Starting phenix.real_space_refine on Wed Sep 17 21:16:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7au2_11923/09_2025/7au2_11923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7au2_11923/09_2025/7au2_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_11923/09_2025/7au2_11923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7au2_11923/09_2025/7au2_11923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7au2_11923/09_2025/7au2_11923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7au2_11923/09_2025/7au2_11923.map" } 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-2.0-5805/lib/python3.9/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 dihedrals: 6 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, E, F Time building chain proxies: 3.85, per 1000 atoms: 0.34 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: 1.17 Conformation dependent library (CDL) restraints added in 516.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.50 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: 1.54 Time building geometry restraints manager: 1.41 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 - 20.80: 6543 20.80 - 41.60: 385 41.60 - 62.40: 76 62.40 - 83.21: 28 83.21 - 104.01: 24 Dihedral angle restraints: 7056 sinusoidal: 3018 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 7053 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: 4.880 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 15.752 104.007 4414 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 aren 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 covalent geometry : bond 0.00522 (11554) covalent geometry : angle 0.70879 (15726) SS BOND : bond 0.00416 ( 10) SS BOND : angle 1.44318 ( 20) hydrogen bonds : bond 0.19012 ( 369) hydrogen bonds : angle 6.49082 ( 957) link_ALPHA1-3 : bond 0.00980 ( 2) link_ALPHA1-3 : angle 2.75765 ( 6) link_BETA1-4 : bond 0.00570 ( 6) link_BETA1-4 : angle 1.99186 ( 18) link_NAG-ASN : bond 0.00364 ( 4) link_NAG-ASN : angle 4.26266 ( 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 : 0.376 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 0.7496 time to fit residues: 110.1948 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 : 0.428 ------------------------------------------------------------------------------- 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: 0.0170 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3592 r_free = 0.3592 target = 0.138926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104865 restraints weight = 11413.681| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.71 r_work: 0.3000 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11576 Z= 0.195 Angle : 0.665 6.821 15782 Z= 0.354 Chirality : 0.048 0.171 1752 Planarity : 0.006 0.049 2004 Dihedral : 8.704 72.443 1760 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.15 % Allowed : 7.36 % Favored : 90.50 % 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 aren not related in a simple way. whole: 0.14 (0.22), residues: 1356 helix: 0.73 (0.25), residues: 452 sheet: -0.68 (0.38), residues: 172 loop : 0.00 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 546 TYR 0.017 0.002 TYR A 808 PHE 0.016 0.002 PHE B 600 TRP 0.010 0.002 TRP B 266 HIS 0.006 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00467 (11554) covalent geometry : angle 0.65178 (15726) SS BOND : bond 0.00196 ( 10) SS BOND : angle 1.12463 ( 20) hydrogen bonds : bond 0.06753 ( 369) hydrogen bonds : angle 5.45577 ( 957) link_ALPHA1-3 : bond 0.01064 ( 2) link_ALPHA1-3 : angle 2.25913 ( 6) link_BETA1-4 : bond 0.00635 ( 6) link_BETA1-4 : angle 2.10237 ( 18) link_NAG-ASN : bond 0.00212 ( 4) link_NAG-ASN : angle 3.65668 ( 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: 26 poor density : 138 time to evaluate : 0.403 Fit side-chains REVERT: A 330 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 824 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.7969 (tmt) REVERT: B 330 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: B 824 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7961 (tmt) outliers start: 26 outliers final: 7 residues processed: 147 average time/residue: 0.7031 time to fit residues: 110.2197 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 216 GLN A 307 GLN B 216 GLN B 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107235 restraints weight = 11415.654| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.73 r_work: 0.3035 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11576 Z= 0.125 Angle : 0.563 5.844 15782 Z= 0.296 Chirality : 0.044 0.143 1752 Planarity : 0.005 0.043 2004 Dihedral : 7.305 55.473 