Starting phenix.real_space_refine on Tue Nov 18 14:17:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5t4d_8354/11_2025/5t4d_8354.cif Found real_map, /net/cci-nas-00/data/ceres_data/5t4d_8354/11_2025/5t4d_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 { model { file = "/net/cci-nas-00/data/ceres_data/5t4d_8354/11_2025/5t4d_8354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5t4d_8354/11_2025/5t4d_8354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5t4d_8354/11_2025/5t4d_8354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5t4d_8354/11_2025/5t4d_8354.map" } 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-2.0-5881/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 3.22, per 1000 atoms: 0.22 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: 1.30 Conformation dependent library (CDL) restraints added in 538.0 milliseconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 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: 0.44 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: 2.28 Time building geometry restraints manager: 1.77 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: 8572 15.83 - 31.65: 224 31.65 - 47.48: 72 47.48 - 63.30: 16 63.30 - 79.13: 12 Dihedral angle restraints: 8896 sinusoidal: 3412 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 8893 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.730 Find NCS groups from input model: 0.120 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:8.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 9.476 79.127 5332 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 covalent geometry : bond 0.01047 (15264) covalent geometry : angle 0.80865 (20784) SS BOND : bond 0.00477 ( 4) SS BOND : angle 2.20016 ( 8) hydrogen bonds : bond 0.24771 ( 913) hydrogen bonds : angle 8.65854 ( 2619) link_NAG-ASN : bond 0.00892 ( 12) link_NAG-ASN : angle 6.18923 ( 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 : 0.547 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: 0.7048 (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: 0.7056 (m110) cc_final: 0.6778 (m-40) outliers start: 4 outliers final: 0 residues processed: 359 average time/residue: 0.5600 time to fit residues: 221.8998 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 : 0.539 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3615 r_free = 0.3615 target = 0.144033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109138 restraints weight = 17127.200| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.84 r_work: 0.2997 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15280 Z= 0.152 Angle : 0.620 8.170 20828 Z= 0.334 Chirality : 0.042 0.141 2428 Planarity : 0.004 0.041 2552 Dihedral : 5.798 42.520 2268 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.64 % Allowed : 9.37 % Favored : 87.99 % 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: 0.38 (0.18), residues: 1828 helix: 0.79 (0.15), residues: 1032 sheet: 0.49 (0.34), residues: 184 loop : -0.61 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 338 TYR 0.021 0.002 TYR C 249 PHE 0.014 0.001 PHE D 676 TRP 0.017 0.002 TRP A 293 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00318 (15264) covalent geometry : angle 0.60350 (20784) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.86141 ( 8) hydrogen bonds : bond 0.05553 ( 913) hydrogen bonds : angle 4.96656 ( 2619) link_NAG-ASN : bond 0.00381 ( 12) link_NAG-ASN : angle 3.46144 ( 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 302 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.553 Fit side-chains REVERT: A 410 LYS cc_start: 0.8420 (tttm) cc_final: 0.8172 (tttp) REVERT: A 411 LYS cc_start: 0.8679 (tmmt) cc_final: 0.8474 (tttt) REVERT: A 440 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8315 (ttp-170) REVERT: A 478 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8138 (pt) REVERT: A 528 ARG cc_start: 0.7493 (tpp-160) cc_final: 0.7277 (mmt-90) REVERT: A 590 MET cc_start: 0.6524 (mtp) cc_final: 0.6213 (mtp) REVERT: A 638 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8375 (mtm180) REVERT: B 410 LYS cc_start: 0.8418 (tttm) cc_final: 0.8167 (tttp) REVERT: B 411 LYS cc_start: 0.8682 (tmmt) cc_final: 0.8479 (tttt) REVERT: B 440 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8311 (ttp-170) REVERT: B 478 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8139 (pt) REVERT: B 528 ARG cc_start: 0.7493 (tpp-160) cc_final: 