Starting phenix.real_space_refine on Wed Mar 4 18:50:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzf_24758/03_2026/7rzf_24758.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzf_24758/03_2026/7rzf_24758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rzf_24758/03_2026/7rzf_24758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzf_24758/03_2026/7rzf_24758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rzf_24758/03_2026/7rzf_24758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzf_24758/03_2026/7rzf_24758.map" } resolution = 3.4 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= 0.003 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 45 5.16 5 C 10044 2.51 5 N 2613 2.21 5 O 2882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15584 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7763 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 51, 'TRANS': 896} Chain breaks: 1 Chain: "B" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7704 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 49, 'TRANS': 890} Chain breaks: 1 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain breaks: 1 Chain: "b" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Time building chain proxies: 3.09, per 1000 atoms: 0.20 Number of scatterers: 15584 At special positions: 0 Unit cell: (156.125, 133.357, 116.009, 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 45 16.00 O 2882 8.00 N 2613 7.00 C 10044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 6 " - pdb=" SG CYS a 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 582.7 milliseconds 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3628 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 13 sheets defined 45.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.624A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.985A pdb=" N PHE A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.514A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 removed outlier: 4.218A pdb=" N VAL A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.524A pdb=" N ARG A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 267 through 273 removed outlier: 3.724A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.531A pdb=" N LEU A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.654A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 403 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.683A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 3.617A pdb=" N TYR A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.802A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.904A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 3.862A pdb=" N ALA A 593 " --> pdb=" O HIS A 589 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.627A pdb=" N LEU A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.725A pdb=" N GLU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 677 through 690 removed outlier: 3.844A pdb=" N ARG A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.663A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 Proline residue: A 717 - end of helix Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.630A pdb=" N LEU A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.954A pdb=" N LEU A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 removed outlier: 3.752A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 877 removed outlier: 3.520A pdb=" N LEU A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 3.516A pdb=" N PHE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 912 removed outlier: 3.736A pdb=" N LYS A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 932 through 945 removed outlier: 3.846A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.506A pdb=" N HIS B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.720A pdb=" N PHE B 168 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 4.269A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.639A pdb=" N ARG B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.599A pdb=" N LEU B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 227 " --> pdb=" O LYS B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.620A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 248 removed outlier: 3.716A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.756A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.518A pdb=" N GLY B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.624A pdb=" N ILE B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.644A pdb=" N ILE B 510 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 514 " --> pdb=" O ILE B 510 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 3.997A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 586 through 613 removed outlier: 4.928A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 651 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 673 through 676 removed outlier: 3.940A pdb=" N GLU B 676 " --> pdb=" O PHE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 