Starting phenix.real_space_refine on Tue Jul 29 14:18:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7au2_11923/07_2025/7au2_11923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7au2_11923/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2025/7au2_11923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2025/7au2_11923.map" model { file = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2025/7au2_11923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7au2_11923/07_2025/7au2_11923.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} 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: E, F, B Time building chain proxies: 12.39, per 1000 atoms: 1.10 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.22 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: 4.52 Time building geometry restraints manager: 3.38 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: 0.11 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.460 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:19.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 266 HIS 0.005 0.002 HIS B 877 PHE 0.024 0.002 PHE B 600 TYR 0.023 0.002 TYR A 791 ARG 0.017 0.001 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 4) link_NAG-ASN : angle 4.26266 ( 12) link_BETA1-4 : bond 0.00570 ( 6) link_BETA1-4 : angle 1.99186 ( 18) link_ALPHA1-3 : bond 0.00980 ( 2) link_ALPHA1-3 : angle 2.75765 ( 6) hydrogen bonds : bond 0.19012 ( 369) hydrogen bonds : angle 6.49082 ( 957) SS BOND : bond 0.00416 ( 10) SS BOND : angle 1.44318 ( 20) covalent geometry : bond 0.00522 (11554) covalent geometry : angle 0.70879 (15726) *********************** 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 : 1.431 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 1.6992 time to fit residues: 251.3309 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 : 1.220 ------------------------------------------------------------------------------- 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 114 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.140801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106808 restraints weight = 11347.217| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.71 r_work: 0.3029 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11576 Z= 0.148 Angle : 0.612 6.366 15782 Z= 0.323 Chirality : 0.046 0.148 1752 Planarity : 0.005 0.048 2004 Dihedral : 8.230 67.242 1760 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.07 % Allowed : 7.27 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1356 helix: 0.87 (0.25), residues: 452 sheet: -0.66 (0.39), residues: 172 loop : 0.05 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 761 HIS 0.005 0.001 HIS A 776 PHE 0.014 0.002 PHE A 206 TYR 0.016 0.002 TYR A 808 ARG 0.010 0.001 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 4) link_NAG-ASN : angle 3.55129 ( 12) link_BETA1-4 : bond 0.00529 ( 6) link_BETA1-4 : angle 2.06622 ( 18) link_ALPHA1-3 : bond 0.01207 ( 2) link_ALPHA1-3 : angle 2.53340 ( 6) hydrogen bonds : bond 0.05718 ( 369) hydrogen bonds : angle 5.36337 ( 957) SS BOND : bond 0.00185 ( 10) SS BOND : angle 0.98896 ( 20) covalent geometry : bond 0.00342 (11554) covalent geometry : angle 0.59762 (15726) *********************** 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 162 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.189 Fit side-chains REVERT: A 330 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 824 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7988 (tmt) REVERT: B 330 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 824 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7973 (tmt) outliers start: 25 outliers final: 6 residues processed: 147 average time/residue: 1.4735 time to fit residues: 231.7561 Evaluate side-chains 141 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 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 114 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 0.0000 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 307 GLN B 216 GLN B 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105590 restraints weight = 11480.039| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.74 r_work: 0.3012 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1216 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= 0.157 Angle : 0.603 6.374 15782 Z= 0.319 Chirality : 0.046 0.149 1752 Planarity : 0.005 0.043 2004 Dihedral : 7.387 55.643 1754 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.15 % Allowed : 8.68 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1356 helix: 1.02 (0.25), residues: 452 sheet: -0.74 (0.38), residues: 172 loop : 0.03 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 266 HIS 0.005 0.001 HIS B 265 PHE 0.014 0.002 PHE B 804 TYR 0.014 0.001 TYR A 808 ARG 0.009 0.001 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 4) link_NAG-ASN : angle 3.35473 ( 12) link_BETA1-4 : bond 0.00510 ( 6) link_BETA1-4 : angle 1.91070 ( 18) link_ALPHA1-3 : bond 0.01047 ( 2) link_ALPHA1-3 : angle 1.75798 ( 6) hydrogen bonds : bond 0.05979 ( 369) hydrogen bonds : angle 5.31810 ( 957) SS BOND : bond 0.00214 ( 10) SS BOND : angle 0.98481 ( 20) covalent geometry : bond 0.00365 (11554) covalent geometry : angle 0.59105 (15726) *********************** 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 168 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.359 Fit side-chains REVERT: A 330 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A 824 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.7965 (tmt) REVERT: B 257 GLU cc_start: 0.8329 (tt0) cc_final: 0.8074 (tt0) REVERT: B 330 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 824 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7965 (tmt) outliers start: 26 outliers final: 10 residues processed: 150 average time/residue: 1.5107 time to fit residues: 242.2762 Evaluate side-chains 147 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 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 305 THR 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 23 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.141027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106796 restraints weight = 11303.691| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.72 r_work: 0.3027 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1396 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= 0.131 Angle : 0.566 5.945 15782 Z= 0.298 Chirality : 0.044 0.161 1752 Planarity : 0.005 0.043 2004 Dihedral : 6.277 39.288 1754 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.31 % Allowed : 8.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1356 helix: 1.14 (0.25), residues: 452 sheet: -0.79 (0.39), residues: 168 loop : 0.00 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 266 HIS 0.004 0.001 HIS B 616 PHE 0.011 0.002 PHE A 804 TYR 0.014 0.001 TYR A 808 ARG 0.008 0.000 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 4) link_NAG-ASN : angle 3.23586 ( 12) link_BETA1-4 : bond 0.00522 ( 6) link_BETA1-4 : angle 1.81399 ( 18) link_ALPHA1-3 : bond 0.01073 ( 2) link_ALPHA1-3 : angle 1.94314 ( 6) hydrogen bonds : bond 0.05217 ( 369) hydrogen bonds : angle 5.20681 ( 957) SS BOND : bond 0.00143 ( 10) SS BOND : angle 0.89907 ( 20) covalent geometry : bond 0.00298 (11554) covalent geometry : angle 0.55457 (15726) *********************** 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 160 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.592 Fit side-chains REVERT: A 330 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: A 824 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7951 (tmt) REVERT: B 330 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: B 824 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.7957 (tmt) outliers start: 28 outliers final: 15 residues processed: 144 average time/residue: 1.8404 time to fit residues: 285.1318 Evaluate side-chains 148 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain B residue 252 ARG 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 824 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 115 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.139394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.104988 restraints weight = 11322.961| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.73 r_work: 0.3001 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11576 Z= 0.176 Angle : 0.617 6.546 15782 Z= 0.326 Chirality : 0.047 0.174 1752 Planarity : 0.005 0.049 2004 Dihedral : 5.928 32.066 1754 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.40 % Allowed : 9.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1356 helix: 1.02 (0.25), residues: 452 sheet: -0.77 (0.39), residues: 168 loop : -0.08 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 266 HIS 0.005 0.002 HIS A 616 PHE 0.015 0.002 PHE A 600 TYR 0.016 0.002 TYR B 808 ARG 0.007 0.001 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 4) link_NAG-ASN : angle 3.46347 ( 12) link_BETA1-4 : bond 0.00522 ( 6) link_BETA1-4 : angle 1.92334 ( 18) link_ALPHA1-3 : bond 0.00995 ( 2) link_ALPHA1-3 : angle 2.08516 ( 6) hydrogen bonds : bond 0.06170 ( 369) hydrogen bonds : angle 5.27380 ( 957) SS BOND : bond 0.00271 ( 10) SS BOND : angle 1.01645 ( 20) covalent geometry : bond 0.00416 (11554) covalent geometry : angle 0.60523 (15726) *********************** 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: 29 poor density : 135 time to evaluate : 1.221 Fit side-chains REVERT: A 330 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 648 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6541 (mmtp) REVERT: A 824 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7925 (tmt) REVERT: B 330 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 648 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6530 (mmtp) REVERT: B 824 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.7930 (tmt) outliers start: 29 outliers final: 16 residues processed: 149 average time/residue: 2.0942 time to fit residues: 333.6233 Evaluate side-chains 153 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 2.736 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.141133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.106581 restraints weight = 11440.582| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.75 r_work: 0.3029 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1577 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= 0.126 Angle : 0.555 5.853 15782 Z= 0.292 Chirality : 0.044 0.146 1752 Planarity : 0.005 0.044 2004 Dihedral : 5.342 28.661 1754 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.81 % Allowed : 9.