Starting phenix.real_space_refine on Fri Jul 3 01:32:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7au2_11923/07_2026/7au2_11923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7au2_11923/07_2026/7au2_11923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2026/7au2_11923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2026/7au2_11923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2026/7au2_11923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2026/7au2_11923.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2026/7au2_11923.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2026/7au2_11923.cif" } resolution = 2.43 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= 0.000 sd= 0.006 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 56 5.16 5 C 7252 2.51 5 N 1886 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5540 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, E, F Time building chain proxies: 5.10, per 1000 atoms: 0.45 Number of scatterers: 11236 At special positions: 0 Unit cell: (91.3379, 102.005, 103.339, 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 56 16.00 O 2042 8.00 N 1886 7.00 C 7252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 793 " - pdb=" SG CYS B 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 879 " distance=2.04 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS B 793 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 879 " distance=2.04 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 592 " " NAG D 1 " - " ASN A 790 " " NAG E 1 " - " ASN B 592 " " NAG F 1 " - " ASN B 790 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 471.2 milliseconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 41.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.688A pdb=" N PHE A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.656A pdb=" N ARG A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.361A pdb=" N ASN A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.513A pdb=" N GLU A 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.841A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.630A pdb=" N VAL A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 486 through 491 removed outlier: 4.533A pdb=" N THR A 491 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.502A pdb=" N LEU A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 520 Processing helix chain 'A' and resid 522 through 538 Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 599 through 606 Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.889A pdb=" N GLY A 641 " --> pdb=" O PRO A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.596A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.677A pdb=" N MET A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.548A pdb=" N ARG A 728 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 764 Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 818 through 829 removed outlier: 3.922A pdb=" N ARG A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 845 Processing helix chain 'A' and resid 870 through 888 removed outlier: 4.127A pdb=" N ARG A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 877 " --> pdb=" O PHE A 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.687A pdb=" N PHE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.656A pdb=" N ARG B 187 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.361A pdb=" N ASN B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.513A pdb=" N GLU B 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.500A pdb=" N LYS B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.840A pdb=" N LEU B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.630A pdb=" N VAL B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 486 through 491 removed outlier: 4.533A pdb=" N THR B 491 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.502A pdb=" N LEU B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'B' and resid 522 through 538 Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 599 through 606 Processing helix chain 'B' and resid 626 through 630 Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.888A pdb=" N GLY B 641 " --> pdb=" O PRO B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.596A pdb=" N ALA B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 removed outlier: 3.677A pdb=" N MET B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.548A pdb=" N ARG B 728 " --> pdb=" O LEU B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 764 Processing helix chain 'B' and resid 807 through 816 Processing helix chain 'B' and resid 818 through 829 removed outlier: 3.921A pdb=" N ARG B 822 " --> pdb=" O PRO B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 845 Processing helix chain 'B' and resid 870 through 888 removed outlier: 4.127A pdb=" N ARG B 876 " --> pdb=" O HIS B 872 