Starting phenix.real_space_refine on Sat Sep 12 08:28:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5t4d_8354/09_2026/5t4d_8354.cif Found real_map, /net/cci-nas-00/data/ceres_data/5t4d_8354/09_2026/5t4d_8354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5t4d_8354/09_2026/5t4d_8354.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5t4d_8354/09_2026/5t4d_8354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5t4d_8354/09_2026/5t4d_8354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5t4d_8354/09_2026/5t4d_8354.map" model { file = "/net/cci-nas-00/data/ceres_data/5t4d_8354/09_2026/5t4d_8354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5t4d_8354/09_2026/5t4d_8354.cif" } resolution = 3.0 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= 0.013 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 72 5.16 5 C 9860 2.51 5 N 2360 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14876 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3677 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 10, 'ASP:plan': 11, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 3.72, per 1000 atoms: 0.25 Number of scatterers: 14876 At special positions: 0 Unit cell: (110.62, 110.62, 102.11, 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 72 16.00 O 2584 8.00 N 2360 7.00 C 9860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 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: 1.32 Conformation dependent library (CDL) restraints added in 552.7 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: 72 helices and 12 sheets defined 60.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 216 through 242 removed outlier: 3.541A pdb=" N THR A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER A 330 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS A 331 " --> pdb=" O ASN A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 331' Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 492 removed outlier: 3.569A pdb=" N CYS A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 Processing helix chain 'A' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 579 removed outlier: 4.521A pdb=" N ASN A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 579 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.683A 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 646 through 653 Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.542A pdb=" N THR B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.708A pdb=" N SER B 330 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS B 331 " --> pdb=" O ASN B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 492 removed outlier: 3.569A pdb=" N CYS B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 579 removed outlier: 4.522A pdb=" N ASN B 578 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 619 removed outlier: 3.747A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.683A 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 646 through 653 Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 removed outlier: 3.541A pdb=" N THR C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.769A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER C 330 " --> pdb=" O ARG C 327 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS C 331 " --> pdb=" O ASN C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 327 through 331' Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 492 removed outlier: 3.570A pdb=" N CYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 484 " --> pdb=" O PHE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 528 Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 579 removed outlier: 4.522A pdb=" N ASN C 578 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 579 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 3.682A 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 646 through 653 Processing helix chain 'C' and resid 655 through 670 Processing helix chain 'C' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 removed outlier: 3.542A pdb=" N THR D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS D 331 " --> pdb=" O ASN D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 492 removed outlier: 3.568A pdb=" N CYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 528 Processing helix chain 'D' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 579 removed outlier: 4.521A pdb=" N ASN D 578 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE D 579 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 3.682A 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 646 through 653 Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 672 through 693 removed outlier: 3.660A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.603A 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: 6.694A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.685A 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: 6.693A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.685A 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: 6.694A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.684A 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: 6.694A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.685A 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 380 921 hydrogen bonds defined for protein. 