1754 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.98 % Allowed : 8.60 % Favored : 89.42 % 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 aren not related in a simple way. whole: 0.35 (0.22), residues: 1356 helix: 1.10 (0.25), residues: 452 sheet: -0.79 (0.38), residues: 172 loop : 0.05 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 546 TYR 0.013 0.001 TYR A 808 PHE 0.012 0.002 PHE A 804 TRP 0.010 0.001 TRP A 266 HIS 0.005 0.001 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00280 (11554) covalent geometry : angle 0.55131 (15726) SS BOND : bond 0.00081 ( 10) SS BOND : angle 0.90523 ( 20) hydrogen bonds : bond 0.05182 ( 369) hydrogen bonds : angle 5.26689 ( 957) link_ALPHA1-3 : bond 0.01135 ( 2) link_ALPHA1-3 : angle 1.69833 ( 6) link_BETA1-4 : bond 0.00539 ( 6) link_BETA1-4 : angle 1.83094 ( 18) link_NAG-ASN : bond 0.00161 ( 4) link_NAG-ASN : angle 3.21457 ( 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 162 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.434 Fit side-chains REVERT: A 330 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 824 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8050 (tmt) REVERT: B 257 GLU cc_start: 0.8317 (tt0) cc_final: 0.8032 (tt0) REVERT: B 283 ASP cc_start: 0.7901 (m-30) cc_final: 0.7695 (m-30) REVERT: B 330 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 824 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7962 (tmt) outliers start: 24 outliers final: 8 residues processed: 146 average time/residue: 0.7106 time to fit residues: 110.9231 Evaluate side-chains 140 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 330 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3616 r_free = 0.3616 target = 0.140877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106437 restraints weight = 11358.450| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.74 r_work: 0.3020 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11576 Z= 0.137 Angle : 0.572 5.803 15782 Z= 0.301 Chirality : 0.045 0.160 1752 Planarity : 0.005 0.042 2004 Dihedral : 6.324 39.928 1754 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.40 % Allowed : 9.01 % Favored : 88.60 % 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 aren not related in a simple way. whole: 0.32 (0.22), residues: 1356 helix: 1.11 (0.25), residues: 452 sheet: -0.75 (0.40), residues: 166 loop : -0.02 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 546 TYR 0.014 0.001 TYR A 808 PHE 0.013 0.002 PHE A 600 TRP 0.010 0.002 TRP A 266 HIS 0.004 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00314 (11554) covalent geometry : angle 0.56033 (15726) SS BOND : bond 0.00284 ( 10) SS BOND : angle 0.91639 ( 20) hydrogen bonds : bond 0.05401 ( 369) hydrogen bonds : angle 5.21259 ( 957) link_ALPHA1-3 : bond 0.01096 ( 2) link_ALPHA1-3 : angle 1.95754 ( 6) link_BETA1-4 : bond 0.00505 ( 6) link_BETA1-4 : angle 1.84196 ( 18) link_NAG-ASN : bond 0.00069 ( 4) link_NAG-ASN : angle 3.22184 ( 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 162 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.291 Fit side-chains REVERT: A 330 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: A 824 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.7962 (tmt) REVERT: B 330 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: B 824 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7938 (tmt) outliers start: 29 outliers final: 13 residues processed: 146 average time/residue: 0.6449 time to fit residues: 100.8422 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 : 0.471 ------------------------------------------------------------------------------- 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 675 VAL Chi-restraints excluded: chain A residue 824 MET 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: 1.9990 chunk 1 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 107 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108123 restraints weight = 11313.550| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.73 r_work: 0.3048 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11576 Z= 0.111 Angle : 0.530 5.566 15782 Z= 0.277 Chirality : 0.043 0.147 1752 Planarity : 0.005 0.040 2004 Dihedral : 5.391 30.731 1754 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.82 % Allowed : 10.25 % Favored : 87.93 % 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 aren not related in a simple way. whole: 0.42 (0.22), residues: 1356 helix: 1.24 (0.25), residues: 452 sheet: -0.75 (0.40), residues: 166 loop : 0.03 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 546 TYR 0.013 0.001 TYR A 808 PHE 0.011 0.001 PHE