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 877 " --> pdb=" O PHE B 873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.776A pdb=" N TYR A 197 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU A 241 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR A 238 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 276 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 240 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 298 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.540A pdb=" N ILE A 443 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 7.409A pdb=" N LEU A 395 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 343 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU A 397 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A 345 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR A 341 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA A 431 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE A 343 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ILE A 433 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N PHE A 345 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR A 429 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 462 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 431 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 464 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 433 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 485 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 463 " --> pdb=" O VAL A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 551 through 552 removed outlier: 4.758A pdb=" N ALA A 551 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET A 716 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 692 " --> pdb=" O MET A 716 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL A 718 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 694 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE A 663 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 693 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 665 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 695 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET A 667 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 664 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 743 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 666 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 788 Processing sheet with id=AA6, first strand: chain 'A' and resid 898 through 900 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 198 removed outlier: 6.776A pdb=" N TYR B 197 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU B 241 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 238 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE B 276 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 240 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 298 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.540A pdb=" N ILE B 443 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 395 through 397 removed outlier: 7.409A pdb=" N LEU B 395 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 343 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU B 397 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE B 345 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N TYR B 341 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA B 431 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE B 343 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ILE B 433 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N PHE B 345 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 429 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL B 462 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 431 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 464 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 433 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 485 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 463 " --> pdb=" O VAL B 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 551 through 552 removed outlier: 4.758A pdb=" N ALA B 551 " --> pdb=" O ARG B 719 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET B 716 " --> pdb=" O ASN B 690 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 692 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 718 " --> pdb=" O VAL B 692 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 694 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE B 663 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL B 693 " --> pdb=" O PHE B 663 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 665 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL B 695 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET B 667 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 664 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 743 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL B 666 " --> pdb=" O ILE B 743 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 784 through 788 369 hydrogen bonds defined for protein. 