0.7471 (t80) cc_final: 0.7147 (t80) REVERT: D 483 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7576 (t80) REVERT: D 511 ASP cc_start: 0.8913 (m-30) cc_final: 0.8392 (m-30) REVERT: D 595 LYS cc_start: 0.8840 (tptt) cc_final: 0.8520 (ttmt) REVERT: D 603 MET cc_start: 0.8708 (ttp) cc_final: 0.8469 (ttp) REVERT: D 688 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7744 (mmmm) outliers start: 19 outliers final: 10 residues processed: 234 average time/residue: 0.1287 time to fit residues: 44.8960 Evaluate side-chains 234 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 483 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU 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 483 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU 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: 0.9990 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095862 restraints weight = 22796.945| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.55 r_work: 0.3023 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.003 0.023 15288 Z= 0.128 Angle : 0.531 8.960 20836 Z= 0.285 Chirality : 0.041 0.335 2428 Planarity : 0.003 0.042 2556 Dihedral : 4.028 19.991 2268 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.94 % Favored : 95.84 % Rotamer: Outliers : 1.05 % Allowed : 17.76 % Favored : 81.18 % 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: 1.22 (0.20), residues: 1828 helix: 1.94 (0.16), residues: 1044 sheet: 0.33 (0.33), residues: 192 loop : -1.10 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 581 TYR 0.016 0.001 TYR D 486 PHE 0.015 0.001 PHE A 676 TRP 0.007 0.001 TRP B 293 HIS 0.001 0.000 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00265 (15276) covalent geometry : angle 0.51311 (20800) hydrogen bonds : bond 0.03920 ( 937) hydrogen bonds : angle 4.09263 ( 2655) link_NAG-ASN : bond 0.00778 ( 12) link_NAG-ASN : angle 3.32777 ( 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 246 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ARG cc_start: 0.7664 (ptp-170) cc_final: 0.7265 (ptp-170) REVERT: A 362 ASN cc_start: 0.7637 (t0) cc_final: 0.7385 (t0) REVERT: A 483 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7620 (t80) REVERT: A 511 ASP cc_start: 0.8952 (m-30) cc_final: 0.8434 (m-30) REVERT: A 595 LYS cc_start: 0.8838 (tptt) cc_final: 0.8550 (ttmt) REVERT: A 597 LEU cc_start: 0.8458 (mt) cc_final: 0.7768 (mt) REVERT: B 245 ASN cc_start: 0.7721 (m-40) cc_final: 0.6900 (p0) REVERT: B 362 ASN cc_start: 0.7603 (t0) cc_final: 0.7361 (t0) REVERT: B 469 PHE cc_start: 0.7523 (t80) cc_final: 0.7112 (t80) REVERT: B 483 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7650 (t80) REVERT: B 511 ASP cc_start: 0.8817 (m-30) cc_final: 0.8524 (m-30) REVERT: B 595 LYS cc_start: 0.8839 (tptt) cc_final: 0.8544 (ttmt) REVERT: B 597 LEU cc_start: 0.8457 (mt) cc_final: 0.7761 (mt) REVERT: C 306 ARG cc_start: 0.7696 (ptp-170) cc_final: 0.7301 (ptp-170) REVERT: C 362 ASN cc_start: 0.7637 (t0) cc_final: 0.7389 (t0) REVERT: C 483 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7608 (t80) REVERT: C 511 ASP cc_start: 0.8944 (m-30) cc_final: 0.8404 (m-30) REVERT: C 595 LYS cc_start: 0.8822 (tptt) cc_final: 0.8533 (ttmt) REVERT: C 597 LEU cc_start: 0.8480 (mt) cc_final: 0.7761 (mt) REVERT: C 668 MET cc_start: 0.9041 (tpp) cc_final: 0.8698 (mmp) REVERT: C 688 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7738 (mmmm) REVERT: D 306 ARG cc_start: 0.7683 (ptp-170) cc_final: 0.7296 (ptp-170) REVERT: D 362 ASN cc_start: 0.7635 (t0) cc_final: 0.7387 (t0) REVERT: D 483 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7672 (t80) REVERT: D 511 ASP cc_start: 0.8888 (m-30) cc_final: 0.8365 (m-30) REVERT: D 595 LYS cc_start: 0.8838 (tptt) cc_final: 0.8542 (ttmt) REVERT: D 597 LEU cc_start: 0.8409 (mt) cc_final: 0.7736 (mt) REVERT: D 603 MET cc_start: 0.8642 (ttp) cc_final: 0.8423 (ttp) REVERT: D 668 MET cc_start: 0.9039 (tpp) cc_final: 0.8698 (mmp) REVERT: D 688 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7721 (mmmm) outliers start: 16 outliers final: 9 residues processed: 239 average time/residue: 0.1175 time to fit residues: 41.7085 Evaluate side-chains 234 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 483 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU 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 483 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU 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: 0.6980 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094982 restraints weight = 22647.906| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.53 r_work: 0.3015 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15288 