B 804 TRP 0.010 0.001 TRP B 266 HIS 0.003 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00243 (11554) covalent geometry : angle 0.51932 (15726) SS BOND : bond 0.00216 ( 10) SS BOND : angle 0.83128 ( 20) hydrogen bonds : bond 0.04661 ( 369) hydrogen bonds : angle 5.12311 ( 957) link_ALPHA1-3 : bond 0.01137 ( 2) link_ALPHA1-3 : angle 1.82388 ( 6) link_BETA1-4 : bond 0.00561 ( 6) link_BETA1-4 : angle 1.64714 ( 18) link_NAG-ASN : bond 0.00114 ( 4) link_NAG-ASN : angle 3.07655 ( 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 152 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.468 Fit side-chains REVERT: A 330 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: A 672 ARG cc_start: 0.5557 (OUTLIER) cc_final: 0.5195 (mtt-85) REVERT: A 824 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7956 (tmt) REVERT: B 330 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: B 672 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.5177 (mtt-85) REVERT: B 824 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7941 (tmt) outliers start: 22 outliers final: 9 residues processed: 140 average time/residue: 0.7130 time to fit residues: 106.8231 Evaluate side-chains 140 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 626 GLU Chi-restraints excluded: chain A residue 672 ARG 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 252 ARG Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 672 ARG 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: 3.9990 chunk 67 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106166 restraints weight = 11456.717| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.74 r_work: 0.3022 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11576 Z= 0.139 Angle : 0.568 5.751 15782 Z= 0.299 Chirality : 0.045 0.148 1752 Planarity : 0.005 0.042 2004 Dihedral : 5.184 26.314 1754 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.48 % Allowed : 9.75 % Favored : 87.77 % 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 aren not related in a simple way. whole: 0.38 (0.22), residues: 1356 helix: 1.19 (0.25), residues: 452 sheet: -0.70 (0.41), residues: 166 loop : -0.00 (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 0.012 0.002 PHE B 600 TRP 0.010 0.002 TRP A 266 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00319 (11554) covalent geometry : angle 0.55695 (15726) SS BOND : bond 0.00241 ( 10) SS BOND : angle 0.89053 ( 20) hydrogen bonds : bond 0.05368 ( 369) hydrogen bonds : angle 5.14705 ( 957) link_ALPHA1-3 : bond 0.00994 ( 2) link_ALPHA1-3 : angle 1.85097 ( 6) link_BETA1-4 : bond 0.00518 ( 6) link_BETA1-4 : angle 1.70816 ( 18) link_NAG-ASN : bond 0.00007 ( 4) link_NAG-ASN : angle 3.23166 ( 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 154 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8371 (tt0) cc_final: 0.8088 (tt0) REVERT: A 330 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: A 648 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6480 (mmtp) REVERT: A 824 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7932 (tmt) REVERT: B 330 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: B 648 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6476 (mmtp) REVERT: B 824 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7927 (tmt) outliers start: 30 outliers final: 17 residues processed: 139 average time/residue: 0.7160 time to fit residues: 106.0055 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 : 0.453 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3595 r_free = 0.3595 target = 0.139143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104723 restraints weight = 11349.286| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.73 r_work: 0.2998 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1611 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= 0.192 Angle : 0.631 6.843 15782 Z= 0.334 Chirality : 0.047 0.172 1752 Planarity : 0.005 0.049 2004 Dihedral : 5.341 24.439 1754 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.81 % Allowed : 9.50 % 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 aren not related in a simple way. whole: 0.24 (0.22), residues: 1356 helix: 1.03 (0.25), residues: 452 sheet: -0.70 (0.41), residues: 166 loop : -0.08 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 546 TYR 0.016 0.002 TYR A 808 PHE 0.015 0.002 PHE A 520 TRP 0.011 0.002 TRP B 266 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00459 (11554) covalent geometry : angle 0.61960 (15726) SS BOND : bond 0.00361 ( 10) SS BOND : angle 1.01893 ( 20) hydrogen bonds : bond 0.06349 ( 369) hydrogen bonds : angle 5.28729 ( 957) link_ALPHA1-3 : bond 