957 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: 1.83 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3574 1.34 - 1.46: 2831 1.46 - 1.58: 5061 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 11554 Sorted by residual: bond pdb=" N ILE A 829 " pdb=" CA ILE A 829 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N ILE B 829 " pdb=" CA ILE B 829 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 bond pdb=" N ASN B 830 " pdb=" CA ASN B 830 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.16e-02 7.43e+03 5.95e+00 bond pdb=" N ASN A 830 " pdb=" CA ASN A 830 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.16e-02 7.43e+03 5.94e+00 bond pdb=" N PHE A 918 " pdb=" CA PHE A 918 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.38e-02 5.25e+03 5.24e+00 ... (remaining 11549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 14726 1.25 - 2.50: 766 2.50 - 3.75: 174 3.75 - 5.00: 39 5.00 - 6.25: 21 Bond angle restraints: 15726 Sorted by residual: angle pdb=" C ASN A 830 " pdb=" N CYS A 831 " pdb=" CA CYS A 831 " ideal model delta sigma weight residual 122.74 128.48 -5.74 1.44e+00 4.82e-01 1.59e+01 angle pdb=" C ASN B 830 " pdb=" N CYS B 831 " pdb=" CA CYS B 831 " ideal model delta sigma weight residual 122.74 128.40 -5.66 1.44e+00 4.82e-01 1.54e+01 angle pdb=" CA CYS A 831 " pdb=" C CYS A 831 " pdb=" O CYS A 831 " ideal model delta sigma weight residual 120.57 116.07 4.50 1.20e+00 6.94e-01 1.41e+01 angle pdb=" CA CYS B 831 " pdb=" C CYS B 831 " pdb=" O CYS B 831 " ideal model delta sigma weight residual 120.57 116.09 4.48 1.20e+00 6.94e-01 1.39e+01 angle pdb=" CA PRO A 583 " pdb=" N PRO A 583 " pdb=" CD PRO A 583 " ideal model delta sigma weight residual 112.00 106.78 5.22 1.40e+00 5.10e-01 1.39e+01 ... (remaining 15721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6200 17.99 - 35.97: 458 35.97 - 53.96: 100 53.96 - 71.94: 26 71.94 - 89.93: 28 Dihedral angle restraints: 6812 sinusoidal: 2774 harmonic: 4038 Sorted by residual: dihedral pdb=" CA PHE A 520 " pdb=" C PHE A 520 " pdb=" N SER A 521 " pdb=" CA SER A 521 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA PHE B 520 " pdb=" C PHE B 520 " pdb=" N SER B 521 " pdb=" CA SER B 521 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA VAL A 242 " pdb=" C VAL A 242 " pdb=" N GLY A 243 " pdb=" CA GLY A 243 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1691 0.105 - 0.210: 57 0.210 - 0.316: 2 0.316 - 0.421: 0 0.421 - 0.526: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CB THR A 617 " pdb=" CA THR A 617 " pdb=" OG1 THR A 617 " pdb=" CG2 THR A 617 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB THR B 617 " pdb=" CA THR B 617 " pdb=" OG1 THR B 617 " pdb=" CG2 THR B 617 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1749 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 582 " 0.041 5.00e-02 4.00e+02 5.96e-02 5.67e+00 pdb=" N PRO A 583 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 582 " -0.041 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO B 583 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 890 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 891 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 891 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 891 " 0.023 5.00e-02 4.00e+02 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 4300 2.89 - 3.40: 10155 3.40 - 3.90: 18642 3.90 - 4.40: 22307 4.40 - 4.90: 36722 Nonbonded interactions: 92126 Sorted by model distance: nonbonded pdb=" N ASP A 833 " pdb=" OD1 ASP A 833 " model vdw 2.392 3.120 nonbonded pdb=" N ASP B 833 " pdb=" OD1 ASP B 833 " model vdw 2.393 3.120 nonbonded pdb=" OE1 GLN B 819 " pdb=" NH1 ARG B 822 " model vdw 2.442 3.120 nonbonded pdb=" OE1 GLN A 819 " pdb=" NH1 ARG A 822 " model vdw 2.442 3.120 nonbonded pdb=" O VAL A 851 " pdb=" O VAL A 899 " model vdw 2.444 3.040 ... (remaining 92121 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.530 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 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 : 0.005 0.086 11576 Z= 0.222 Angle : 0.724 7.985 15782 Z= 0.391 Chirality : 0.049 0.526 1752 Planarity : 0.005 0.060 2004 Dihedral : 14.970 89.928 4170 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.83 % Allowed : 7.93 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1356 helix: 0.45 (0.25), residues: 438 sheet: -0.62 (0.38), residues: 172 loop : -0.04 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 546 TYR 0.023 0.002 TYR A 791 PHE 0.024 0.002 PHE B 600 TRP 0.010 0.001 TRP A 266 HIS 0.005 0.002 HIS B 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (11554) covalent geometry : angle 0.70879 / 0.39 (15726) SS BOND : bond 0.00416 / 0.25 ( 10) SS BOND : angle 1.44318 / 1.00 ( 20) hydrogen bonds : bond 0.19012 / 12.32 ( 369) hydrogen bonds : angle 6.49082 / 4.51 ( 957) link_ALPHA1-3 : bond 0.00980 / 0.58 ( 2) link_ALPHA1-3 : angle 2.75765 / 1.35 ( 6) link_BETA1-4 : bond 0.00570 / 0.38 ( 6) link_BETA1-4 : angle 1.99186 / 1.24 ( 18) link_NAG-ASN : bond 0.00364 / 0.24 ( 4) link_NAG-ASN : angle 4.26266 / 2.