Z= 0.143 Angle : 0.550 8.904 20836 Z= 0.294 Chirality : 0.042 0.331 2428 Planarity : 0.004 0.041 2556 Dihedral : 4.063 19.927 2268 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.10 % Favored : 95.68 % Rotamer: Outliers : 1.18 % Allowed : 18.75 % Favored : 80.07 % 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: 1.16 (0.20), residues: 1828 helix: 1.87 (0.16), residues: 1048 sheet: 0.21 (0.34), residues: 192 loop : -1.07 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 581 TYR 0.016 0.001 TYR B 486 PHE 0.029 0.001 PHE D 469 TRP 0.008 0.001 TRP B 293 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00312 (15276) covalent geometry : angle 0.53270 (20800) hydrogen bonds : bond 0.03999 ( 937) hydrogen bonds : angle 4.14358 ( 2655) link_NAG-ASN : bond 0.00764 ( 12) link_NAG-ASN : angle 3.30171 ( 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 236 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASN cc_start: 0.7808 (m-40) cc_final: 0.6978 (p0) REVERT: A 306 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.7228 (ptp-170) REVERT: A 362 ASN cc_start: 0.7657 (t0) cc_final: 0.7416 (t0) REVERT: A 469 PHE cc_start: 0.7464 (t80) cc_final: 0.7109 (t80) REVERT: A 483 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7637 (t80) REVERT: A 511 ASP cc_start: 0.8951 (m-30) cc_final: 0.8424 (m-30) REVERT: A 581 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7816 (ttt90) REVERT: A 595 LYS cc_start: 0.8835 (tptt) cc_final: 0.8556 (ttmt) REVERT: B 245 ASN cc_start: 0.7717 (m-40) cc_final: 0.6902 (p0) REVERT: B 362 ASN cc_start: 0.7619 (t0) cc_final: 0.7382 (t0) REVERT: B 483 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7648 (t80) REVERT: B 511 ASP cc_start: 0.8814 (m-30) cc_final: 0.8515 (m-30) REVERT: B 595 LYS cc_start: 0.8838 (tptt) cc_final: 0.8542 (ttmt) REVERT: C 306 ARG cc_start: 0.7657 (ptp-170) cc_final: 0.7135 (ptp-170) REVERT: C 362 ASN cc_start: 0.7653 (t0) cc_final: 0.7412 (t0) REVERT: C 483 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7626 (t80) REVERT: C 511 ASP cc_start: 0.8964 (m-30) cc_final: 0.8431 (m-30) REVERT: C 581 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7825 (ttt90) REVERT: C 595 LYS cc_start: 0.8838 (tptt) cc_final: 0.8543 (ttmt) REVERT: C 688 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7728 (mmmm) REVERT: D 306 ARG cc_start: 0.7656 (ptp-170) cc_final: 0.7134 (ptp-170) REVERT: D 362 ASN cc_start: 0.7650 (t0) cc_final: 0.7411 (t0) REVERT: D 483 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7692 (t80) REVERT: D 511 ASP cc_start: 0.8880 (m-30) cc_final: 0.8358 (m-30) REVERT: D 581 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7826 (ttt90) REVERT: D 595 LYS cc_start: 0.8854 (tptt) cc_final: 0.8545 (ttmt) REVERT: D 597 LEU cc_start: 0.8435 (mt) cc_final: 0.7769 (mt) REVERT: D 603 MET cc_start: 0.8715 (ttp) cc_final: 0.8463 (ttp) REVERT: D 668 MET cc_start: 0.9048 (tpp) cc_final: 0.8713 (mmp) REVERT: D 688 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7716 (mmmm) outliers start: 18 outliers final: 8 residues processed: 230 average time/residue: 0.1213 time to fit residues: 41.5768 Evaluate side-chains 227 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU 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 483 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU 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 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 141 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096435 restraints weight = 22578.221| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.52 r_work: 0.3039 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15288 Z= 0.129 Angle : 0.541 8.880 20836 Z= 0.290 Chirality : 0.041 0.329 2428 Planarity : 0.004 0.041 2556 Dihedral : 3.988 20.112 2268 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.16 % Favored : 95.62 % Rotamer: Outliers : 0.92 % Allowed : 18.95 % Favored : 80.13 % 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: 1.21 (0.20), residues: 1828 helix: 1.90 (0.16), residues: 1048 sheet: 0.23 (0.34), residues: 192 loop : -1.03 (0.26), residues: 588 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 0.017 0.001 PHE A 676 TRP 0.010 0.001 TRP C 293 HIS 0.001 0.000 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00272 (15276) covalent geometry : angle 0.52443 (20800) hydrogen bonds : bond 0.03868 ( 937) hydrogen bonds : angle 4.11715 ( 2655) link_NAG-ASN : bond 0.00784 ( 12) link_NAG-ASN : angle 3.28012 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2879.95 seconds wall clock time: 50 minutes 15.07 seconds (3015.07 seconds total)