0.7276 (mmt-90) REVERT: B 590 MET cc_start: 0.6690 (mtp) cc_final: 0.6361 (mtp) REVERT: B 638 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8373 (mtm180) REVERT: C 410 LYS cc_start: 0.8421 (tttm) cc_final: 0.8160 (tttp) REVERT: C 440 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8303 (ttp-170) REVERT: C 478 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8059 (pt) REVERT: C 590 MET cc_start: 0.6715 (mtp) cc_final: 0.6380 (mtp) REVERT: C 638 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8392 (mtm180) REVERT: D 410 LYS cc_start: 0.8419 (tttm) cc_final: 0.8166 (tttp) REVERT: D 411 LYS cc_start: 0.8674 (tmmt) cc_final: 0.8461 (tttt) REVERT: D 440 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8313 (ttp-170) REVERT: D 478 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8140 (pt) REVERT: D 528 ARG cc_start: 0.7480 (tpp-160) cc_final: 0.7263 (mmt-90) REVERT: D 590 MET cc_start: 0.6536 (mtp) cc_final: 0.6216 (mtp) REVERT: D 638 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8386 (mtm180) outliers start: 40 outliers final: 7 residues processed: 294 average time/residue: 0.5444 time to fit residues: 177.1150 Evaluate side-chains 222 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 440 ARG Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 602 ILE 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: 2.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109111 restraints weight = 17153.567| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.63 r_work: 0.3010 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3256 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= 0.139 Angle : 0.564 7.625 20828 Z= 0.300 Chirality : 0.041 0.144 2428 Planarity : 0.004 0.042 2552 Dihedral : 4.791 31.945 2268 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.23 % Allowed : 12.07 % Favored : 84.70 % 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: 1.08 (0.19), residues: 1828 helix: 1.58 (0.16), residues: 1036 sheet: 0.06 (0.33), residues: 192 loop : -0.51 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 338 TYR 0.019 0.002 TYR C 249 PHE 0.030 0.001 PHE A 480 TRP 0.015 0.002 TRP B 293 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00301 (15264) covalent geometry : angle 0.55472 (20784) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.77421 ( 8) hydrogen bonds : bond 0.04498 ( 913) hydrogen bonds : angle 4.56643 ( 2619) link_NAG-ASN : bond 0.00271 ( 12) link_NAG-ASN : angle 2.54267 ( 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 301 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.550 Fit side-chains REVERT: A 272 THR cc_start: 0.8842 (m) cc_final: 0.8537 (p) REVERT: A 410 LYS cc_start: 0.8512 (tttm) cc_final: 0.8263 (tttm) REVERT: A 440 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8320 (ttp-170) REVERT: A 528 ARG cc_start: 0.7541 (tpp-160) cc_final: 0.7225 (mmt-90) REVERT: A 638 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.8323 (mtm180) REVERT: A 688 LYS cc_start: 0.7624 (mptp) cc_final: 0.7014 (tptp) REVERT: A 693 GLN cc_start: 0.7022 (tt0) cc_final: 0.6787 (tp40) REVERT: B 272 THR cc_start: 0.8850 (m) cc_final: 0.8536 (p) REVERT: B 410 LYS cc_start: 0.8504 (tttm) cc_final: 0.8251 (tttm) REVERT: B 440 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8312 (ttp-170) REVERT: B 528 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.7226 (mmt-90) REVERT: B 638 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8333 (mtm180) REVERT: B 688 LYS cc_start: 0.7618 (mptp) cc_final: 0.7015 (tptp) REVERT: B 693 GLN cc_start: 0.7013 (tt0) cc_final: 0.6779 (tp40) REVERT: C 272 THR cc_start: 0.8847 (m) cc_final: 0.8554 (p) REVERT: C 410 LYS cc_start: 0.8493 (tttm) cc_final: 0.8251 (tttm) REVERT: C 440 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8316 (ttp-170) REVERT: C 638 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8317 (mtm180) REVERT: C 688 LYS cc_start: 0.7644 (mptp) cc_final: 0.7037 (tptp) REVERT: D 272 THR cc_start: 0.8843 (m) cc_final: 0.8540 (p) REVERT: D 410 LYS cc_start: 0.8516 (tttm) cc_final: 0.8265 (tttm) REVERT: D 440 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8318 (ttp-170) REVERT: D 528 ARG cc_start: 0.7547 (tpp-160) cc_final: 0.7232 (mmt-90) REVERT: D 638 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8326 (mtm180) REVERT: D 688 LYS cc_start: 0.7624 (mptp) cc_final: 0.7013 (tptp) outliers start: 49 outliers final: 