2619 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: 2.52 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4454 1.34 - 1.45: 3166 1.45 - 1.57: 7536 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 15264 Sorted by residual: bond pdb=" CA ALA B 356 " pdb=" C ALA B 356 " ideal model delta sigma weight residual 1.528 1.505 0.022 1.08e-02 8.57e+03 4.21e+00 bond pdb=" CA ALA C 356 " pdb=" C ALA C 356 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.08e-02 8.57e+03 4.10e+00 bond pdb=" CA ALA D 356 " pdb=" C ALA D 356 " ideal model delta sigma weight residual 1.528 1.506 0.021 1.08e-02 8.57e+03 3.93e+00 bond pdb=" CA ALA A 356 " pdb=" C ALA A 356 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.08e-02 8.57e+03 3.61e+00 bond pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.30e-02 5.92e+03 2.73e+00 ... (remaining 15259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 20228 2.20 - 4.40: 484 4.40 - 6.60: 60 6.60 - 8.80: 8 8.80 - 10.99: 4 Bond angle restraints: 20784 Sorted by residual: angle pdb=" N ALA C 303 " pdb=" CA ALA C 303 " pdb=" C ALA C 303 " ideal model delta sigma weight residual 111.28 116.09 -4.81 1.09e+00 8.42e-01 1.95e+01 angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 111.28 116.07 -4.79 1.09e+00 8.42e-01 1.93e+01 angle pdb=" N ALA A 303 " pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 111.28 116.06 -4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N ALA D 303 " pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 111.28 116.06 -4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" C LYS D 294 " pdb=" N MET D 295 " pdb=" CA MET D 295 " ideal model delta sigma weight residual 121.70 128.56 -6.86 1.80e+00 3.09e-01 1.45e+01 ... (remaining 20779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 8368 15.83 - 31.65: 208 31.65 - 47.48: 56 47.48 - 63.30: 0 63.30 - 79.13: 12 Dihedral angle restraints: 8644 sinusoidal: 3160 harmonic: 5484 Sorted by residual: 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 180.00 148.04 31.96 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA ASN D 432 " pdb=" C ASN D 432 " pdb=" N ILE D 433 " pdb=" CA ILE D 433 " ideal model delta harmonic sigma weight residual 180.00 148.04 31.96 0 5.00e+00 4.00e-02 4.09e+01 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 180.00 148.08 31.92 0 5.00e+00 4.00e-02 4.08e+01 ... (remaining 8641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1277 0.034 - 0.068: 799 0.068 - 0.103: 235 0.103 - 0.137: 95 0.137 - 0.171: 22 Chirality restraints: 2428 Sorted by residual: chirality pdb=" CG LEU D 677 " pdb=" CB LEU D 677 " pdb=" CD1 LEU D 677 " pdb=" CD2 LEU D 677 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CG LEU B 677 " pdb=" CB LEU B 677 " pdb=" CD1 LEU B 677 " pdb=" CD2 LEU B 677 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CG LEU A 314 " pdb=" CB LEU A 314 " pdb=" CD1 LEU A 314 " pdb=" CD2 LEU A 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 2425 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 380 " 0.018 2.00e-02 2.50e+03 1.50e-02 5.60e+00 pdb=" CG TRP B 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 380 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 380 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 380 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 380 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 380 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 380 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 380 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 380 " 0.018 2.00e-02 2.50e+03 1.50e-02 5.59e+00 pdb=" CG TRP D 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP D 380 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 380 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 380 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 380 " 0.018 2.00e-02 2.50e+03 1.49e-02 5.52e+00 pdb=" CG TRP A 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 380 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 380 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 380 " 0.002 2.00e-02 2.50e+03 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 279 2.68 - 3.23: 16182 3.23 - 3.79: 24255 3.79 - 4.34: 31807 4.34 - 4.90: 52246 Nonbonded interactions: 124769 Sorted by model distance: nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.121 3.040 nonbonded pdb=" O LEU A 586 " pdb=" OG1 THR A 589 " model vdw 2.216 3.040 ... (remaining 124764 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: 0.05 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.550 Find NCS groups from input model: 0.140 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.051 15280 Z= 0.472 Angle : 0.849 12.891 20828 Z= 0.455 Chirality : 0.049 0.171 2428 Planarity : 0.005 0.052 2552 Dihedral : 8.909 79.127 5080 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.26 % Allowed : 1.58 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -2.69 (0.17), residues: 1828 helix: -2.42 (0.12), residues: 1004 sheet: 0.11 (0.31), residues: 192 loop : -0.88 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 420 TYR 0.026 0.002 TYR D 249 PHE 0.025 0.002 PHE C 310 TRP 0.040 0.005 TRP D 380 HIS 0.005 0.003 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.47 (15264) covalent geometry : angle 0.80865 / 0.45 (20784) SS BOND : bond 0.00477 / 0.24 ( 4) SS BOND : angle 2.20016 / 1.23 ( 8) hydrogen bonds : bond 0.24771 / 16.42 ( 913) hydrogen bonds : angle 8.65854 / 6.18 ( 2619) link_NAG-ASN : bond 0.00892 / 0.58 ( 12) link_NAG-ASN : angle 6.18923 / 5.23 ( 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 363 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 359 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7875 (m-40) cc_final: 0.7657 (m-40) REVERT: A 410 LYS cc_start: 0.8414 (tttm) cc_final: 0.8109 (tttm) REVERT: A 508 ASN cc_start: 0.7052 (m110) cc_final: 0.6776 (m-40) REVERT: B 269 ASN cc_start: 0.7879 (m-40) cc_final: 0.7667 (m-40) REVERT: B 410 LYS cc_start: 0.8414 (tttm) cc_final: 0.8107 (tttm) REVERT: B 508 ASN cc_start: 0.7047 (m110) cc_final: 0.6770 (m-40) REVERT: C 410 LYS cc_start: 0.8429 (tttm) cc_final: 0.8119 (tttp) REVERT: C 508 ASN cc_start: 0.7127 (m110) cc_final: 0.6822 (m-40) REVERT: D 269 ASN cc_start: 0.7871 (m-40) cc_final: 0.7658 (m-40) REVERT: D 410 LYS cc_start: 0.8412 (tttm) cc_final: 0.8107 (tttp) REVERT: D 508 ASN cc_start: 0.7057 (m110) cc_final: 0.6779 (m-40) outliers start: 4 outliers final: 0 residues processed: 359 average time/residue: 0.5414 time to fit residues: 215.4671 Evaluate side-chains 196 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN A 543 ASN A 636 GLN B 458 GLN B 543 ASN B 636 GLN C 458 GLN C 537 GLN C 543 ASN C 636 GLN D 458 GLN D 543 ASN D 636 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108922 restraints weight = 17175.725| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.84 r_work: 0.3002 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15280 Z= 0.151 Angle : 0.611 7.975 20828 Z= 0.332 Chirality : 0.042 0.145 2428 Planarity : 0.005 0.041 2552 Dihedral : 4.956 33.745 2016 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.90 % Allowed : 9.04 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.44 (0.19), residues: 1828 helix: 0.84 (0.15), residues: 1032 sheet: 0.57 (0.34), residues: 184 loop : -0.61 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 338 TYR 0.021 0.002 TYR C 249 PHE 0.015 0.002 PHE A 676 TRP 0.017 0.002 TRP B 293 HIS 0.003 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (15264) covalent geometry : angle 0.59662 / 0.33 (20784) SS BOND : bond 0.00085 / 0.04 ( 4) SS BOND : angle 0.84934 / 0.48 ( 8) hydrogen bonds : bond 0.05132 / 3.37 ( 913) hydrogen bonds : angle 4.89180 / 3.49 ( 2619) link_NAG-ASN : bond 0.00354 / 0.24 ( 12) link_NAG-ASN : angle 3.21054 / 2.72 ( 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 323 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 0.555 Fit side-chains REVERT: A 410 LYS cc_start: 0.8398 (tttm) cc_final: 0.8155 (tttm) REVERT: A 411 LYS cc_start: 0.8663 (tmmt) cc_final: 0.8450 (tttt) REVERT: A 440 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8311 (ttp-170) REVERT: A 478 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8049 (pt) REVERT: A 508 ASN cc_start: 0.7489 (m110) cc_final: 0.7280 (m-40) REVERT: A 528 ARG cc_start: 0.7500 (tpp-160) cc_final: 0.7270 (mmt-90) REVERT: A 590 MET cc_start: 0.6454 (mtp) cc_final: 0.6159 (mtp) REVERT: A 638 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8299 (mtm180) REVERT: A 688 LYS cc_start: 0.7521 (mmtt) cc_final: 0.7027 (tttp) REVERT: A 693 GLN cc_start: 0.7218 (tt0) cc_final: 0.6873 (tp40) REVERT: B 410 LYS cc_start: 0.8395 (tttm) cc_final: 0.8150 (tttm) REVERT: B 411 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8459 (tttt) REVERT: B 440 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8294 (ttp-170) REVERT: B 478 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8060 (pt) REVERT: B 508 ASN cc_start: 0.7501 (m110) cc_final: 0.7299 (m-40) REVERT: B 528 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.7276 (mmt-90) REVERT: B 590 MET cc_start: 0.6469 (mtp) cc_final: 0.6166 (mtp) REVERT: B 638 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8301 (mtm180) REVERT: B 688 LYS cc_start: 0.7510 (mmtt) cc_final: 0.7011 (tttp) REVERT: B 693 GLN cc_start: 0.7225 (tt0) cc_final: 0.6881 (tp40) REVERT: C 410 LYS cc_start: 0.8426 (tttm) cc_final: 0.8180 (tttm) REVERT: C 440 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8291 (ttp-170) REVERT: C 478 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7816 (pt) REVERT: C 508 ASN cc_start: 0.7498 (m110) cc_final: 0.7271 (m-40) REVERT: C 590 MET cc_start: 0.6492 (mtp) cc_final: 0.6188 (mtp) REVERT: C 638 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8385 (mtm180) REVERT: C 688 LYS cc_start: 0.7489 (mmtt) cc_final: 0.6988 (tttp) REVERT: D 410 LYS cc_start: 0.8392 (tttm) cc_final: 0.8146 (tttm) REVERT: D 411 LYS cc_start: 0.8656 (tmmt) cc_final: 0.8444 (tttt) REVERT: D 440 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8287 (ttp-170) REVERT: D 478 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8090 (pt) REVERT: D 528 ARG cc_start: 0.7511 (tpp-160) cc_final: 0.7277 (mmt-90) REVERT: D 590 MET cc_start: 0.6471 (mtp) cc_final: 0.6154 (mtp) REVERT: D 638 ARG cc_start: 0.8592 (mtm-85) cc_final: 0.8354 (mtm180) REVERT: D 688 LYS cc_start: 0.7482 (mmtt) cc_final: 0.6988 (tttp) outliers start: 44 outliers final: 11 residues processed: 315 average time/residue: 0.5450 time to fit residues: 190.8098 Evaluate side-chains 221 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 602 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN A 578 ASN B 323 GLN B 578 ASN C 323 GLN C 578 ASN D 323 GLN D 578 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.104489 restraints weight = 17325.919| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.77 r_work: 0.2987 