677 through 691 Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.943A pdb=" N ASP B 705 " --> pdb=" O LYS B 701 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 Proline residue: B 717 - end of helix removed outlier: 4.303A pdb=" N ARG B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 Processing helix chain 'B' and resid 801 through 815 removed outlier: 4.081A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 823 removed outlier: 3.520A pdb=" N ALA B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 876 removed outlier: 3.739A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.693A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.616A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 932 through 945 removed outlier: 3.646A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET B 943 " --> pdb=" O PHE B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 4.587A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.364A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 87 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 4.492A pdb=" N PHE A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 366 " --> pdb=" O PHE A 370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AA4, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.731A pdb=" N ARG A 491 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 557 through 558 removed outlier: 6.124A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 558 removed outlier: 6.124A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 724 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 832 through 840 removed outlier: 4.561A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 836 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN A 844 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 778 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 69 removed outlier: 6.208A pdb=" N LYS B 74 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL B 258 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU B 76 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLY B 260 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE B 78 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 91 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 86 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AB1, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB2, first strand: chain 'B' and resid 549 through 553 removed outlier: 6.011A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLY B 731 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LYS B 562 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.189A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.189A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY B 790 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER B 852 " --> pdb=" O GLY B 790 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU B 792 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE B 850 " --> pdb=" O GLU B 792 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR B 794 " --> pdb=" O PHE B 848 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE B 848 " --> pdb=" O TYR B 794 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN B 796 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 846 " --> pdb=" O GLN B 796 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 798 " --> pdb=" O GLN B 844 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4371 1.33 - 1.45: 2822 1.45 - 1.57: 8688 1.57 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 15970 Sorted by residual: bond pdb=" N ASP B 586 " pdb=" CA ASP B 586 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.73e+01 bond pdb=" N ASP B 99 " pdb=" CA ASP B 99 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.73e+01 bond pdb=" N VAL B 707 " pdb=" CA VAL B 707 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.19e-02 7.06e+03 1.16e+01 bond pdb=" N ILE B 235 " pdb=" CA ILE B 235 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.66e+00 bond pdb=" N VAL B 769 " pdb=" CA VAL B 769 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.48e+00 ... (remaining 15965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19814 2.05 - 4.10: 1508 4.10 - 6.14: 219 6.14 - 8.19: 40 8.19 - 10.24: 10 Bond angle restraints: 21591 Sorted by residual: angle pdb=" N LEU B 763 " pdb=" CA LEU B 763 " pdb=" C LEU B 763 " ideal model delta sigma weight residual 112.57 103.72 8.85 1.13e+00 7.83e-01 6.13e+01 angle pdb=" N SER B 96 " pdb=" CA SER B 96 " pdb=" C SER B 96 " ideal model delta sigma weight residual 112.54 106.53 6.01 1.22e+00 6.72e-01 2.43e+01 angle pdb=" C ILE A 912 " pdb=" CA ILE A 912 " pdb=" CB ILE A 912 " ideal model delta sigma weight residual 111.29 103.29 8.00 1.64e+00 3.72e-01 2.38e+01 angle pdb=" C ALA A 367 " pdb=" CA ALA A 367 " pdb=" CB ALA A 367 " ideal model delta sigma weight residual 116.54 111.42 5.12 1.15e+00 7.56e-01 1.98e+01 angle pdb=" CA HIS B 291 " pdb=" C HIS B 291 " pdb=" O HIS B 291 " ideal model delta sigma weight