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.440 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 0.7341 time to fit residues: 108.1984 Evaluate side-chains 131 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN A 469 GLN A 616 HIS A 782 HIS A 881 ASN B 216 GLN B 469 GLN B 616 HIS B 782 HIS B 881 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104650 restraints weight = 11413.882| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.71 r_work: 0.2998 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11576 Z= 0.204 Angle : 0.664 6.677 15782 Z= 0.354 Chirality : 0.048 0.169 1752 Planarity : 0.006 0.046 2004 Dihedral : 5.388 32.749 1516 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.98 % Allowed : 7.69 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.22), residues: 1356 helix: 0.58 (0.24), residues: 464 sheet: -0.66 (0.38), residues: 172 loop : -0.07 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 546 TYR 0.016 0.002 TYR A 808 PHE 0.016 0.002 PHE B 600 TRP 0.010 0.002 TRP A 761 HIS 0.006 0.002 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (11554) covalent geometry : angle 0.65231 / 0.35 (15726) SS BOND : bond 0.00167 / 0.11 ( 10) SS BOND : angle 1.14419 / 0.67 ( 20) hydrogen bonds : bond 0.07203 / 4.56 ( 369) hydrogen bonds : angle 5.50671 / 3.77 ( 957) link_ALPHA1-3 : bond 0.00547 / 0.32 ( 2) link_ALPHA1-3 : angle 1.49927 / 0.94 ( 6) link_BETA1-4 : bond 0.00583 / 0.38 ( 6) link_BETA1-4 : angle 1.92099 / 1.19 ( 18) link_NAG-ASN : bond 0.00184 / 0.12 ( 4) link_NAG-ASN : angle 3.64497 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.445 Fit side-chains REVERT: A 330 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: A 824 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7853 (ttt) REVERT: B 330 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 824 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.7971 (tmt) outliers start: 24 outliers final: 8 residues processed: 148 average time/residue: 0.6578 time to fit residues: 104.1486 Evaluate side-chains 144 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 824 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS A 216 GLN A 307 GLN B 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108660 restraints weight = 11447.408| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.73 r_work: 0.3056 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11576 Z= 0.106 Angle : 0.534 5.439 15782 Z= 0.282 Chirality : 0.043 0.136 1752 Planarity : 0.005 0.042 2004 Dihedral : 4.677 20.749 1510 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.74 % Allowed : 8.43 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.22), residues: 1356 helix: 1.17 (0.25), residues: 452 sheet: -0.57 (0.38), residues: 168 loop : 0.04 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 546 TYR 0.012 0.001 TYR A 775 PHE 0.012 0.001 PHE B 206 TRP 0.010 0.001 TRP A 761 HIS 0.004 0.001 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (11554) covalent geometry : angle 0.52423 / 0.28 (15726) SS BOND : bond 0.00226 / 0.14 ( 10) SS BOND : angle 0.81932 / 0.52 ( 20) hydrogen bonds : bond 0.04710 / 2.98 ( 369) hydrogen bonds : angle 5.24489 / 3.60 ( 957) link_ALPHA1-3 : bond 0.00717 / 0.42 ( 2) link_ALPHA1-3 : angle 1.34560 / 0.84 ( 6) link_BETA1-4 : bond 0.00518 / 0.34 ( 6) link_BETA1-4 : angle 1.54819 / 1.01 ( 18) link_NAG-ASN : bond 0.00267 / 0.17 ( 4) link_NAG-ASN : angle 3.07755 / 2.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.268 Fit side-chains REVERT: A 283 ASP cc_start: 0.7896 (m-30) cc_final: 0.7657 (m-30) REVERT: A 330 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: A 824 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8040 (tmt) REVERT: B 257 GLU cc_start: 0.8318 (tt0) cc_final: 0.8020 (tt0) REVERT: B 330 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: B 824 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7992 (tmt) outliers start: 21 outliers final: 7 residues processed: 150 average time/residue: 0.5646 time to fit residues: 90.8745 Evaluate side-chains 142 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 817 MET Chi-restraints excluded: chain B residue 824 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105167 restraints weight = 11354.913| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.73 r_work: 0.3003 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11576 Z= 0.170 Angle : 0.612 6.164 15782 Z= 0.325 Chirality : 0.046 0.152 1752 Planarity : 0.005 0.046 2004 Dihedral : 4.945 24.165 1510 