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15280 Z= 0.137 Angle : 0.564 7.566 20828 Z= 0.298 Chirality : 0.040 0.141 2428 Planarity : 0.004 0.042 2552 Dihedral : 4.667 31.792 2016 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.70 % Allowed : 11.87 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.09 (0.19), residues: 1828 helix: 1.60 (0.16), residues: 1032 sheet: 0.15 (0.33), residues: 192 loop : -0.54 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 528 TYR 0.019 0.002 TYR C 527 PHE 0.013 0.001 PHE D 600 TRP 0.014 0.002 TRP D 293 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (15264) covalent geometry : angle 0.55487 / 0.30 (20784) SS BOND : bond 0.00088 / 0.04 ( 4) SS BOND : angle 0.77684 / 0.44 ( 8) hydrogen bonds : bond 0.04461 / 2.94 ( 913) hydrogen bonds : angle 4.55083 / 3.25 ( 2619) link_NAG-ASN : bond 0.00293 / 0.20 ( 12) link_NAG-ASN : angle 2.43688 / 2.02 ( 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 276 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.577 Fit side-chains REVERT: A 272 THR cc_start: 0.8837 (m) cc_final: 0.8507 (p) REVERT: A 410 LYS cc_start: 0.8439 (tttm) cc_final: 0.8182 (tttp) REVERT: A 411 LYS cc_start: 0.8707 (tmmt) cc_final: 0.8474 (tttt) REVERT: A 440 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8281 (ttp-170) REVERT: A 508 ASN cc_start: 0.7561 (m110) cc_final: 0.7303 (m-40) REVERT: A 528 ARG cc_start: 0.7532 (tpp-160) cc_final: 0.7296 (mmt-90) REVERT: A 590 MET cc_start: 0.7844 (mtp) cc_final: 0.7548 (mtp) REVERT: A 638 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8276 (mtm180) REVERT: A 688 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7195 (tptp) REVERT: A 693 GLN cc_start: 0.7124 (tt0) cc_final: 0.6877 (tp40) REVERT: B 272 THR cc_start: 0.8844 (m) cc_final: 0.8507 (p) REVERT: B 410 LYS cc_start: 0.8426 (tttm) cc_final: 0.8169 (tttp) REVERT: B 411 LYS cc_start: 0.8700 (tmmt) cc_final: 0.8467 (tttt) REVERT: B 440 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8282 (ttp-170) REVERT: B 508 ASN cc_start: 0.7551 (m110) cc_final: 0.7294 (m-40) REVERT: B 528 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7300 (mmt-90) REVERT: B 590 MET cc_start: 0.7841 (mtp) cc_final: 0.7547 (mtp) REVERT: B 638 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.8282 (mtm180) REVERT: B 688 LYS cc_start: 0.7590 (mmtt) cc_final: 0.7191 (tptp) REVERT: B 693 GLN cc_start: 0.7113 (tt0) cc_final: 0.6864 (tp40) REVERT: C 272 THR cc_start: 0.8855 (m) cc_final: 0.8520 (p) REVERT: C 410 LYS cc_start: 0.8448 (tttm) cc_final: 0.8209 (tttm) REVERT: C 440 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8282 (ttp-170) REVERT: C 508 ASN cc_start: 0.7546 (m110) cc_final: 0.7290 (m-40) REVERT: C 590 MET cc_start: 0.7851 (mtp) cc_final: 0.7547 (mtp) REVERT: C 638 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8259 (mtm180) REVERT: D 272 THR cc_start: 0.8841 (m) cc_final: 0.8513 (p) REVERT: D 410 LYS cc_start: 0.8432 (tttm) cc_final: 0.8175 (tttp) REVERT: D 411 LYS cc_start: 0.8706 (tmmt) cc_final: 0.8471 (tttt) REVERT: D 440 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8277 (ttp-170) REVERT: D 528 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.7296 (mmt-90) REVERT: D 590 MET cc_start: 0.7840 (mtp) cc_final: 0.7541 (mtp) REVERT: D 638 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8268 (mtm180) REVERT: D 688 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7206 (tptp) outliers start: 41 outliers final: 14 residues processed: 264 average time/residue: 0.5043 time to fit residues: 149.2809 Evaluate side-chains 222 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 141 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3598 r_free = 0.3598 target = 0.142853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.110003 restraints weight = 17102.969| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.61 r_work: 0.3032 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15280 Z= 0.122 Angle : 0.526 7.924 20828 Z= 0.279 Chirality : 0.039 0.147 2428 Planarity : 0.004 0.039 2552 Dihedral : 4.464 30.047 2016 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.30 % Allowed : 13.85 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.32 (0.20), residues: 1828 helix: 1.85 (0.16), residues: 1024 sheet: 0.12 (0.32), residues: 192 loop : -0.51 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 338 TYR 0.017 0.002 TYR C 527 PHE 0.014 0.001 PHE D 600 TRP 0.011 0.001 TRP C 293 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15264) covalent geometry : angle 0.52053 / 0.28 (20784) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 0.72882 / 0.41 ( 8) hydrogen bonds : bond 0.04030 / 2.66 ( 913) hydrogen bonds : angle 4.39057 / 3.13 ( 2619) link_NAG-ASN : bond 0.00238 / 0.16 ( 12) link_NAG-ASN : angle 1.89190 / 1.53 ( 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 273 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.528 Fit side-chains REVERT: A 272 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8641 (p) REVERT: A 410 LYS cc_start: 0.8526 (tttm) cc_final: 0.8272 (tttm) REVERT: A 440 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8312 (ttp-170) REVERT: A 508 ASN cc_start: 0.7640 (m110) cc_final: 0.7406 (m-40) REVERT: A 585 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: A 638 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8293 (mtm180) REVERT: A 688 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7312 (tptp) REVERT: B 272 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8664 (p) REVERT: B 410 LYS cc_start: 0.8524 (tttm) cc_final: 0.8272 (tttm) REVERT: B 440 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8309 (ttp-170) REVERT: B 508 ASN cc_start: 0.7638 (m110) cc_final: 0.7408 (m-40) REVERT: B 585 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: B 638 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8306 (mtm180) REVERT: B 688 LYS cc_start: 0.7544 (mmtt) cc_final: 0.7319 (tptp) REVERT: C 272 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8679 (p) REVERT: C 410 LYS cc_start: 0.8539 (tttm) cc_final: 0.8246 (tttp) REVERT: C 440 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8304 (ttp-170) REVERT: C 508 ASN cc_start: 0.7644 (m110) cc_final: 0.7384 (m-40) REVERT: C 590 MET cc_start: 0.8051 (mtp) cc_final: 0.7833 (mtp) REVERT: C 638 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8218 (mtm180) REVERT: C 688 LYS cc_start: 0.7400 (mmmt) cc_final: 0.7109 (tptp) REVERT: D 272 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8668 (p) REVERT: D 410 LYS cc_start: 0.8528 (tttm) cc_final: 0.8301 (tttm) REVERT: D 440 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8296 (ttp-170) REVERT: D 585 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: D 638 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8298 (mtm180) REVERT: D 688 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7324 (tptp) outliers start: 50 outliers final: 26 residues processed: 251 average time/residue: 0.4941 time to fit residues: 139.0502 Evaluate side-chains 241 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 585 GLN Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 170 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN B 537 GLN D 537 GLN D 681 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105478 restraints weight = 17122.695| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.62 r_work: 0.2950 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15280 Z= 0.160 Angle : 0.554 8.884 20828 Z= 0.294 Chirality : 0.041 0.192 2428 Planarity : 0.004 0.040 2552 Dihedral : 4.618 26.188 2016 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.69 % Allowed : 13.39 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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 (0.19), residues: 1828 helix: 1.75 (0.16), residues: 1032 sheet: -0.40 (0.31), residues: 200 loop : -0.56 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 528 TYR 0.019 0.002 TYR A 249 PHE 0.017 0.001 PHE D 600 TRP 0.012 0.002 TRP A 293 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15264) covalent geometry : angle 0.54992 / 0.29 (20784) SS BOND : bond 0.00174 / 0.09 ( 4) SS BOND : angle 0.88259 / 0.50 ( 8) hydrogen bonds : bond 0.04309 / 2.84 ( 913) hydrogen bonds : angle 4.42099 / 3.15 ( 2619) link_NAG-ASN : bond 0.00189 / 0.13 ( 12) link_NAG-ASN : angle 1.73416 / 1.36 ( 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 265 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 0.473 Fit side-chains REVERT: A 410 LYS cc_start: 0.8624 (tttm) cc_final: 0.8359 (tttm) REVERT: A 440 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8358 (ttp-170) REVERT: A 508 ASN cc_start: 0.7714 (m110) cc_final: 0.7492 (m-40) REVERT: A 590 MET cc_start: 0.7318 (mtp) cc_final: 0.6956 (mtp) REVERT: A 688 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7366 (tptp) REVERT: B 338 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7298 (tpp80) REVERT: B 410 LYS cc_start: 0.8623 (tttm) cc_final: 0.8356 (tttm) REVERT: B 440 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8349 (ttp-170) REVERT: B 508 ASN cc_start: 0.7719 (m110) cc_final: 0.7472 (m-40) REVERT: B 590 MET cc_start: 0.7333 (mtp) cc_final: 0.6966 (mtp) REVERT: B 688 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7414 (tttp) REVERT: C 338 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7295 (tpp80) REVERT: C 410 LYS cc_start: 0.8640 (tttm) cc_final: 0.8354 (tttm) REVERT: C 440 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8350 (ttp-170) REVERT: C 508 ASN cc_start: 0.7715 (m110) cc_final: 0.7468 (m-40) REVERT: C 638 ARG cc_start: 0.8592 (mtm-85) cc_final: 0.8291 (mtm180) REVERT: C 688 LYS cc_start: 0.7465 (mmmt) cc_final: 0.7177 (tptt) REVERT: D 338 ARG cc_start: 0.7535 (tpp80) cc_final: 0.7272 (tpp80) REVERT: D 410 LYS cc_start: 0.8653 (tttm) cc_final: 0.8342 (tttm) REVERT: D 440 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8343 (ttp-170) REVERT: D 590 MET cc_start: 0.7307 (mtp) cc_final: 0.6946 (mtp) REVERT: D 688 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7406 (tttp) outliers start: 56 outliers final: 30 residues processed: 243 average time/residue: 0.5149 time to fit residues: 139.8477 Evaluate side-chains 233 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 0.9980 chunk 172 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN B 537 GLN D 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.141897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108884 restraints weight = 17096.799| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.60 r_work: 0.3019 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15280 Z= 0.124 Angle : 0.515 8.962 20828 Z= 0.276 Chirality : 0.039 0.162 2428 Planarity : 0.004 0.039 2552 Dihedral : 4.372 24.765 2016 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.90 % Allowed : 14.45 