residual 120.19 116.55 3.64 8.40e-01 1.42e+00 1.88e+01 ... (remaining 21586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8904 18.00 - 36.00: 625 36.00 - 53.99: 114 53.99 - 71.99: 17 71.99 - 89.99: 10 Dihedral angle restraints: 9670 sinusoidal: 4060 harmonic: 5610 Sorted by residual: dihedral pdb=" CA LYS A 511 " pdb=" C LYS A 511 " pdb=" N LYS A 512 " pdb=" CA LYS A 512 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN B 800 " pdb=" C GLN B 800 " pdb=" N SER B 801 " pdb=" CA SER B 801 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ARG A 261 " pdb=" C ARG A 261 " pdb=" N GLU A 262 " pdb=" CA GLU A 262 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 9667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1728 0.074 - 0.148: 509 0.148 - 0.223: 71 0.223 - 0.297: 8 0.297 - 0.371: 5 Chirality restraints: 2321 Sorted by residual: chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CG LEU B 77 " pdb=" CB LEU B 77 " pdb=" CD1 LEU B 77 " pdb=" CD2 LEU B 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA LEU B 763 " pdb=" N LEU B 763 " pdb=" C LEU B 763 " pdb=" CB LEU B 763 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 2318 not shown) Planarity restraints: 2791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 461 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO B 461 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO B 461 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 462 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 666 " 0.032 2.00e-02 2.50e+03 2.18e-02 9.53e+00 pdb=" CG TYR A 666 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 666 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 666 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 666 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 666 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 666 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 666 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 866 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.15e+00 pdb=" C PHE B 866 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE B 866 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU B 867 " 0.018 2.00e-02 2.50e+03 ... (remaining 2788 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 6 2.14 - 2.83: 4881 2.83 - 3.52: 21112 3.52 - 4.21: 35831 4.21 - 4.90: 61454 Nonbonded interactions: 123284 Sorted by model distance: nonbonded pdb=" CZ ARG B 229 " pdb=" OE2 GLU B 233 " model vdw 1.454 3.270 nonbonded pdb=" NE ARG B 229 " pdb=" OE2 GLU B 233 " model vdw 1.702 3.120 nonbonded pdb=" NH2 ARG B 229 " pdb=" OE2 GLU B 233 " model vdw 1.711 3.120 nonbonded pdb=" O HIS A 134 " pdb=" OG SER A 154 " model vdw 2.090 3.040 nonbonded pdb=" OG1 THR A 623 " pdb=" O GLY A 626 " model vdw 2.136 3.040 ... (remaining 123279 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 47 through 962 or resid 989 through 1011)) selection = (chain 'B' and resid 47 through 1011) } 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.120 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.009 0.074 15971 Z= 0.422 Angle : 1.186 10.238 21593 Z= 0.680 Chirality : 0.069 0.371 2321 Planarity : 0.008 0.062 2791 Dihedral : 12.934 89.990 6039 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.41 % Allowed : 1.94 % Favored : 97.64 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.16), residues: 1889 helix: -3.00 (0.13), residues: 776 sheet: -1.87 (0.26), residues: 347 loop : -2.55 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG B 711 TYR 0.052 0.004 TYR A 666 PHE 0.047 0.004 PHE B 866 TRP 0.050 0.004 TRP B 695 HIS 0.016 0.003 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00853 (15970) covalent geometry : angle 1.18582 (21591) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.25096 ( 2) hydrogen bonds : bond 0.16661 ( 675) hydrogen bonds : angle 7.80704 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 358 THR cc_start: 0.7562 (t) cc_final: 0.7278 (m) REVERT: A 426 ASP cc_start: 0.7180 (p0) cc_final: 0.6959 (p0) REVERT: A 779 TYR cc_start: 0.6866 (p90) cc_final: 0.5854 (p90) REVERT: B 62 ARG cc_start: 0.3970 (mtm-85) cc_final: 0.3731 (mtm-85) REVERT: B 332 HIS cc_start: 0.5921 (t-90) cc_final: 0.5648 (t70) REVERT: B 429 ARG cc_start: 0.6480 (tpt-90) cc_final: 0.6009 (tpt90) REVERT: B 855 PRO cc_start: 0.7719 (Cg_exo) cc_final: 0.7473 (Cg_endo) REVERT: B 993 GLN cc_start: 0.7136 (mp10) cc_final: 0.6936 (mp10) outliers start: 7 outliers final: 2 residues processed: 229 average time/residue: 0.1218 time to fit residues: 41.8626 Evaluate side-chains 136 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 688 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN B 93 HIS B 232 GLN B 442 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 770 GLN B 844 GLN ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 GLN b 3 ASN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.142074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108920 restraints weight = 