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.15 % Allowed : 9.09 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.22), residues: 1356 helix: 1.05 (0.25), residues: 452 sheet: -0.76 (0.39), residues: 168 loop : -0.04 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 546 TYR 0.014 0.002 TYR A 808 PHE 0.015 0.002 PHE A 600 TRP 0.010 0.002 TRP A 266 HIS 0.005 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (11554) covalent geometry : angle 0.60102 / 0.32 (15726) SS BOND : bond 0.00249 / 0.16 ( 10) SS BOND : angle 1.07748 / 0.64 ( 20) hydrogen bonds : bond 0.06173 / 3.90 ( 369) hydrogen bonds : angle 5.28454 / 3.62 ( 957) link_ALPHA1-3 : bond 0.00587 / 0.35 ( 2) link_ALPHA1-3 : angle 1.51820 / 0.95 ( 6) link_BETA1-4 : bond 0.00415 / 0.27 ( 6) link_BETA1-4 : angle 1.79207 / 1.10 ( 18) link_NAG-ASN : bond 0.00058 / 0.04 ( 4) link_NAG-ASN : angle 3.33207 / 2.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.370 Fit side-chains REVERT: A 330 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: A 824 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7952 (tmt) REVERT: B 330 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 824 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7942 (tmt) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 0.6765 time to fit residues: 103.5635 Evaluate side-chains 149 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104623 restraints weight = 11294.203| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.72 r_work: 0.2995 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 11576 Z= 0.191 Angle : 0.632 6.802 15782 Z= 0.335 Chirality : 0.047 0.167 1752 Planarity : 0.006 0.051 2004 Dihedral : 5.052 24.701 1510 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.81 % Allowed : 9.09 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1356 helix: 0.93 (0.25), residues: 452 sheet: -0.78 (0.39), residues: 168 loop : -0.10 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 546 TYR 0.015 0.002 TYR B 808 PHE 0.015 0.002 PHE B 857 TRP 0.012 0.002 TRP A 266 HIS 0.006 0.002 HIS A 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (11554) covalent geometry : angle 0.62023 / 0.33 (15726) SS BOND : bond 0.00233 / 0.16 ( 10) SS BOND : angle 1.11293 / 0.67 ( 20) hydrogen bonds : bond 0.06358 / 4.01 ( 369) hydrogen bonds : angle 5.32828 / 3.65 ( 957) link_ALPHA1-3 : bond 0.00536 / 0.32 ( 2) link_ALPHA1-3 : angle 1.55331 / 0.97 ( 6) link_BETA1-4 : bond 0.00464 / 0.30 ( 6) link_BETA1-4 : angle 1.83157 / 1.12 ( 18) link_NAG-ASN : bond 0.00093 / 0.05 ( 4) link_NAG-ASN : angle 3.53264 / 2.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.438 Fit side-chains REVERT: A 330 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 648 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6547 (mmtp) REVERT: A 824 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7933 (tmt) REVERT: B 330 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 648 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6534 (mmtp) REVERT: B 824 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8021 (ttt) outliers start: 34 outliers final: 16 residues processed: 146 average time/residue: 0.6590 time to fit residues: 103.1896 Evaluate side-chains 146 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 616 HIS Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105726 restraints weight = 11425.897| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.74 r_work: 0.3016 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11576 Z= 0.139 Angle : 0.574 6.115 15782 Z= 0.304 Chirality : 0.044 0.138 1752 Planarity : 0.005 0.046 2004 Dihedral : 4.836 22.901 1510 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.64 % Allowed : 9.67 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1356 helix: 1.09 (0.25), residues: 452 sheet: -0.76 (0.40), residues: 166 loop : -0.10 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 546 TYR 0.014 0.001 TYR B 808 PHE 0.012 0.002 PHE A 600 TRP 0.011 0.002 TRP B 266 HIS 0.004 0.001 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11554) covalent geometry : angle 0.56278 / 0.30 (15726) SS BOND : bond 0.00262 / 0.17 ( 10) SS BOND : angle 0.94639 / 0.58 ( 20) hydrogen bonds : bond 0.05422 / 3.42 ( 369) hydrogen bonds : angle 5.23367 / 3.59 ( 957) link_ALPHA1-3 : bond 0.00567 / 0.34 ( 2) link_ALPHA1-3 : angle 1.44251 / 0.90 ( 6) link_BETA1-4 : bond 0.00449 / 0.29 ( 6) link_BETA1-4 : angle 1.66179 / 1.04 ( 18) link_NAG-ASN : bond 0.00047 / 0.03 ( 4) link_NAG-ASN : angle 3.33081 / 2.