0.00842 ( 2) link_ALPHA1-3 : angle 1.85839 ( 6) link_BETA1-4 : bond 0.00567 ( 6) link_BETA1-4 : angle 1.86348 ( 18) link_NAG-ASN : bond 0.00118 ( 4) link_NAG-ASN : angle 3.54885 ( 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 162 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: A 648 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6542 (mmtp) REVERT: A 674 GLU cc_start: 0.6749 (tp30) cc_final: 0.6261 (tt0) REVERT: A 824 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7929 (tmt) REVERT: B 330 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: B 405 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7029 (mptp) REVERT: B 602 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8685 (ttt90) REVERT: B 648 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6542 (mmtp) REVERT: B 674 GLU cc_start: 0.6752 (tp30) cc_final: 0.6262 (tt0) REVERT: B 824 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8016 (ttt) outliers start: 34 outliers final: 18 residues processed: 146 average time/residue: 0.7051 time to fit residues: 109.5858 Evaluate side-chains 152 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 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 602 ARG 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: 0.6980 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 103 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3645 r_free = 0.3645 target = 0.143198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.109245 restraints weight = 11326.504| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.72 r_work: 0.3066 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11576 Z= 0.096 Angle : 0.511 5.172 15782 Z= 0.267 Chirality : 0.042 0.136 1752 Planarity : 0.004 0.043 2004 Dihedral : 4.704 19.349 1754 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.40 % Allowed : 11.40 % 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 aren not related in a simple way. whole: 0.47 (0.23), residues: 1356 helix: 1.27 (0.25), residues: 452 sheet: -0.52 (0.41), residues: 162 loop : 0.00 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 546 TYR 0.012 0.001 TYR A 808 PHE 0.009 0.001 PHE A 600 TRP 0.011 0.001 TRP A 761 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00198 (11554) covalent geometry : angle 0.50074 (15726) SS BOND : bond 0.00215 ( 10) SS BOND : angle 0.76914 ( 20) hydrogen bonds : bond 0.04172 ( 369) hydrogen bonds : angle 5.05062 ( 957) link_ALPHA1-3 : bond 0.00855 ( 2) link_ALPHA1-3 : angle 1.57521 ( 6) link_BETA1-4 : bond 0.00579 ( 6) link_BETA1-4 : angle 1.48280 ( 18) link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 3.05625 ( 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 143 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8282 (tt0) cc_final: 0.7980 (tt0) REVERT: A 330 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: A 405 LYS cc_start: 0.7910 (mtpt) cc_final: 0.6895 (mptp) REVERT: A 824 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.7959 (tmt) REVERT: B 330 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 405 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7006 (mptp) REVERT: B 648 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6511 (mmtp) REVERT: B 824 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7968 (tmt) outliers start: 17 outliers final: 12 residues processed: 136 average time/residue: 0.7404 time to fit residues: 107.4406 Evaluate side-chains 139 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 96 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3612 r_free = 0.3612 target = 0.140482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106113 restraints weight = 11272.004| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.73 r_work: 0.3018 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1654 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= 0.155 Angle : 0.581 5.934 15782 Z= 0.306 Chirality : 0.045 0.143 1752 Planarity : 0.005 0.044 2004 Dihedral : 4.899 22.922 1754 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.90 % Allowed : 11.07 % 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 aren not related in a simple way. whole: 0.35 (0.23), residues: 1356 helix: 1.13 (0.25), residues: 452 sheet: -0.64 (0.41), residues: 166 loop : -0.03 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 546 TYR 0.015 0.001 TYR A 808 PHE 0.013 0.002 PHE B 520 TRP 0.010 0.002 TRP B 266 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00362 (11554) covalent geometry : angle 0.57057 (15726) SS BOND : bond 0.00233 ( 10) SS BOND : angle 0.87393 ( 20) hydrogen bonds : bond 0.05641 ( 369) hydrogen bonds : angle 5.15839 ( 957) link_ALPHA1-3 : bond 0.00882 ( 2) link_ALPHA1-3 : angle 1.68187 ( 6) link_BETA1-4 : bond 0.00535 ( 6) link_BETA1-4 : angle 1.67708 ( 18) link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 3.29716 ( 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 144 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 405 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7026 (mptp) REVERT: A 648 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6486 (mmtp) REVERT: A 824 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7931 (tmt) REVERT: B 330 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: B 405 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7004 (mptp) REVERT: B 648 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6483 (mmtp) REVERT: B 824 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7923 (tmt) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 0.6927 time to fit residues: 101.4800 Evaluate side-chains 140 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3607 r_free = 0.3607 target = 0.140203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105709 restraints weight = 11405.966| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.74 r_work: 0.3018 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1685 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= 0.149 Angle : 0.578 6.179 15782 Z= 0.304 Chirality : 0.045 0.145 1752 Planarity : 0.005 0.046 2004 Dihedral : 4.911 22.903 1754 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.98 % Allowed : 11.07 % Favored : 86.94 % 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 aren not related in a simple way. whole: 0.31 (0.22), residues: 1356 helix: 1.10 (0.25), residues: 452 sheet: -0.64 (0.41), residues: 166 loop : -0.05 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 546 TYR 0.015 0.001 TYR A 808 PHE 0.012 0.002 PHE A 600 TRP 0.010 0.002 TRP B 266 HIS 0.004 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00349 (11554) covalent geometry : angle 0.56722 (15726) SS BOND : bond 0.00196 ( 10) SS BOND : angle 0.86322 ( 20) hydrogen bonds : bond 0.05489 ( 369) hydrogen bonds : angle 5.17188 ( 957) link_ALPHA1-3 : bond 0.00780 ( 2) link_ALPHA1-3 : angle 1.67878 ( 6) link_BETA1-4 : bond 0.00548 ( 6) link_BETA1-4 : angle 1.65625 ( 18) link_NAG-ASN : bond 0.00043 ( 4) link_NAG-ASN : angle 3.34534 ( 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 149 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: A 405 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7000 (mptp) REVERT: A 648 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6533 (mmtp) REVERT: A 824 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.7942 (tmt) REVERT: B 330 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: B 405 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7002 (mptp) REVERT: B 648 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6531 (mmtp) REVERT: B 824 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.7940 (tmt) outliers start: 24 outliers final: 14 residues processed: 141 average time/residue: 0.7139 time to fit residues: 107.5606 Evaluate side-chains 144 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 0.1980 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3629 r_free = 0.3629 target = 0.141949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107825 restraints weight = 11333.673| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.73 r_work: 0.3045 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11576 Z= 0.114 Angle : 0.531 5.425 15782 Z= 0.278 Chirality : 0.043 0.134 1752 Planarity : 0.004 0.043 2004 Dihedral : 4.643 20.673 1754 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.82 % Allowed : 11.32 % Favored : 86.86 % 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 aren not related in a simple way. whole: 0.42 (0.23), residues: 1356 helix: 1.24 (0.25), residues: 452 sheet: -0.63 (0.42), residues: 166 loop : -0.00 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.013 0.001 TYR A 808 PHE 0.010 0.001 PHE B 600 TRP 0.009 0.001 TRP A 761 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00254 (11554) covalent geometry : angle 0.52076 (15726) SS BOND : bond 0.00117 ( 10) SS BOND : angle 0.78411 ( 20) hydrogen bonds : bond 0.04689 ( 369) hydrogen bonds : angle 5.06939 ( 957) link_ALPHA1-3 : bond 0.00783 ( 2) link_ALPHA1-3 : angle 1.56711 ( 6) link_BETA1-4 : bond 0.00516 ( 6) link_BETA1-4 : angle 1.52114 ( 18) link_NAG-ASN : bond 0.00072 ( 4) link_NAG-ASN : angle 3.13934 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4273.12 seconds wall clock time: 73 minutes 23.51 seconds (4403.51 seconds total)