31339.993| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.23 r_work: 0.3501 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15971 Z= 0.138 Angle : 0.673 8.627 21593 Z= 0.349 Chirality : 0.045 0.187 2321 Planarity : 0.005 0.042 2791 Dihedral : 5.649 58.724 2067 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.24 % Allowed : 7.72 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.17), residues: 1889 helix: -1.15 (0.16), residues: 789 sheet: -1.44 (0.25), residues: 366 loop : -1.97 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 477 TYR 0.023 0.002 TYR A 594 PHE 0.031 0.002 PHE B 866 TRP 0.018 0.002 TRP A 776 HIS 0.006 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00298 (15970) covalent geometry : angle 0.67309 (21591) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.45672 ( 2) hydrogen bonds : bond 0.04855 ( 675) hydrogen bonds : angle 5.60753 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.7481 (tpp) cc_final: 0.6921 (tpp) REVERT: A 145 GLU cc_start: 0.8041 (tp30) cc_final: 0.7210 (tm-30) REVERT: A 514 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7033 (pt0) REVERT: A 620 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8194 (tp) REVERT: A 723 LEU cc_start: 0.8600 (pp) cc_final: 0.8363 (pp) REVERT: A 742 MET cc_start: 0.8098 (tpp) cc_final: 0.7852 (tpp) REVERT: A 779 TYR cc_start: 0.6850 (p90) cc_final: 0.5838 (p90) REVERT: A 990 GLU cc_start: 0.7469 (pm20) cc_final: 0.7112 (pm20) REVERT: B 62 ARG cc_start: 0.4073 (mtm-85) cc_final: 0.3719 (mtm-85) REVERT: B 332 HIS cc_start: 0.5950 (t-90) cc_final: 0.5702 (t70) REVERT: B 429 ARG cc_start: 0.6082 (tpt-90) cc_final: 0.5610 (tpt90) REVERT: B 627 MET cc_start: 0.7066 (ttm) cc_final: 0.6812 (ttp) REVERT: B 744 MET cc_start: 0.8027 (tmm) cc_final: 0.7732 (tmm) REVERT: B 855 PRO cc_start: 0.7384 (Cg_exo) cc_final: 0.6981 (Cg_endo) REVERT: B 857 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6308 (p-80) REVERT: B 870 MET cc_start: 0.7133 (mpp) cc_final: 0.6430 (mmm) REVERT: B 917 ASN cc_start: 0.7165 (t0) cc_final: 0.6846 (t0) REVERT: b 1 PHE cc_start: 0.6005 (t80) cc_final: 0.5471 (t80) outliers start: 21 outliers final: 13 residues processed: 207 average time/residue: 0.1036 time to fit residues: 33.9833 Evaluate side-chains 156 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 92 optimal weight: 0.0470 chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN B 134 HIS B 245 HIS ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 ASN B 844 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.139211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.106104 restraints weight = 31594.407| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.13 r_work: 0.3464 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15971 Z= 0.191 Angle : 0.682 9.728 21593 Z= 0.352 Chirality : 0.046 0.173 2321 Planarity : 0.005 0.040 2791 Dihedral : 5.498 59.869 2067 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.18 % Allowed : 10.02 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.18), residues: 1889 helix: -0.33 (0.18), residues: 787 sheet: -1.07 (0.25), residues: 370 loop : -1.85 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 477 TYR 0.024 0.002 TYR A 666 PHE 0.037 0.002 PHE B 866 TRP 0.021 0.002 TRP A 776 HIS 0.008 0.001 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00441 (15970) covalent geometry : angle 0.68223 (21591) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.46025 ( 2) hydrogen bonds : bond 0.04831 ( 675) hydrogen bonds : angle 5.28710 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.497 Fit side-chains REVERT: A 113 MET cc_start: 0.7523 (tpp) cc_final: 0.6957 (tpp) REVERT: A 145 GLU cc_start: 0.7741 (tp30) cc_final: 0.7185 (tm-30) REVERT: A 168 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.5568 (t80) REVERT: A 224 TYR cc_start: 0.8112 (t80) cc_final: 0.7841 (t80) REVERT: A 699 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7292 (mt-10) REVERT: A 779 TYR cc_start: 0.7007 (p90) cc_final: 0.5831 (p90) REVERT: B 62 ARG cc_start: 0.3740 (mtm-85) cc_final: 0.3198 (mtm-85) REVERT: B 267 LEU cc_start: 0.3977 (OUTLIER) cc_final: 0.3641 (mt) REVERT: B 429 ARG cc_start: 0.6299 (tpt-90) cc_final: 0.5930 (tpt90) REVERT: B 857 HIS cc_start: 0.6617 (OUTLIER) cc_final: 0.6090 (p-80) REVERT: B 866 PHE cc_start: 0.8761 (t80) cc_final: 0.7713 (t80) REVERT: B 870 MET cc_start: 0.7105 (mpp) cc_final: 0.6852 (mmm) REVERT: B 917 ASN cc_start: 0.7316 (t0) cc_final: 0.7003 (t0) REVERT: b 1 PHE cc_start: 0.6202 (t80) cc_final: 0.5890 (t80) outliers start: 37 outliers final: 22 residues processed: 192 average time/residue: 0.1122 time to fit residues: 33.7607 Evaluate side-chains 168 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 150 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 98 optimal weight: 50.0000 chunk 31 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 332 HIS A 982 GLN B 108 HIS B 752 HIS b 5 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.139672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.105310 