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: A 648 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6517 (mmtp) REVERT: A 824 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7939 (tmt) REVERT: B 257 GLU cc_start: 0.8365 (tt0) cc_final: 0.8070 (tt0) REVERT: B 330 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: B 648 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6506 (mmtp) REVERT: B 824 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7930 (tmt) outliers start: 32 outliers final: 18 residues processed: 141 average time/residue: 0.6800 time to fit residues: 102.7777 Evaluate side-chains 147 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 915 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105545 restraints weight = 11367.445| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.72 r_work: 0.3010 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11576 Z= 0.156 Angle : 0.591 6.297 15782 Z= 0.312 Chirality : 0.045 0.149 1752 Planarity : 0.005 0.048 2004 Dihedral : 4.860 23.612 1510 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.56 % Allowed : 9.83 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.22), residues: 1356 helix: 1.04 (0.25), residues: 452 sheet: -0.72 (0.40), residues: 166 loop : -0.10 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 546 TYR 0.015 0.001 TYR B 808 PHE 0.013 0.002 PHE A 804 TRP 0.011 0.002 TRP B 266 HIS 0.004 0.001 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11554) covalent geometry : angle 0.57973 / 0.31 (15726) SS BOND : bond 0.00219 / 0.14 ( 10) SS BOND : angle 0.95798 / 0.59 ( 20) hydrogen bonds : bond 0.05750 / 3.63 ( 369) hydrogen bonds : angle 5.24954 / 3.60 ( 957) link_ALPHA1-3 : bond 0.00516 / 0.30 ( 2) link_ALPHA1-3 : angle 1.49649 / 0.94 ( 6) link_BETA1-4 : bond 0.00427 / 0.28 ( 6) link_BETA1-4 : angle 1.70086 / 1.05 ( 18) link_NAG-ASN : bond 0.00041 / 0.02 ( 4) link_NAG-ASN : angle 3.37281 / 2.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 405 LYS cc_start: 0.8069 (mtpt) cc_final: 0.6953 (mmtt) REVERT: A 648 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6514 (mmtp) REVERT: A 674 GLU cc_start: 0.6721 (tp30) cc_final: 0.6242 (tt0) REVERT: A 824 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7918 (tmt) REVERT: B 257 GLU cc_start: 0.8361 (tt0) cc_final: 0.8125 (tt0) REVERT: B 330 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 648 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6510 (mmtp) REVERT: B 674 GLU cc_start: 0.6716 (tp30) cc_final: 0.6235 (tt0) REVERT: B 824 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7916 (tmt) outliers start: 31 outliers final: 20 residues processed: 147 average time/residue: 0.6479 time to fit residues: 101.9403 Evaluate side-chains 154 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 616 HIS Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 915 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107474 restraints weight = 11342.480| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.73 r_work: 0.3042 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11576 Z= 0.110 Angle : 0.532 5.569 15782 Z= 0.280 Chirality : 0.043 0.136 1752 Planarity : 0.005 0.044 2004 Dihedral : 4.598 21.005 1510 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.90 % Allowed : 10.66 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1356 helix: 1.18 (0.25), residues: 452 sheet: -0.69 (0.41), residues: 166 loop : -0.03 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 546 TYR 0.014 0.001 TYR A 808 PHE 0.011 0.001 PHE B 804 TRP 0.010 0.001 TRP B 761 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11554) covalent geometry : angle 0.52166 / 0.28 (15726) SS BOND : bond 0.00119 / 0.08 ( 10) SS BOND : angle 0.85723 / 0.53 ( 20) hydrogen bonds : bond 0.04689 / 2.96 ( 369) hydrogen bonds : angle 5.15218 / 3.54 ( 957) link_ALPHA1-3 : bond 0.00537 / 0.32 ( 2) link_ALPHA1-3 : angle 1.38936 / 0.87 ( 6) link_BETA1-4 : bond 0.00439 / 0.29 ( 6) link_BETA1-4 : angle 1.54644 / 0.98 ( 18) link_NAG-ASN : bond 0.00083 / 0.05 ( 4) link_NAG-ASN : angle 3.09326 / 2.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: A 405 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7019 (mmtt) REVERT: A 824 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7929 (tmt) REVERT: B 257 GLU cc_start: 0.8282 (tt0) cc_final: 0.8027 (tt0) REVERT: B 330 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 405 LYS cc_start: 0.8009 (mtpt) cc_final: 0.6913 (mptp) REVERT: B 824 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7935 (tmt) outliers start: 23 outliers final: 14 residues processed: 143 average time/residue: 0.6664 time to fit residues: 102.2926 Evaluate side-chains 141 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 915 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108711 restraints weight = 11305.513| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.72 r_work: 0.3058 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11576 Z= 0.102 Angle : 0.512 5.075 15782 Z= 0.268 Chirality : 0.042 0.135 1752 Planarity : 0.004 0.044 2004 Dihedral : 4.429 19.949 1510 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.90 % Allowed : 10.91 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1356 