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.34 (0.20), residues: 1828 helix: 1.98 (0.16), residues: 1020 sheet: -0.24 (0.32), residues: 192 loop : -0.57 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 528 TYR 0.016 0.002 TYR B 527 PHE 0.016 0.001 PHE D 600 TRP 0.008 0.001 TRP D 293 HIS 0.001 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15264) covalent geometry : angle 0.51188 / 0.28 (20784) SS BOND : bond 0.00164 / 0.08 ( 4) SS BOND : angle 0.73102 / 0.41 ( 8) hydrogen bonds : bond 0.03935 / 2.59 ( 913) hydrogen bonds : angle 4.28922 / 3.06 ( 2619) link_NAG-ASN : bond 0.00195 / 0.13 ( 12) link_NAG-ASN : angle 1.50301 / 1.18 ( 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 265 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.595 Fit side-chains REVERT: A 410 LYS cc_start: 0.8587 (tttm) cc_final: 0.8327 (tttp) REVERT: A 440 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8308 (ttp-170) REVERT: A 508 ASN cc_start: 0.7723 (m110) cc_final: 0.7493 (m-40) REVERT: A 590 MET cc_start: 0.7731 (mtp) cc_final: 0.7352 (mtp) REVERT: A 688 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7325 (tptp) REVERT: B 410 LYS cc_start: 0.8598 (tttm) cc_final: 0.8337 (tttp) REVERT: B 440 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8307 (ttp-170) REVERT: B 508 ASN cc_start: 0.7732 (m110) cc_final: 0.7503 (m-40) REVERT: B 590 MET cc_start: 0.7748 (mtp) cc_final: 0.7358 (mtp) REVERT: B 688 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7327 (tptp) REVERT: C 410 LYS cc_start: 0.8609 (tttm) cc_final: 0.8329 (tttp) REVERT: C 440 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8313 (ttp-170) REVERT: C 485 PHE cc_start: 0.7877 (t80) cc_final: 0.7642 (t80) REVERT: C 508 ASN cc_start: 0.7686 (m110) cc_final: 0.7446 (m-40) REVERT: C 590 MET cc_start: 0.7345 (mtp) cc_final: 0.6998 (mtp) REVERT: C 638 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8250 (mtm180) REVERT: C 688 LYS cc_start: 0.7416 (mmmt) cc_final: 0.7204 (tptp) REVERT: D 410 LYS cc_start: 0.8611 (tttm) cc_final: 0.8329 (tttm) REVERT: D 440 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8304 (ttp-170) REVERT: D 590 MET cc_start: 0.7730 (mtp) cc_final: 0.7343 (mtp) REVERT: D 688 LYS cc_start: 0.7562 (mmtt) cc_final: 0.7326 (tptp) outliers start: 44 outliers final: 22 residues processed: 249 average time/residue: 0.4958 time to fit residues: 138.7137 Evaluate side-chains 238 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN A 636 GLN A 653 ASN B 537 GLN B 636 GLN B 681 ASN C 537 GLN D 537 GLN D 636 GLN D 653 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108506 restraints weight = 17050.138| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.60 r_work: 0.2979 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15280 Z= 0.133 Angle : 0.531 9.371 20828 Z= 0.284 Chirality : 0.040 0.171 2428 Planarity : 0.004 0.039 2552 Dihedral : 4.364 23.414 2016 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.17 % Allowed : 14.78 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.34 (0.20), residues: 1828 helix: 1.97 (0.16), residues: 1020 sheet: -0.37 (0.31), residues: 200 loop : -0.49 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 528 TYR 0.016 0.002 TYR C 527 PHE 0.017 0.001 PHE B 600 TRP 0.008 0.001 TRP C 293 HIS 0.002 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15264) covalent geometry : angle 0.52798 / 0.28 (20784) SS BOND : bond 0.00160 / 0.08 ( 4) SS BOND : angle 0.80474 / 0.45 ( 8) hydrogen bonds : bond 0.04004 / 2.64 ( 913) hydrogen bonds : angle 4.27672 / 3.04 ( 2619) link_NAG-ASN : bond 0.00178 / 0.12 ( 12) link_NAG-ASN : angle 1.45722 / 1.13 ( 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 270 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.576 Fit side-chains REVERT: A 410 LYS cc_start: 0.8617 (tttm) cc_final: 0.8380 (tttp) REVERT: A 440 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8315 (ttp-170) REVERT: A 508 ASN cc_start: 0.7741 (m110) cc_final: 0.7526 (m-40) REVERT: A 590 MET cc_start: 0.7705 (mtp) cc_final: 0.7458 (mtp) REVERT: A 688 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7380 (tptp) REVERT: B 410 LYS cc_start: 0.8627 (tttm) cc_final: 0.8388 (tttp) REVERT: B 440 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8317 (ttp-170) REVERT: B 508 ASN cc_start: 0.7747 (m110) cc_final: 0.7531 (m-40) REVERT: B 590 MET cc_start: 0.7762 (mtp) cc_final: 0.7496 (mtp) REVERT: B 688 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7372 (tttp) REVERT: C 410 LYS cc_start: 0.8625 (tttm) cc_final: 0.8351 (tttp) REVERT: C 440 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8312 (ttp-170) REVERT: C 485 PHE cc_start: 0.7923 (t80) cc_final: 0.7636 (t80) REVERT: C 508 ASN cc_start: 0.7702 (m110) cc_final: 0.7466 (m-40) REVERT: C 590 MET cc_start: 0.7330 (mtp) cc_final: 0.6959 (mtp) REVERT: C 638 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.8240 (mtm180) REVERT: C 688 LYS cc_start: 0.7400 (mmmt) cc_final: 0.7170 (tptp) REVERT: D 338 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7415 (tpp-160) REVERT: D 410 LYS cc_start: 0.8645 (tttm) cc_final: 0.8367 (tttp) REVERT: D 440 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8321 (ttp-170) REVERT: D 590 MET cc_start: 0.7739 (mtp) cc_final: 0.7480 (mtp) REVERT: D 688 LYS cc_start: 0.7575 (mmtt) cc_final: 0.7324 (tptp) outliers start: 48 outliers final: 32 residues processed: 258 average time/residue: 0.5353 time to