restraints weight = 31404.996| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.06 r_work: 0.3476 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15971 Z= 0.145 Angle : 0.603 8.427 21593 Z= 0.312 Chirality : 0.044 0.227 2321 Planarity : 0.004 0.039 2791 Dihedral : 5.238 59.677 2067 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.77 % Allowed : 10.96 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1889 helix: 0.02 (0.18), residues: 798 sheet: -0.75 (0.26), residues: 367 loop : -1.76 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 477 TYR 0.021 0.002 TYR A 779 PHE 0.031 0.001 PHE B 866 TRP 0.029 0.002 TRP A 776 HIS 0.007 0.001 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00330 (15970) covalent geometry : angle 0.60320 (21591) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.52488 ( 2) hydrogen bonds : bond 0.04301 ( 675) hydrogen bonds : angle 5.02466 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.644 Fit side-chains REVERT: A 112 HIS cc_start: 0.7065 (t-170) cc_final: 0.6850 (t70) REVERT: A 145 GLU cc_start: 0.7878 (tp30) cc_final: 0.7332 (tm-30) REVERT: A 146 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.6720 (p-80) REVERT: A 224 TYR cc_start: 0.8013 (t80) cc_final: 0.7724 (t80) REVERT: A 723 LEU cc_start: 0.8607 (pp) cc_final: 0.7726 (mt) REVERT: A 776 TRP cc_start: 0.6593 (t-100) cc_final: 0.6011 (t-100) REVERT: A 779 TYR cc_start: 0.7169 (p90) cc_final: 0.5759 (p90) REVERT: A 982 GLN cc_start: 0.6930 (tp40) cc_final: 0.6674 (tp40) REVERT: B 267 LEU cc_start: 0.3962 (OUTLIER) cc_final: 0.3738 (mt) REVERT: B 470 LYS cc_start: 0.8488 (tppt) cc_final: 0.8219 (mtmt) REVERT: B 798 ASP cc_start: 0.7675 (t0) cc_final: 0.7461 (m-30) REVERT: B 857 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.6029 (p-80) REVERT: B 866 PHE cc_start: 0.8825 (t80) cc_final: 0.7761 (t80) REVERT: B 870 MET cc_start: 0.7189 (mpp) cc_final: 0.6897 (mmm) REVERT: B 917 ASN cc_start: 0.7326 (t0) cc_final: 0.7003 (t0) REVERT: B 943 MET cc_start: 0.7987 (mmt) cc_final: 0.7753 (mmt) REVERT: b 5 HIS cc_start: 0.6282 (OUTLIER) cc_final: 0.5856 (m-70) outliers start: 47 outliers final: 27 residues processed: 190 average time/residue: 0.1037 time to fit residues: 31.4078 Evaluate side-chains 173 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 134 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.138185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104752 restraints weight = 31636.674| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.24 r_work: 0.3441 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15971 Z= 0.172 Angle : 0.638 8.377 21593 Z= 0.327 Chirality : 0.044 0.146 2321 Planarity : 0.004 0.038 2791 Dihedral : 5.295 59.689 2067 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.95 % Allowed : 11.79 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 1889 helix: 0.17 (0.18), residues: 791 sheet: -0.61 (0.26), residues: 363 loop : -1.81 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 477 TYR 0.021 0.002 TYR A 779 PHE 0.032 0.002 PHE B 866 TRP 0.020 0.002 TRP A 776 HIS 0.021 0.001 HIS b 5 Details of bonding type rmsd covalent geometry : bond 0.00399 (15970) covalent geometry : angle 0.63799 (21591) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.50829 ( 2) hydrogen bonds : bond 0.04459 ( 675) hydrogen bonds : angle 5.04235 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 0.603 Fit side-chains REVERT: A 112 HIS cc_start: 0.7123 (t-170) cc_final: 0.6835 (t70) REVERT: A 145 GLU cc_start: 0.8011 (tp30) cc_final: 0.7504 (tm-30) REVERT: A 146 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.6836 (p-80) REVERT: A 168 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.5737 (t80) REVERT: A 699 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 1011 HIS cc_start: 0.6339 (t-90) cc_final: 0.6035 (t-170) REVERT: B 254 MET cc_start: 0.5821 (tmm) cc_final: 0.5470 (mmt) REVERT: B 267 LEU cc_start: 0.3895 (OUTLIER) cc_final: 0.3569 (mt) REVERT: B 470 LYS cc_start: 0.8474 (tppt) cc_final: 0.8142 (mtmm) REVERT: B 490 ASP cc_start: 0.4469 (m-30) cc_final: 0.4190 (p0) REVERT: B 702 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: B 798 ASP cc_start: 0.7794 (t0) cc_final: 0.7568 (m-30) REVERT: B 823 LEU cc_start: 0.6501 (mt) cc_final: 0.5910 (mt) REVERT: B 857 HIS cc_start: 0.6557 (OUTLIER) cc_final: 0.6107 (p-80) REVERT: B 870 MET cc_start: 0.7407 (mpp) cc_final: 0.6813 (mmm) REVERT: B 943 MET cc_start: 0.8009 (mmt) cc_final: 0.7790 (mmt) outliers start: 50 outliers final: 35 residues processed: 177 average time/residue: 0.1040 time to fit residues: 29.5200 Evaluate side-chains 172 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 152 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 120 optimal weight: 0.0470 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A 982 GLN B 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.136731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.103025 restraints weight = 