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1356 helix: 1.18 (0.25), residues: 452 sheet: -0.73 (0.40), residues: 166 loop : -0.04 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 266 HIS 0.004 0.001 HIS B 616 PHE 0.011 0.002 PHE A 600 TYR 0.015 0.001 TYR A 808 ARG 0.007 0.000 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 4) link_NAG-ASN : angle 3.24839 ( 12) link_BETA1-4 : bond 0.00551 ( 6) link_BETA1-4 : angle 1.68778 ( 18) link_ALPHA1-3 : bond 0.01011 ( 2) link_ALPHA1-3 : angle 1.79843 ( 6) hydrogen bonds : bond 0.05059 ( 369) hydrogen bonds : angle 5.17373 ( 957) SS BOND : bond 0.00177 ( 10) SS BOND : angle 0.87814 ( 20) covalent geometry : bond 0.00284 (11554) covalent geometry : angle 0.54331 (15726) *********************** 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 167 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 824 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7922 (tmt) REVERT: B 330 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: B 824 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7922 (tmt) outliers start: 34 outliers final: 21 residues processed: 149 average time/residue: 2.3003 time to fit residues: 365.6538 Evaluate side-chains 151 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 252 ARG 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 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 103 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.138024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103638 restraints weight = 11430.077| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.73 r_work: 0.2985 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11576 Z= 0.229 Angle : 0.676 6.850 15782 Z= 0.357 Chirality : 0.049 0.179 1752 Planarity : 0.006 0.055 2004 Dihedral : 5.645 26.806 1754 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.06 % Allowed : 9.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1356 helix: 0.86 (0.25), residues: 452 sheet: -0.73 (0.41), residues: 166 loop : -0.13 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 855 HIS 0.006 0.002 HIS A 616 PHE 0.017 0.003 PHE A 520 TYR 0.017 0.002 TYR A 808 ARG 0.006 0.001 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 4) link_NAG-ASN : angle 3.72085 ( 12) link_BETA1-4 : bond 0.00585 ( 6) link_BETA1-4 : angle 2.02440 ( 18) link_ALPHA1-3 : bond 0.00845 ( 2) link_ALPHA1-3 : angle 2.04199 ( 6) hydrogen bonds : bond 0.06973 ( 369) hydrogen bonds : angle 5.36405 ( 957) SS BOND : bond 0.00373 ( 10) SS BOND : angle 1.13200 ( 20) covalent geometry : bond 0.00555 (11554) covalent geometry : angle 0.66363 (15726) *********************** 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 169 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: A 405 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7094 (mptp) REVERT: A 648 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6599 (mmtp) REVERT: A 674 GLU cc_start: 0.6809 (tp30) cc_final: 0.6325 (tt0) REVERT: A 824 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8036 (ttt) REVERT: B 330 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: B 405 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7072 (mptp) REVERT: B 648 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6584 (mmtp) REVERT: B 674 GLU cc_start: 0.6789 (tp30) cc_final: 0.6335 (tt0) REVERT: B 824 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8043 (ttt) outliers start: 37 outliers final: 18 residues processed: 150 average time/residue: 1.5754 time to fit residues: 253.2255 Evaluate side-chains 153 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 129 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.141277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106974 restraints weight = 11403.513| |-----------------------------------------------------------------------------| r_work (start): 0.3181 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: 3.82 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 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 0.022 11576 Z= 0.114 Angle : 0.546 5.719 15782 Z= 0.287 Chirality : 0.043 0.135 1752 Planarity : 0.005 0.047 2004 Dihedral : 5.096 25.600 1754 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.15 % Allowed : 10.74 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1356 helix: 1.15 (0.25), residues: 452 sheet: -0.72 (0.41), residues: 166 loop : -0.05 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 761 HIS 0.004 0.001 HIS A 616 PHE 0.012 0.001 PHE A 600 TYR 0.015 0.001 TYR A 808 ARG 0.007 0.000 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 4) link_NAG-ASN : angle 3.27154 ( 12) link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 1.61187 ( 18) link_ALPHA1-3 : bond 0.00995 ( 2) link_ALPHA1-3 : angle 1.76078 ( 6) hydrogen bonds : bond 0.04886 ( 369) hydrogen bonds : angle 5.19906 ( 957) SS BOND : bond 0.00438 ( 10) SS BOND : angle 0.90507 ( 20) covalent geometry : bond 0.00247 (11554) covalent geometry : angle 0.53497 (15726) *********************** 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 147 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: A 405 LYS cc_start: 0.8036 (mtpt) cc_final: 0.6978 (mptp) REVERT: A 824 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7930 (tmt) REVERT: B 330 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: B 405 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7000 (mptp) REVERT: B 648 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6510 (mmtp) REVERT: B 824 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7939 (tmt) outliers start: 26 outliers final: 15 residues processed: 138 average time/residue: 1.6233 time to fit residues: 239.4351 Evaluate side-chains 141 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 252 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105163 restraints weight = 11329.958| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.73 r_work: 0.3006 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11576 Z= 0.171 Angle : 0.606 6.329 15782 Z= 0.319 Chirality : 0.046 0.156 1752 Planarity : 0.005 0.049 2004 Dihedral : 5.195 27.022 1754 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.31 % Allowed : 10.58 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1356 helix: 1.03 (0.25), residues: 452 sheet: -0.73 (0.41), residues: 166 loop : -0.10 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 266 HIS 0.004 0.001 HIS B 265 PHE 0.013 0.002 PHE B 520 TYR 0.017 0.002 TYR A 808 ARG 0.006 0.001 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 