fit residues: 153.7661 Evaluate side-chains 242 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN B 537 GLN B 653 ASN C 537 GLN C 645 ASN C 653 ASN D 537 GLN D 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109361 restraints weight = 17252.501| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.62 r_work: 0.3023 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15280 Z= 0.130 Angle : 0.555 9.122 20828 Z= 0.293 Chirality : 0.040 0.169 2428 Planarity : 0.004 0.037 2552 Dihedral : 4.402 22.804 2016 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.17 % Allowed : 15.11 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.46 (0.20), residues: 1828 helix: 2.01 (0.16), residues: 1020 sheet: -0.22 (0.32), residues: 192 loop : -0.37 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 397 TYR 0.016 0.002 TYR C 527 PHE 0.016 0.001 PHE B 600 TRP 0.007 0.001 TRP A 293 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15264) covalent geometry : angle 0.54334 / 0.29 (20784) SS BOND : bond 0.00708 / 0.36 ( 4) SS BOND : angle 4.83556 / 2.71 ( 8) hydrogen bonds : bond 0.03934 / 2.59 ( 913) hydrogen bonds : angle 4.26261 / 3.02 ( 2619) link_NAG-ASN : bond 0.00180 / 0.12 ( 12) link_NAG-ASN : angle 1.51347 / 1.14 ( 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 259 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.508 Fit side-chains REVERT: A 338 ARG cc_start: 0.7425 (tpp80) cc_final: 0.7190 (tpp80) REVERT: A 410 LYS cc_start: 0.8667 (tttm) cc_final: 0.8343 (tttp) REVERT: A 440 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8302 (ttp-170) REVERT: A 485 PHE cc_start: 0.7934 (t80) cc_final: 0.7703 (t80) REVERT: A 508 ASN cc_start: 0.7742 (m110) cc_final: 0.7531 (m-40) REVERT: A 578 ASN cc_start: 0.6882 (m-40) cc_final: 0.6533 (p0) REVERT: A 688 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7337 (tptp) REVERT: B 410 LYS cc_start: 0.8672 (tttm) cc_final: 0.8347 (tttp) REVERT: B 440 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8295 (ttp-170) REVERT: B 485 PHE cc_start: 0.7929 (t80) cc_final: 0.7694 (t80) REVERT: B 508 ASN cc_start: 0.7761 (m110) cc_final: 0.7544 (m-40) REVERT: B 578 ASN cc_start: 0.6877 (m-40) cc_final: 0.6534 (p0) REVERT: B 688 LYS cc_start: 0.7584 (mmtt) cc_final: 0.7336 (tptp) REVERT: C 321 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8978 (tp) REVERT: C 338 ARG cc_start: 0.7535 (tpp80) cc_final: 0.7122 (mmt-90) REVERT: C 410 LYS cc_start: 0.8636 (tttm) cc_final: 0.8365 (tttp) REVERT: C 440 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8308 (ttp-170) REVERT: C 485 PHE cc_start: 0.7969 (t80) cc_final: 0.7689 (t80) REVERT: C 508 ASN cc_start: 0.7716 (m110) cc_final: 0.7492 (m-40) REVERT: C 590 MET cc_start: 0.7281 (mtp) cc_final: 0.6922 (mtp) REVERT: C 636 GLN cc_start: 0.8941 (mt0) cc_final: 0.8657 (mt0) REVERT: C 638 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8247 (mtm180) REVERT: C 688 LYS cc_start: 0.7380 (mmmt) cc_final: 0.7157 (tptp) REVERT: D 410 LYS cc_start: 0.8644 (tttm) cc_final: 0.8358 (tttm) REVERT: D 440 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8304 (ttp-170) REVERT: D 485 PHE cc_start: 0.7924 (t80) cc_final: 0.7693 (t80) REVERT: D 578 ASN cc_start: 0.6896 (m-40) cc_final: 0.6551 (p0) REVERT: D 688 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7337 (tptp) outliers start: 48 outliers final: 33 residues processed: 245 average time/residue: 0.5056 time to fit residues: 138.6629 Evaluate side-chains 240 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 126 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 55 optimal weight: 0.0060 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN A 645 ASN B 537 GLN B 645 ASN C 537 GLN D 537 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110540 restraints weight = 17269.418| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.62 r_work: 0.3043 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15280 Z= 0.120 Angle : 0.535 9.410 20828 Z= 0.284 Chirality : 0.040 0.156 2428 Planarity : 0.004 0.035 2552 Dihedral : 4.290 22.169 2016 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.77 % Allowed : 15.63 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.52 (0.20), residues: 1828 helix: 2.05 (0.16), residues: 1020 sheet: -0.14 (0.33), residues: 192 loop : -0.33 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 397 TYR 0.016 0.001 TYR C 527 PHE 0.016 0.001 PHE D 600 TRP 0.006 0.001 TRP C 293 HIS 0.001 0.000 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (15264) covalent geometry : angle 0.52663 / 0.28 (20784) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 4.09964 / 2.30 ( 8) hydrogen bonds : bond 0.03803 / 2.51 ( 913) hydrogen bonds : angle 4.24326 / 3.00 ( 2619) link_NAG-ASN : bond 0.00187 / 0.13 ( 12) link_NAG-ASN : angle 1.31570 / 1.01 ( 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 269 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.574 Fit side-chains REVERT: A 410 LYS cc_start: 0.8662 (tttm) cc_final: 0.8347 (tttp) REVERT: A 485 PHE cc_start: 0.7970 (t80) cc_final: 0.7743 (t80) REVERT: A 508 ASN cc_start: 0.7729 (m110) cc_final: 0.7514 (m-40) REVERT: A 578 ASN cc_start: 0.6932 (m-40) cc_final: 0.6588 (p0) REVERT: A 688 LYS cc_start: 0.7575 (mmtt) cc_final: 0.7336 (tptp) REVERT: B 338 ARG cc_start: 0.7145 (tpp-160) cc_final: 0.6761 (mpt90) REVERT: B 410 LYS cc_start: 0.8665 (tttm) cc_final: 0.8352 (tttp) REVERT: B 485 PHE cc_start: 0.7972 (t80) cc_final: 0.7732 (t80) REVERT: B 508 ASN cc_start: 0.7707 (m110) cc_final: 0.7490 (m-40) REVERT: B 578 ASN cc_start: 0.6932 (m-40) cc_final: 0.6595 (p0) REVERT: B 688 LYS cc_start: 0.7574 (mmtt) cc_final: 0.7325 (tptp) REVERT: C 410 LYS cc_start: 0.8587 (tttm) cc_final: 0.8315 (tttm) REVERT: C 485 PHE cc_start: 0.7983 (t80) cc_final: 0.7694 (t80) REVERT: C 508 ASN cc_start: 0.7691 (m110) cc_final: 0.7473 (m-40) REVERT: C 578 ASN cc_start: 0.6932 (m-40) cc_final: 0.6601 (p0) REVERT: C 590 MET cc_start: 0.7234 (mtp) cc_final: 0.7025 (mtp) REVERT: C 638 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8246 (mtm180) REVERT: D 410 LYS cc_start: 0.8630 (tttm) cc_final: 0.8346 (tttp) REVERT: D 485 PHE cc_start: 0.7969 (t80) cc_final: 0.7730 (t80) REVERT: D 578 ASN cc_start: 0.6941 (m-40) cc_final: 0.6595 (p0) REVERT: D 688 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7333 (tptp) outliers start: 42 outliers final: 30 residues processed: 256 average time/residue: 0.5037 time to fit residues: 144.6728 Evaluate side-chains 245 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 150 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN A 636 GLN B 537 GLN B 636 GLN C 537 GLN C 636 GLN D 537 GLN D 636 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110242 restraints weight = 17250.406| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.63 r_work: 0.3036 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15280 Z= 0.128 Angle : 0.547 9.506 20828 Z= 0.291 Chirality : 0.040 0.168 2428 Planarity : 0.004 0.035 2552 Dihedral : 4.297 21.974 2016 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.70 % Allowed : 15.70 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.51 (0.20), residues: 1828 helix: 2.03 (0.16), residues: 1020 sheet: -0.14 (0.33), residues: 192 loop : -0.32 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 397 TYR 0.016 0.001 TYR C 527 PHE 0.016 0.001 PHE B 600 TRP 0.008 0.001 TRP C 455 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (15264) covalent geometry : angle 0.53921 / 0.29 (20784) SS BOND : bond 0.00473 / 0.24 ( 4) SS BOND : angle 4.03351 / 2.26 ( 8) hydrogen bonds : bond 0.03909 / 2.58 ( 913) hydrogen bonds : angle 4.27740 / 3.01 ( 2619) link_NAG-ASN : bond 0.00172 / 0.12 ( 12) link_NAG-ASN : angle 1.33681 / 1.03 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.443 Fit side-chains REVERT: A 410 LYS cc_start: 0.8668 (tttm) cc_final: 0.8354 (tttp) REVERT: A 440 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8355 (ttp-170) REVERT: A 485 PHE cc_start: 0.8009 (t80) cc_final: 0.7731 (t80) REVERT: A 508 ASN cc_start: 0.7724 (m110) cc_final: 0.7517 (m-40) REVERT: A 578 ASN cc_start: 0.6890 (m-40) cc_final: 0.6657 (p0) REVERT: A 688 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7397 (tttp) REVERT: B 410 LYS cc_start: 0.8667 (tttm) cc_final: 0.8353 (tttp) REVERT: B 440 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8353 (ttp-170) REVERT: B 485 PHE cc_start: 0.7979 (t80) cc_final: 0.7706 (t80) REVERT: B 578 ASN cc_start: 0.6897 (m-40) cc_final: 0.6671 (p0) REVERT: B 688 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7396 (tttp) REVERT: C 410 LYS cc_start: 0.8624 (tttm) cc_final: 0.8344 (tttp) REVERT: C 440 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8378 (ttp-170) REVERT: C 485 PHE cc_start: 0.8007 (t80) cc_final: 0.7700 (t80) REVERT: C 508 ASN cc_start: 0.7741 (m110) cc_final: 0.7522 (m-40) REVERT: C 578 ASN cc_start: 0.6952 (m-40) cc_final: 0.6620 (p0) REVERT: C 590 MET cc_start: 0.7235 (mtp) cc_final: 0.7007 (mtp) REVERT: C 638 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8270 (mtm180) REVERT: D 410 LYS cc_start: 0.8634 (tttm) cc_final: 0.8352 (tttp) REVERT: D 440 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8362 (ttp-170) REVERT: D 485 PHE cc_start: 0.7977 (t80) cc_final: 0.7703 (t80) REVERT: D 578 ASN cc_start: 0.6901 (m-40) cc_final: 0.6665 (p0) REVERT: D 688 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7411 (tttp) outliers start: 41 outliers final: 32 residues processed: 236 average time/residue: 0.4998 time to fit residues: 131.5050 Evaluate side-chains 241 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN B 537 GLN C 537 GLN D 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111129 restraints weight = 17162.566| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.62 r_work: 0.3044 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15280 Z= 0.124 Angle : 0.543 9.532 20828 Z= 0.290 Chirality : 0.040 0.158 2428 Planarity : 0.004 0.035 2552 Dihedral : 4.268 22.063 2016 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.31 % Allowed : 16.16 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.55 (0.20), residues: 1828 helix: 2.05 (0.16), residues: 1020 sheet: -0.11 (0.33), residues: 192 loop : -0.27 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 397 TYR 0.015 0.001 TYR C 553 PHE 0.016 0.001 PHE B 600 TRP 0.010 0.001 TRP C 455 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15264) covalent geometry : angle 0.53528 / 0.29 (20784) SS BOND : bond 0.00440 / 0.22 ( 4) SS BOND : angle 3.82842 / 2.15 ( 8) hydrogen bonds : bond 0.03865 / 2.56 ( 913) hydrogen bonds : angle 4.27701 / 3.01 ( 2619) link_NAG-ASN : bond 0.00178 / 0.12 ( 12) link_NAG-ASN : angle 1.28625 / 0.99 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4713.43 seconds wall clock time: 81 minutes 10.99 seconds (4870.99 seconds total)