31603.897| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.23 r_work: 0.3413 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15971 Z= 0.186 Angle : 0.653 8.797 21593 Z= 0.334 Chirality : 0.045 0.175 2321 Planarity : 0.004 0.041 2791 Dihedral : 5.361 59.416 2067 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.12 % Allowed : 11.84 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 1889 helix: 0.17 (0.18), residues: 791 sheet: -0.55 (0.26), residues: 364 loop : -1.85 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 477 TYR 0.022 0.002 TYR A 779 PHE 0.035 0.002 PHE B 866 TRP 0.029 0.002 TRP B 355 HIS 0.011 0.001 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00434 (15970) covalent geometry : angle 0.65297 (21591) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.54326 ( 2) hydrogen bonds : bond 0.04585 ( 675) hydrogen bonds : angle 5.09234 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 0.542 Fit side-chains REVERT: A 168 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.5978 (t80) REVERT: A 226 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 952 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7476 (m-70) REVERT: A 982 GLN cc_start: 0.6925 (tp40) cc_final: 0.6691 (tp40) REVERT: A 1011 HIS cc_start: 0.6333 (t-90) cc_final: 0.6035 (t-170) REVERT: B 254 MET cc_start: 0.5835 (tmm) cc_final: 0.5524 (mmt) REVERT: B 470 LYS cc_start: 0.8474 (tppt) cc_final: 0.8106 (mtmm) REVERT: B 490 ASP cc_start: 0.4454 (m-30) cc_final: 0.4166 (p0) REVERT: B 676 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: B 702 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: B 781 GLN cc_start: 0.7613 (tp40) cc_final: 0.7349 (tp40) REVERT: B 798 ASP cc_start: 0.7813 (t0) cc_final: 0.7477 (m-30) REVERT: B 857 HIS cc_start: 0.6395 (OUTLIER) cc_final: 0.6112 (p-80) REVERT: B 870 MET cc_start: 0.7488 (mpp) cc_final: 0.6970 (mmm) REVERT: B 943 MET cc_start: 0.7996 (mmt) cc_final: 0.7778 (mmt) outliers start: 53 outliers final: 42 residues processed: 184 average time/residue: 0.0970 time to fit residues: 29.4601 Evaluate side-chains 183 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 952 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 84 optimal weight: 3.9990 chunk 110 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN B 108 HIS ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.138119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103486 restraints weight = 31430.435| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.17 r_work: 0.3434 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15971 Z= 0.128 Angle : 0.585 8.562 21593 Z= 0.300 Chirality : 0.043 0.142 2321 Planarity : 0.004 0.040 2791 Dihedral : 5.096 57.383 2067 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.06 % Allowed : 12.96 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.19), residues: 1889 helix: 0.46 (0.18), residues: 795 sheet: -0.40 (0.27), residues: 361 loop : -1.71 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 477 TYR 0.017 0.001 TYR A 779 PHE 0.028 0.001 PHE B 866 TRP 0.042 0.002 TRP B 355 HIS 0.006 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00291 (15970) covalent geometry : angle 0.58453 (21591) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.14653 ( 2) hydrogen bonds : bond 0.04040 ( 675) hydrogen bonds : angle 4.85176 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 0.671 Fit side-chains REVERT: A 113 MET cc_start: 0.7293 (tpp) cc_final: 0.6993 (mpp) REVERT: A 145 GLU cc_start: 0.8079 (tp30) cc_final: 0.7557 (tm-30) REVERT: A 168 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6012 (t80) REVERT: A 226 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7418 (mt) REVERT: A 698 ASP cc_start: 0.8264 (t0) cc_final: 0.8008 (m-30) REVERT: A 723 LEU cc_start: 0.8611 (pp) cc_final: 0.7835 (mt) REVERT: A 742 MET cc_start: 0.8094 (tpp) cc_final: 0.7689 (tpp) REVERT: A 779 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6057 (p90) REVERT: A 952 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7380 (m-70) REVERT: A 982 GLN cc_start: 0.6928 (tp40) cc_final: 0.6697 (tp40) REVERT: A 1011 HIS cc_start: 0.6270 (t-90) cc_final: 0.6013 (t-170) REVERT: B 267 LEU cc_start: 0.3666 (OUTLIER) cc_final: 0.3360 (mt) REVERT: B 430 PRO cc_start: 0.4196 (Cg_exo) cc_final: 0.3918 (Cg_endo) REVERT: B 470 LYS cc_start: 0.8470 (tppt) cc_final: 0.8138 (mtmm) REVERT: B 676 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6758 (tt0) REVERT: B 684 TYR cc_start: 0.7580 (t80) cc_final: 0.7332 (t80) REVERT: B 702 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: B 781 GLN cc_start: 0.7651 (tp40) cc_final: 0.7393 (tp40) REVERT: B 798 ASP cc_start: 0.7763 (t0) cc_final: 0.7415 (m-30) REVERT: B 808 LEU cc_start: 0.8653 (tp) cc_final: 0.8355 (tp) REVERT: B 855 PRO cc_start: 0.6879 (Cg_exo) cc_final: 0.6448 (Cg_endo) REVERT: B 857 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.5896 (p-80) REVERT: B 943 MET cc_start: 0.8019 (mmt) cc_final: 0.7812 (mmt) outliers start: 