13 residues processed: 287 average time/residue: 0.5255 time to fit residues: 167.6605 Evaluate side-chains 224 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN C 313 ASN D 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101952 restraints weight = 17264.635| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.73 r_work: 0.2946 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3592 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= 0.145 Angle : 0.548 7.933 20828 Z= 0.291 Chirality : 0.040 0.155 2428 Planarity : 0.004 0.040 2552 Dihedral : 4.539 30.200 2268 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.63 % Allowed : 13.65 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.14 (0.19), residues: 1828 helix: 1.73 (0.16), residues: 1036 sheet: -0.15 (0.31), residues: 192 loop : -0.62 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 338 TYR 0.018 0.002 TYR D 249 PHE 0.020 0.001 PHE B 480 TRP 0.012 0.001 TRP D 293 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00323 (15264) covalent geometry : angle 0.54152 (20784) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.88516 ( 8) hydrogen bonds : bond 0.04271 ( 913) hydrogen bonds : angle 4.45626 ( 2619) link_NAG-ASN : bond 0.00258 ( 12) link_NAG-ASN : angle 2.02864 ( 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 283 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.940 Fit side-chains REVERT: A 272 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 410 LYS cc_start: 0.8485 (tttm) cc_final: 0.8209 (tttp) REVERT: A 440 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8291 (ttp-170) REVERT: A 590 MET cc_start: 0.7836 (mtp) cc_final: 0.7601 (mtp) REVERT: A 638 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8234 (mtm180) REVERT: A 688 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6880 (tptp) REVERT: B 272 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 410 LYS cc_start: 0.8473 (tttm) cc_final: 0.8199 (tttp) REVERT: B 440 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8280 (ttp-170) REVERT: B 590 MET cc_start: 0.7857 (mtp) cc_final: 0.7623 (mtp) REVERT: B 638 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8240 (mtm180) REVERT: B 688 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6893 (tptp) REVERT: C 272 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8603 (p) REVERT: C 338 ARG cc_start: 0.7400 (tpp80) cc_final: 0.7168 (tpp80) REVERT: C 410 LYS cc_start: 0.8514 (tttm) cc_final: 0.8212 (tttp) REVERT: C 440 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8267 (ttp-170) REVERT: C 590 MET cc_start: 0.7550 (mtp) cc_final: 0.7178 (mtp) REVERT: C 595 LYS cc_start: 0.8694 (tptt) cc_final: 0.8446 (tttm) REVERT: C 638 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8235 (mtm180) REVERT: C 688 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6905 (tptp) REVERT: D 272 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8513 (p) REVERT: D 410 LYS cc_start: 0.8484 (tttm) cc_final: 0.8209 (tttp) REVERT: D 440 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8286 (ttp-170) REVERT: D 590 MET cc_start: 0.7984 (mtp) cc_final: 0.7753 (mtp) REVERT: D 638 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.8233 (mtm180) REVERT: D 688 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6885 (tptp) outliers start: 55 outliers final: 26 residues processed: 258 average time/residue: 0.5785 time to fit residues: 164.5700 Evaluate side-chains 250 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR 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 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain B residue 272 THR 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 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 688 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 522 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 C residue 688 LYS Chi-restraints excluded: chain D residue 272 THR 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 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 170 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 537 GLN A 578 ASN B 430 ASN B 578 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100203 restraints weight = 17237.347| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.70 r_work: 0.2896 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15280 Z= 0.189 Angle : 0.578 8.544 20828 Z= 0.308 Chirality : 0.042 0.188 2428 Planarity : 0.004 