4) link_NAG-ASN : angle 3.45159 ( 12) link_BETA1-4 : bond 0.00550 ( 6) link_BETA1-4 : angle 1.78114 ( 18) link_ALPHA1-3 : bond 0.00865 ( 2) link_ALPHA1-3 : angle 1.76849 ( 6) hydrogen bonds : bond 0.05987 ( 369) hydrogen bonds : angle 5.26561 ( 957) SS BOND : bond 0.00199 ( 10) SS BOND : angle 0.98771 ( 20) covalent geometry : bond 0.00404 (11554) covalent geometry : angle 0.59471 (15726) *********************** 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 158 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 405 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7033 (mptp) REVERT: A 411 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: A 648 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6545 (mmtp) REVERT: A 674 GLU cc_start: 0.6736 (tp30) cc_final: 0.6243 (tt0) REVERT: A 824 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7921 (tmt) REVERT: B 330 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: B 405 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7021 (mptp) REVERT: B 411 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: B 648 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6519 (mmtp) REVERT: B 674 GLU cc_start: 0.6731 (tp30) cc_final: 0.6246 (tt0) REVERT: B 824 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8011 (ttt) outliers start: 28 outliers final: 17 residues processed: 151 average time/residue: 1.5377 time to fit residues: 248.2834 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 : 1.236 ------------------------------------------------------------------------------- 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 411 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 268 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 411 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.139575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104552 restraints weight = 11341.157| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.75 r_work: 0.2997 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1711 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= 0.173 Angle : 0.612 6.563 15782 Z= 0.323 Chirality : 0.046 0.158 1752 Planarity : 0.005 0.050 2004 Dihedral : 5.210 29.359 1754 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.23 % Allowed : 10.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1356 helix: 1.01 (0.25), residues: 452 sheet: -0.80 (0.40), residues: 166 loop : -0.10 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 266 HIS 0.005 0.001 HIS A 616 PHE 0.013 0.002 PHE A 520 TYR 0.016 0.002 TYR B 808 ARG 0.007 0.001 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 4) link_NAG-ASN : angle 3.50017 ( 12) link_BETA1-4 : bond 0.00557 ( 6) link_BETA1-4 : angle 1.75803 ( 18) link_ALPHA1-3 : bond 0.00819 ( 2) link_ALPHA1-3 : angle 1.77918 ( 6) hydrogen bonds : bond 0.05948 ( 369) hydrogen bonds : angle 5.27712 ( 957) SS BOND : bond 0.00233 ( 10) SS BOND : angle 0.98460 ( 20) covalent geometry : bond 0.00410 (11554) covalent geometry : angle 0.60090 (15726) ********************** 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 155 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 405 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7003 (mptp) REVERT: A 411 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: A 648 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6536 (mmtp) REVERT: A 674 GLU cc_start: 0.6771 (tp30) cc_final: 0.6281 (tt0) REVERT: A 824 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7965 (tmt) REVERT: B 330 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: B 405 LYS cc_start: 0.8032 (mtpt) cc_final: 0.6979 (mptp) REVERT: B 411 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: B 648 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6550 (mmtp) REVERT: B 674 GLU cc_start: 0.6764 (tp30) cc_final: 0.6279 (tt0) REVERT: B 824 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7963 (tmt) outliers start: 27 outliers final: 17 residues processed: 149 average time/residue: 1.7687 time to fit residues: 283.2909 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 : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 411 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 330 GLU Chi-restraints excluded: chain B residue 411 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 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 = 0.3603 r_free = 0.3603 target = 0.139874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105539 restraints weight = 11346.166| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.73 r_work: 0.3013 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11576 Z= 0.152 Angle : 0.588 6.182 15782 Z= 0.310 Chirality : 0.045 0.145 1752 Planarity : 0.005 0.048 2004 Dihedral : 5.091 29.795 1754 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.23 % Allowed : 11.07 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1356 helix: 1.07 (0.25), residues: 452 sheet: -0.80 (0.40), residues: 166 loop : -0.07 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 266 HIS 0.004 0.001 HIS B 616 PHE 0.012 0.002 PHE A 600 TYR 0.015 0.001 TYR B 808 ARG 0.007 0.000 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 4) link_NAG-ASN : angle 3.41777 ( 12) link_BETA1-4 : bond 0.00555 ( 6) link_BETA1-4 : angle 1.69105 ( 18) link_ALPHA1-3 : bond 0.00789 ( 2) link_ALPHA1-3 : angle 1.68654 ( 6) hydrogen bonds : bond 0.05587 ( 369) hydrogen bonds : angle 5.24590 ( 957) SS BOND : bond 0.00235 ( 10) SS BOND : angle 0.95199 ( 20) covalent geometry : bond 0.00356 (11554) covalent geometry : angle 0.57672 (15726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9340.63 seconds wall clock time: 167 minutes 43.57 seconds (10063.57 seconds total)