helix: 1.27 (0.25), residues: 452 sheet: -0.64 (0.41), residues: 166 loop : 0.04 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 546 TYR 0.013 0.001 TYR B 808 PHE 0.010 0.001 PHE A 804 TRP 0.010 0.001 TRP B 761 HIS 0.003 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (11554) covalent geometry : angle 0.50267 / 0.27 (15726) SS BOND : bond 0.00109 / 0.07 ( 10) SS BOND : angle 0.75824 / 0.48 ( 20) hydrogen bonds : bond 0.04375 / 2.77 ( 369) hydrogen bonds : angle 5.01727 / 3.44 ( 957) link_ALPHA1-3 : bond 0.00522 / 0.31 ( 2) link_ALPHA1-3 : angle 1.39563 / 0.87 ( 6) link_BETA1-4 : bond 0.00420 / 0.27 ( 6) link_BETA1-4 : angle 1.48833 / 0.95 ( 18) link_NAG-ASN : bond 0.00086 / 0.05 ( 4) link_NAG-ASN : angle 2.89249 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 405 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7033 (mmtt) REVERT: A 626 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6246 (pm20) REVERT: A 824 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7946 (tmt) REVERT: B 330 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: B 405 LYS cc_start: 0.8080 (mtpt) cc_final: 0.6993 (mmtt) REVERT: B 626 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6244 (pm20) REVERT: B 824 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7949 (tmt) outliers start: 23 outliers final: 13 residues processed: 136 average time/residue: 0.6822 time to fit residues: 99.3974 Evaluate side-chains 143 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 915 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 57 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.106839 restraints weight = 11428.684| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.73 r_work: 0.3033 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11576 Z= 0.129 Angle : 0.549 5.844 15782 Z= 0.288 Chirality : 0.044 0.135 1752 Planarity : 0.005 0.043 2004 Dihedral : 4.583 21.635 1510 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.74 % Allowed : 11.07 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1356 helix: 1.20 (0.25), residues: 452 sheet: -0.49 (0.42), residues: 160 loop : -0.04 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.014 0.001 TYR B 808 PHE 0.012 0.002 PHE B 520 TRP 0.010 0.002 TRP B 266 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11554) covalent geometry : angle 0.53946 / 0.29 (15726) SS BOND : bond 0.00155 / 0.10 ( 10) SS BOND : angle 0.82116 / 0.52 ( 20) hydrogen bonds : bond 0.05072 / 3.21 ( 369) hydrogen bonds : angle 5.07951 / 3.48 ( 957) link_ALPHA1-3 : bond 0.00493 / 0.29 ( 2) link_ALPHA1-3 : angle 1.44728 / 0.90 ( 6) link_BETA1-4 : bond 0.00391 / 0.25 ( 6) link_BETA1-4 : angle 1.59098 / 0.99 ( 18) link_NAG-ASN : bond 0.00026 / 0.02 ( 4) link_NAG-ASN : angle 3.05164 / 2.03 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 405 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7003 (mmtt) REVERT: A 824 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7915 (tmt) REVERT: B 330 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 405 LYS cc_start: 0.8073 (mtpt) cc_final: 0.6986 (mmtt) REVERT: B 824 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7921 (tmt) outliers start: 21 outliers final: 13 residues processed: 140 average time/residue: 0.6334 time to fit residues: 94.9990 Evaluate side-chains 142 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 915 CYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 915 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 0.0770 chunk 39 optimal weight: 0.0070 chunk 51 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108843 restraints weight = 11395.158| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.74 r_work: 0.3061 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11576 Z= 0.099 Angle : 0.509 5.080 15782 Z= 0.266 Chirality : 0.042 0.133 1752 Planarity : 0.004 0.044 2004 Dihedral : 4.388 19.347 1510 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.57 % Allowed : 11.40 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1356 helix: 1.32 (0.25), residues: 452 sheet: -0.44 (0.42), residues: 158 loop : 0.02 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 546 TYR 0.013 0.001 TYR B 808 PHE 0.010 0.001 PHE A 804 TRP 0.010 0.001 TRP B 761 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (11554) covalent geometry : angle 0.49932 / 0.26 (15726) SS BOND : bond 0.00062 / 0.04 ( 10) SS BOND : angle 0.74313 / 0.47 ( 20) hydrogen bonds : bond 0.04266 / 2.70 ( 369) hydrogen bonds : angle 4.98970 / 3.42 ( 957) link_ALPHA1-3 : bond 0.00490 / 0.29 ( 2) link_ALPHA1-3 : angle 1.39750 / 0.87 ( 6) link_BETA1-4 : bond 0.00425 / 0.28 ( 6) link_BETA1-4 : angle 1.46396 / 0.94 ( 18) link_NAG-ASN : bond 0.00093 / 0.06 ( 4) link_NAG-ASN : angle 2.87867 / 1.92 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3986.01 seconds wall clock time: 68 minutes 36.31 seconds (4116.31 seconds total)