0.041 2552 Dihedral : 4.723 27.537 2268 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.16 % Allowed : 14.25 % 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: 0.92 (0.19), residues: 1828 helix: 1.63 (0.16), residues: 1036 sheet: -0.60 (0.29), residues: 200 loop : -0.70 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 528 TYR 0.021 0.002 TYR A 249 PHE 0.018 0.002 PHE D 423 TRP 0.012 0.002 TRP C 414 HIS 0.005 0.002 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00443 (15264) covalent geometry : angle 0.57350 (20784) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.88079 ( 8) hydrogen bonds : bond 0.04513 ( 913) hydrogen bonds : angle 4.48012 ( 2619) link_NAG-ASN : bond 0.00162 ( 12) link_NAG-ASN : angle 1.87733 ( 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 278 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 0.539 Fit side-chains REVERT: A 410 LYS cc_start: 0.8551 (tttm) cc_final: 0.8301 (tttp) REVERT: A 440 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8276 (ttp-170) REVERT: A 688 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6904 (tptp) REVERT: B 410 LYS cc_start: 0.8545 (tttm) cc_final: 0.8294 (tttp) REVERT: B 440 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8261 (ttp-170) REVERT: B 688 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6905 (tptp) REVERT: C 272 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8646 (p) REVERT: C 410 LYS cc_start: 0.8624 (tttm) cc_final: 0.8325 (tttp) REVERT: C 440 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8264 (ttp-170) REVERT: C 595 LYS cc_start: 0.8694 (tptt) cc_final: 0.8466 (tttm) REVERT: C 688 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6929 (tptp) REVERT: D 410 LYS cc_start: 0.8549 (tttm) cc_final: 0.8300 (tttm) REVERT: D 440 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8270 (ttp-170) REVERT: D 688 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6921 (tptp) outliers start: 63 outliers final: 34 residues processed: 248 average time/residue: 0.5103 time to fit residues: 141.1536 Evaluate side-chains 253 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 315 LEU 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 A residue 688 LYS 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 B residue 688 LYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 315 LEU 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 C residue 688 LYS 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 Chi-restraints excluded: chain D residue 688 LYS 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: 2.9990 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100773 restraints weight = 17212.607| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.80 r_work: 0.2930 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15280 Z= 0.131 Angle : 0.522 8.570 20828 Z= 0.280 Chirality : 0.040 0.170 2428 Planarity : 0.004 0.038 2552 Dihedral : 4.412 25.301 2268 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.42 % Allowed : 14.64 % Favored : 80.94 % 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: 1.20 (0.19), residues: 1828 helix: 1.93 (0.16), residues: 1020 sheet: -0.58 (0.30), residues: 200 loop : -0.62 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 338 TYR 0.016 0.002 TYR C 527 PHE 0.016 0.001 PHE D 600 TRP 0.008 0.001 TRP D 293 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00286 (15264) covalent geometry : angle 0.51847 (20784) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.70777 ( 8) hydrogen bonds : bond 0.04067 ( 913) hydrogen bonds : angle 4.34737 ( 2619) link_NAG-ASN : bond 0.00184 ( 12) link_NAG-ASN : angle 1.61373 ( 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 286 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 0.420 Fit side-chains REVERT: A 332 SER cc_start: 0.8288 (t) cc_final: 0.7982 (t) REVERT: A 338 ARG cc_start: 0.7472 (tpp80) cc_final: 0.7243 (tpp80) REVERT: A 410 LYS cc_start: 0.8486 (tttm) cc_final: 0.8242 (tttm) REVERT: A 440 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8310 (ttp-170) REVERT: A 688 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6891 (tptp) REVERT: B 332 SER cc_start: 0.8295 (t) cc_final: 0.8056 (t) REVERT: B 338 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7220 (tpp80) REVERT: B 410 LYS cc_start: 0.8477 (tttm) cc_final: 0.8233 (tttm) REVERT: B 440 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8322 (ttp-170) REVERT: B 688 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6893 (tptp) REVERT: C 272 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8750 (p) REVERT: C 332 SER cc_start: 0.8302 (t) cc_final: 0.8087 (t) REVERT: C 410 LYS cc_start: 0.8545 (tttm) cc_final: 0.8254 (tttm) REVERT: C 440 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8319 (ttp-170) REVERT: C 485 PHE cc_start: 0.7908 (t80) cc_final: 0.7611 (t80) REVERT: C 595 LYS cc_start: 0.8662 (tptt) cc_final: 0.8375 (tttm) REVERT: C 688 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6897 (tptp) REVERT: D 332 SER cc_start: 0.8301 (t) cc_final: 0.8071 (t) REVERT: D 397 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7933 (mtt-85) REVERT: D 410 LYS cc_start: 0.8481 (tttm) cc_final: 0.8236 (tttm) REVERT: D 440 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8308 (ttp-170) REVERT: D 636 GLN cc_start: 0.8991 (mt0) cc_final: 0.8653 (mt0) REVERT: D 688 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6892 (tptp) outliers start: 67 outliers final: 29 residues processed: 260 average time/residue: 0.4936 time to fit residues: 144.0285 Evaluate side-chains 248 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL 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 A residue 688 LYS 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 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 B residue 688 LYS Chi-restraints excluded: chain C residue 272 THR 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 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 C residue 688 LYS 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 Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 153 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 145 optimal weight: 0.0010 chunk 122 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 430 ASN B 313 ASN B 430 ASN D 313 ASN D 430 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110956 restraints weight = 17003.842| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.61 r_work: 0.3033 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15280 Z= 0.111 Angle : 0.510 9.227 20828 Z= 0.275 Chirality : 0.039 0.144 2428 Planarity : 0.004 0.036 2552 Dihedral : 4.128 23.982 2268 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.43 % Allowed : 16.56 % Favored : 80.01 % 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 (0.19), residues: 1828 helix: 2.09 (0.16), residues: 1020 sheet: -0.17 (0.32), residues: 192 loop : -0.55 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 397 TYR 0.016 0.001 TYR C 527 PHE 0.015 0.001 PHE D 600 TRP 0.007 0.001 TRP D 455 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00223 (15264) covalent geometry : angle 0.50751 (20784) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.73229 ( 8) hydrogen bonds : bond 0.03704 ( 913) hydrogen bonds : angle 4.21439 ( 2619) link_NAG-ASN : bond 0.00226 ( 12) link_NAG-ASN : angle 1.38824 ( 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 287 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.446 Fit side-chains REVERT: A 332 SER cc_start: 0.8310 (t) cc_final: 0.8043 (t) REVERT: A 338 ARG cc_start: 0.7344 (tpp80) cc_final: 0.7082 (tpp80) REVERT: A 410 LYS cc_start: 0.8451 (tttm) cc_final: 0.8223 (tttm) REVERT: A 485 PHE cc_start: 0.7950 (t80) cc_final: 0.7667 (t80) REVERT: A 688 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6879 (tptp) REVERT: B 338 ARG cc_start: 0.7421 (tpp80) cc_final: 0.7149 (tpp80) REVERT: B 410 LYS cc_start: 0.8465 (tttm) cc_final: 0.8229 (tttp) REVERT: B 485 PHE cc_start: 0.7951 (t80) cc_final: 0.7666 (t80) REVERT: B 688 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6896 (tptp) REVERT: C 332 SER cc_start: 0.8335 (t) cc_final: 0.8119 (t) REVERT: C 410 LYS cc_start: 0.8554 (tttm) cc_final: 0.8276 (tttp) REVERT: C 485 PHE cc_start: 0.7914 (t80) cc_final: 0.7627 (t80) REVERT: C 595 LYS cc_start: 0.8676 (tptt) cc_final: 0.8406 (tttm) REVERT: C 688 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6925 (tptp) REVERT: D 272 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8691 (p) REVERT: D 332 SER cc_start: 0.8256 (t) cc_final: 0.8047 (t) REVERT: D 410 LYS cc_start: 0.8448 (tttm) cc_final: 0.8219 (tttm) REVERT: D 485 PHE cc_start: 0.7935 (t80) cc_final: 0.7642 (t80) REVERT: D 578 ASN cc_start: 0.6830 (m-40) cc_final: 0.6541 (p0) REVERT: D 688 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6905 (tptp) outliers start: 52 outliers final: 25 residues processed: 265 average time/residue: 0.4941 time to fit residues: 146.7219 Evaluate side-chains 247 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL 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 A residue 688 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 318 VAL 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 C residue 688 LYS Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 350 VAL 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 Chi-restraints excluded: chain D residue 688 LYS 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: 0.9990 chunk 77 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 636 GLN A 645 ASN B 537 GLN B 636 GLN B 645 ASN C 537 GLN C 636 GLN C 645 ASN D 537 GLN D 636 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.140718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107963 restraints weight = 17143.159| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.59 r_work: 0.2983 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4168 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= 0.132 Angle : 0.529 9.581 20828 Z= 0.284 Chirality : 0.040 0.169 2428 Planarity : 0.004 0.036 2552 Dihedral : 4.144 22.912 2268 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.30 % Allowed : 15.90 % Favored : 80.80 % 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: 1.41 (0.19), residues: 1828 helix: 2.04 (0.16), residues: 1020 sheet: -0.19 (0.32), residues: 192 loop : -0.54 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 338 TYR 0.016 0.002 TYR C 527 PHE 0.016 0.001 PHE D 600 TRP 0.008 0.001 TRP C 414 HIS 0.002 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00287 (15264) covalent geometry : angle 0.52637 (20784) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.83677 ( 8) hydrogen bonds : bond 0.03929 ( 913) hydrogen bonds : angle 4.23436 ( 2619) link_NAG-ASN : bond 0.00185 ( 12) link_NAG-ASN : angle 1.41538 ( 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 275 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.571 Fit side-chains REVERT: A 321 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8978 (tp) REVERT: A 332 SER cc_start: 0.8472 (t) cc_final: 0.8169 (t) REVERT: A 338 ARG cc_start: 0.7529 (tpp80) cc_final: 0.7253 (tpp80) REVERT: A 410 LYS cc_start: 0.8609 (tttm) cc_final: 0.8374 (tttp) REVERT: A 440 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8410 (ttp-170) REVERT: A 485 PHE cc_start: 0.7991 (t80) cc_final: 0.7722 (t80) REVERT: A 578 ASN cc_start: 0.6922 (m-40) cc_final: 0.6579 (p0) REVERT: A 688 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7062 (tptp) REVERT: B 338 ARG cc_start: 0.7522 (tpp80) cc_final: 0.7230 (tpp80) REVERT: B 410 LYS cc_start: 0.8609 (tttm) cc_final: 0.8374 (tttm) REVERT: B 440 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8405 (ttp-170) REVERT: B 485 PHE cc_start: 0.7999 (t80) cc_final: 0.7734 (t80) REVERT: B 578 ASN cc_start: 0.6925 (m-40) cc_final: 0.6583 (p0) REVERT: B 688 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7070 (tptp) REVERT: C 332 SER cc_start: 0.8270 (t) cc_final: 0.7896 (t) REVERT: C 338 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7101 (tpp-160) REVERT: C 410 LYS cc_start: 0.8675 (tttm) cc_final: 0.8408 (tttm) REVERT: C 440 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8398 (ttp-170) REVERT: C 485 PHE cc_start: 0.7993 (t80) cc_final: 0.7703 (t80) REVERT: C 578 ASN cc_start: 0.6916 (m-40) cc_final: 0.6595 (p0) REVERT: C 688 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7097 (tptp) REVERT: D 332 SER cc_start: 0.8266 (t) cc_final: 0.8008 (t) REVERT: D 410 LYS cc_start: 0.8574 (tttm) cc_final: 0.8330 (tttp) REVERT: D 440 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8392 (ttp-170) REVERT: D 485 PHE cc_start: 0.7990 (t80) cc_final: 0.7725 (t80) REVERT: D 578 ASN cc_start: 0.6966 (m-40) cc_final: 0.6746 (p0) REVERT: D 688 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7087 (tptp) outliers start: 50 outliers final: 25 residues processed: 263 average time/residue: 0.4922 time to fit residues: 145.3136 Evaluate side-chains 251 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 350 VAL 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 A residue 688 LYS 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 522 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 350 VAL 