52 outliers final: 38 residues processed: 190 average time/residue: 0.1070 time to fit residues: 32.0674 Evaluate side-chains 186 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 952 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 91 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 514 GLN A 589 HIS B 190 HIS ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.134618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.101462 restraints weight = 32285.188| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.15 r_work: 0.3359 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 15971 Z= 0.259 Angle : 0.757 9.547 21593 Z= 0.386 Chirality : 0.048 0.160 2321 Planarity : 0.005 0.043 2791 Dihedral : 5.640 57.961 2067 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.54 % Allowed : 12.49 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 1889 helix: -0.03 (0.18), residues: 793 sheet: -0.62 (0.26), residues: 363 loop : -2.00 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 838 TYR 0.025 0.003 TYR A 779 PHE 0.046 0.002 PHE B 866 TRP 0.037 0.003 TRP B 355 HIS 0.013 0.002 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00614 (15970) covalent geometry : angle 0.75725 (21591) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.39865 ( 2) hydrogen bonds : bond 0.05196 ( 675) hydrogen bonds : angle 5.31827 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.6894 (m170) REVERT: A 113 MET cc_start: 0.7467 (tpp) cc_final: 0.7202 (mpp) REVERT: A 145 GLU cc_start: 0.8180 (tp30) cc_final: 0.7676 (tm-30) REVERT: A 168 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6105 (t80) REVERT: A 226 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7507 (mt) REVERT: A 266 ASP cc_start: 0.7539 (p0) cc_final: 0.7264 (p0) REVERT: A 427 LYS cc_start: 0.7910 (tptm) cc_final: 0.7339 (tptp) REVERT: A 553 ASP cc_start: 0.7420 (t70) cc_final: 0.7134 (t70) REVERT: A 779 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6121 (p90) REVERT: A 952 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7457 (m-70) REVERT: B 267 LEU cc_start: 0.3739 (OUTLIER) cc_final: 0.3392 (mt) REVERT: B 430 PRO cc_start: 0.4238 (Cg_exo) cc_final: 0.3983 (Cg_endo) REVERT: B 470 LYS cc_start: 0.8492 (tppt) cc_final: 0.8186 (mtmm) REVERT: B 676 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: B 781 GLN cc_start: 0.7636 (tp40) cc_final: 0.7426 (tp-100) REVERT: B 798 ASP cc_start: 0.7970 (t0) cc_final: 0.7597 (m-30) REVERT: B 857 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.6111 (p-80) REVERT: B 870 MET cc_start: 0.7519 (mpp) cc_final: 0.6964 (mmm) outliers start: 60 outliers final: 46 residues processed: 184 average time/residue: 0.1075 time to fit residues: 31.4403 Evaluate side-chains 185 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 952 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 982 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.137825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103999 restraints weight = 31629.160| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.21 r_work: 0.3424 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15971 Z= 0.127 Angle : 0.605 9.105 21593 Z= 0.309 Chirality : 0.043 0.192 2321 Planarity : 0.004 0.047 2791 Dihedral : 5.165 57.527 2067 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.24 % Allowed : 12.91 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 1889 helix: 0.46 (0.18), residues: 789 sheet: -0.59 (0.26), residues: 367 loop : -1.76 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 477 TYR 0.016 0.001 TYR A 779 PHE 0.035 0.001 PHE B 866 TRP 0.041 0.002 TRP B 355 HIS 0.006 0.001 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00288 (15970) covalent geometry : angle 0.60525 (21591) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.03839 ( 2) hydrogen bonds : bond 0.04059 ( 675) hydrogen bonds : angle 4.90040 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 143 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.6863 (m170) REVERT: A 113 MET cc_start: 0.7582 (tpp) cc_final: 0.7316 (mpp) REVERT: A 156 GLU cc_start: 0.7974 (pm20) cc_final: 0.7506 (pm20) REVERT: A 168 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6069 (t80) REVERT: A 180 ASP cc_start: 0.8296 (t0) cc_final: 0.7920 (p0) REVERT: A 266 ASP cc_start: 0.7646 (p0) cc_final: 0.7417 (p0) REVERT: A 553 ASP cc_start: 0.7271 (t70) cc_final: 0.7014 (t70) REVERT: A 698 ASP cc_start: 0.8327 (t0) cc_final: 0.8018 (m-30) REVERT: A 723 LEU cc_start: 0.8573 (pp) cc_final: 0.7824 (mt) REVERT: A 742 MET cc_start: 0.8122 (tpp) cc_final: 0.7714 (tpp) REVERT: A 779 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6085 (p90) REVERT: A 952 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.7318 (m-70) REVERT: A 982 GLN cc_start: 0.6940 (tp40) cc_final: 0.6707 (tp40) REVERT: B 267 LEU cc_start: 0.3649 (OUTLIER) cc_final: 0.3361 (mt) REVERT: B 430 PRO cc_start: 0.4254 (Cg_exo) cc_final: 0.3999 (Cg_endo) REVERT: B 470 LYS cc_start: 0.8470 (tppt) cc_final: 0.8174 (mtmm) REVERT: B 598 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7733 (mt-10) REVERT: B 676 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: B 684 TYR cc_start: 0.7655 (t80) cc_final: 0.7332 (t80) REVERT: B 781 GLN cc_start: 0.7592 (tp40) cc_final: 0.7381 (tp40) REVERT: B 798 ASP cc_start: 0.7751 (t0) cc_final: 0.7414 (m-30) REVERT: B 808 LEU cc_start: 0.8668 (tp) cc_final: 0.8395 (tp) REVERT: B 817 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 857 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.5991 (p-80) REVERT: B 870 MET cc_start: 0.7613 (mpp) cc_final: 0.7197 (mmm) outliers start: 55 outliers final: 44 residues processed: 183 average time/residue: 0.1079 time to fit residues: 31.4255 Evaluate side-chains 189 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 952 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 25 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.137149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.103805 restraints weight = 31681.956| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.06 r_work: 0.3410 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15971 Z= 0.163 Angle : 0.636 9.077 21593 Z= 0.324 Chirality : 0.044 0.164 2321 Planarity : 0.004 0.041 2791 Dihedral : 5.203 55.804 2067 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.42 % Allowed : 12.96 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1889 helix: 0.36 (0.18), residues: 799 sheet: -0.72 (0.26), residues: 374 loop : -1.79 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 164 TYR 0.021 0.002 TYR A 594 PHE 0.039 0.002 PHE B 866 TRP 0.039 0.002 TRP B 355 HIS 0.008 0.001 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00382 (15970) covalent geometry : angle 0.63635 (21591) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.19473 ( 2) hydrogen bonds : bond 0.04351 ( 675) hydrogen bonds : angle 4.96204 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.6940 (m170) REVERT: A 113 MET cc_start: 0.7615 (tpp) cc_final: 0.7334 (mpp) REVERT: A 145 GLU cc_start: 0.8120 (tp30) cc_final: 0.7536 (tm-30) REVERT: A 156 GLU cc_start: 0.7972 (pm20) cc_final: 0.7729 (pm20) REVERT: A 168 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.6070 (t80) REVERT: A 553 ASP cc_start: 0.7228 (t70) cc_final: 0.6972 (t70) REVERT: A 698 ASP cc_start: 0.8403 (t0) cc_final: 0.8060 (m-30) REVERT: A 723 LEU cc_start: 0.8609 (pp) cc_final: 0.7845 (mt) REVERT: A 742 MET cc_start: 0.8126 (tpp) cc_final: 0.7794 (tpp) REVERT: A 779 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6040 (p90) REVERT: A 952 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7321 (m-70) REVERT: A 982 GLN cc_start: 0.6924 (tp40) cc_final: 0.6701 (tp40) REVERT: B 267 LEU cc_start: 0.3678 (OUTLIER) cc_final: 0.3386 (mt) REVERT: B 359 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6695 (pt) REVERT: B 430 PRO cc_start: 0.4273 (Cg_exo) cc_final: 0.4008 (Cg_endo) REVERT: B 466 MET cc_start: 0.6934 (ptm) cc_final: 0.6640 (ptm) REVERT: B 470 LYS cc_start: 0.8404 (tppt) cc_final: 0.8126 (mtmm) REVERT: B 598 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7733 (mt-10) REVERT: B 676 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: B 781 GLN cc_start: 0.7586 (tp40) cc_final: 0.7351 (tp40) REVERT: B 798 ASP cc_start: 0.7743 (t0) cc_final: 0.7394 (m-30) REVERT: B 817 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: B 857 HIS cc_start: 0.6550 (OUTLIER) cc_final: 0.6085 (p-80) REVERT: B 870 MET cc_start: 0.7650 (mpp) cc_final: 0.7266 (mmm) outliers start: 58 outliers final: 48 residues processed: 180 average time/residue: 0.1034 time to fit residues: 29.6145 Evaluate side-chains 188 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 952 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 993 GLN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 48 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.138281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.104237 restraints weight = 31438.320| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.23 r_work: 0.3438 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15971 Z= 0.122 Angle : 0.591 8.739 21593 Z= 0.301 Chirality : 0.043 0.159 2321 Planarity : 0.004 0.041 2791 Dihedral : 4.993 54.736 2067 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.42 % Allowed : 12.96 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.19), residues: 1889 helix: 0.61 (0.18), residues: 794 sheet: -0.46 (0.26), residues: 358 loop : -1.67 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 477 TYR 0.018 0.001 TYR A 594 PHE 0.035 0.001 PHE B 866 TRP 0.040 0.002 TRP B 355 HIS 0.005 0.001 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00277 (15970) covalent geometry : angle 0.59054 (21591) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.07418 ( 2) hydrogen bonds : bond 0.03932 ( 675) hydrogen bonds : angle 4.80606 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3677.68 seconds wall clock time: 63 minutes 48.72 seconds (3828.72 seconds total)