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 C residue 688 LYS Chi-restraints excluded: chain D residue 318 VAL 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 Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN B 537 GLN C 537 GLN C 653 ASN D 537 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107833 restraints weight = 17164.254| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.60 r_work: 0.3000 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15280 Z= 0.135 Angle : 0.546 9.512 20828 Z= 0.291 Chirality : 0.040 0.164 2428 Planarity : 0.004 0.036 2552 Dihedral : 4.195 22.489 2268 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.44 % Allowed : 17.02 % Favored : 80.54 % 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: 1.43 (0.20), residues: 1828 helix: 1.99 (0.16), residues: 1024 sheet: -0.08 (0.33), residues: 192 loop : -0.45 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 397 TYR 0.016 0.002 TYR C 527 PHE 0.020 0.001 PHE A 423 TRP 0.008 0.001 TRP C 414 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00296 (15264) covalent geometry : angle 0.54088 (20784) SS BOND : bond 0.00391 ( 4) SS BOND : angle 2.59344 ( 8) hydrogen bonds : bond 0.03966 ( 913) hydrogen bonds : angle 4.28014 ( 2619) link_NAG-ASN : bond 0.00180 ( 12) link_NAG-ASN : angle 1.43434 ( 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 245 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.589 Fit side-chains REVERT: A 332 SER cc_start: 0.8502 (t) cc_final: 0.8020 (t) REVERT: A 338 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7249 (tpp80) REVERT: A 410 LYS cc_start: 0.8584 (tttm) cc_final: 0.8343 (tttp) REVERT: A 440 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8403 (ttp-170) REVERT: A 485 PHE cc_start: 0.8003 (t80) cc_final: 0.7732 (t80) REVERT: A 578 ASN cc_start: 0.6934 (m-40) cc_final: 0.6583 (p0) REVERT: A 688 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7043 (tptp) REVERT: B 338 ARG cc_start: 0.7632 (tpp80) cc_final: 0.7318 (tpp80) REVERT: B 410 LYS cc_start: 0.8596 (tttm) cc_final: 0.8356 (tttm) REVERT: B 440 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8409 (ttp-170) REVERT: B 485 PHE cc_start: 0.8004 (t80) cc_final: 0.7723 (t80) REVERT: B 578 ASN cc_start: 0.6936 (m-40) cc_final: 0.6606 (p0) REVERT: B 590 MET cc_start: 0.8132 (tpp) cc_final: 0.7684 (mtp) REVERT: B 688 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7065 (tptp) REVERT: C 338 ARG cc_start: 0.7424 (tpp80) cc_final: 0.7034 (tpp-160) REVERT: C 410 LYS cc_start: 0.8655 (tttm) cc_final: 0.8386 (tttp) REVERT: C 440 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8429 (ttp-170) REVERT: C 485 PHE cc_start: 0.7998 (t80) cc_final: 0.7711 (t80) REVERT: C 578 ASN cc_start: 0.7092 (m-40) cc_final: 0.6685 (p0) REVERT: C 688 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7114 (tptp) REVERT: D 332 SER cc_start: 0.8346 (t) cc_final: 0.8073 (t) REVERT: D 410 LYS cc_start: 0.8588 (tttm) cc_final: 0.8339 (tttp) REVERT: D 440 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8413 (ttp-170) REVERT: D 485 PHE cc_start: 0.7996 (t80) cc_final: 0.7729 (t80) REVERT: D 578 ASN cc_start: 0.7050 (m-40) cc_final: 0.6829 (p0) REVERT: D 590 MET cc_start: 0.8181 (tpp) cc_final: 0.7673 (mtp) REVERT: D 688 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7084 (tptp) outliers start: 37 outliers final: 22 residues processed: 235 average time/residue: 0.5086 time to fit residues: 133.6134 Evaluate side-chains 231 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 644 ILE Chi-restraints excluded: chain A residue 688 LYS 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 522 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 688 LYS Chi-restraints excluded: chain D residue 318 VAL 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 644 ILE Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 150 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 101 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3605 r_free = 0.3605 target = 0.143895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111578 restraints weight = 17255.941| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.59 r_work: 0.3052 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15280 Z= 0.118 Angle : 0.544 9.611 20828 Z= 0.289 Chirality : 0.040 0.147 2428 Planarity : 0.004 0.035 2552 Dihedral : 4.090 22.505 2268 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.98 % Allowed : 17.94 % Favored : 80.08 % 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: 1.57 (0.20), residues: 1828 helix: 2.09 (0.16), residues: 1020 sheet: 0.01 (0.34), residues: 192 loop : -0.37 (0.26), 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 0.018 0.001 PHE A 423 TRP 0.006 0.001 TRP C 293 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00243 (15264) covalent geometry : angle 0.53501 (20784) SS BOND : bond 0.00488 ( 4) SS BOND : angle 4.08555 ( 8) hydrogen bonds : bond 0.03753 ( 913) hydrogen bonds : angle 4.26245 ( 2619) link_NAG-ASN : bond 0.00203 ( 12) link_NAG-ASN : angle 1.40969 ( 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 243 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.576 Fit side-chains REVERT: A 338 ARG cc_start: 0.7501 (tpp80) cc_final: 0.7199 (tpp80) REVERT: A 410 LYS cc_start: 0.8535 (tttm) cc_final: 0.8296 (tttm) REVERT: A 440 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8388 (ttp-170) REVERT: A 485 PHE cc_start: 0.7996 (t80) cc_final: 0.7710 (t80) REVERT: A 578 ASN cc_start: 0.6962 (m-40) cc_final: 0.6631 (p0) REVERT: A 688 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7081 (tptp) REVERT: B 338 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7197 (tpp80) REVERT: B 410 LYS cc_start: 0.8542 (tttm) cc_final: 0.8303 (tttm) REVERT: B 440 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8387 (ttp-170) REVERT: B 485 PHE cc_start: 0.7991 (t80) cc_final: 0.7699 (t80) REVERT: B 578 ASN cc_start: 0.6970 (m-40) cc_final: 0.6640 (p0) REVERT: B 590 MET cc_start: 0.8147 (tpp) cc_final: 0.7661 (mtp) REVERT: B 688 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7088 (tptp) REVERT: C 338 ARG cc_start: 0.7435 (tpp80) cc_final: 0.7069 (tpp-160) REVERT: C 410 LYS cc_start: 0.8610 (tttm) cc_final: 0.8340 (tttp) REVERT: C 440 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8401 (ttp-170) REVERT: C 485 PHE cc_start: 0.7972 (t80) cc_final: 0.7666 (t80) REVERT: C 578 ASN cc_start: 0.7095 (m-40) cc_final: 0.6703 (p0) REVERT: C 595 LYS cc_start: 0.8695 (tptt) cc_final: 0.8398 (tttm) REVERT: C 688 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7075 (tptt) REVERT: D 332 SER cc_start: 0.8348 (t) cc_final: 0.8092 (t) REVERT: D 410 LYS cc_start: 0.8563 (tttm) cc_final: 0.8318 (tttp) REVERT: D 440 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8387 (ttp-170) REVERT: D 485 PHE cc_start: 0.8002 (t80) cc_final: 0.7719 (t80) REVERT: D 585 GLN cc_start: 0.6823 (mp10) cc_final: 0.6572 (mp10) REVERT: D 590 MET cc_start: 0.8180 (tpp) cc_final: 0.7786 (mtp) REVERT: D 688 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7125 (tptp) outliers start: 30 outliers final: 19 residues processed: 235 average time/residue: 0.4913 time to fit residues: 129.3705 Evaluate side-chains 235 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 440 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 LYS 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 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 688 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 0.0010 chunk 72 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 636 GLN C 537 GLN C 636 GLN D 537 GLN D 636 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111328 restraints weight = 17067.063| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.61 r_work: 0.3039 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4432 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 : 0.541 9.536 20828 Z= 0.287 Chirality : 0.040 0.152 2428 Planarity : 0.004 0.035 2552 Dihedral : 4.048 22.209 2268 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.98 % Allowed : 18.07 % Favored : 79.95 % 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: 1.56 (0.20), residues: 1828 helix: 2.06 (0.16), residues: 1024 sheet: -0.02 (0.34), residues: 192 loop : -0.34 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 397 TYR 0.015 0.001 TYR C 527 PHE 0.018 0.001 PHE A 423 TRP 0.006 0.001 TRP D 293 HIS 0.001 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00253 (15264) covalent geometry : angle 0.53342 (20784) SS BOND : bond 0.00312 ( 4) SS BOND : angle 3.85439 ( 8) hydrogen bonds : bond 0.03779 ( 913) hydrogen bonds : angle 4.23748 ( 2619) link_NAG-ASN : bond 0.00195 ( 12) link_NAG-ASN : angle 1.30018 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4707.67 seconds wall clock time: 81 minutes 5.55 seconds (4865.55 seconds total)