Starting phenix.real_space_refine on Fri Jun 5 23:06:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9osf_70805/06_2026/9osf_70805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9osf_70805/06_2026/9osf_70805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9osf_70805/06_2026/9osf_70805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9osf_70805/06_2026/9osf_70805.map" model { file = "/net/cci-nas-00/data/ceres_data/9osf_70805/06_2026/9osf_70805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9osf_70805/06_2026/9osf_70805.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 130 5.16 5 C 15242 2.51 5 N 4022 2.21 5 O 4400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23794 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5909 Classifications: {'peptide': 747} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 715} Chain breaks: 2 Chain: "B" Number of atoms: 5988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5988 Classifications: {'peptide': 755} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 727} Chain breaks: 2 Chain: "C" Number of atoms: 5909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5909 Classifications: {'peptide': 747} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 715} Chain breaks: 2 Chain: "D" Number of atoms: 5988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5988 Classifications: {'peptide': 755} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 727} Chain breaks: 2 Time building chain proxies: 5.68, per 1000 atoms: 0.24 Number of scatterers: 23794 At special positions: 0 Unit cell: (106.5, 166.14, 202.776, 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 130 16.00 O 4400 8.00 N 4022 7.00 C 15242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 292 " distance=2.04 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 334 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 788 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 292 " distance=2.04 Simple disulfide: pdb=" SG CYS C 83 " - pdb=" SG CYS C 334 " distance=2.04 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 788 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 28 sheets defined 44.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 39 through 53 Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.725A pdb=" N GLN A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.655A pdb=" N SER A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 112 " --> pdb=" O HIS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 removed outlier: 3.643A pdb=" N VAL A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.652A pdb=" N LEU A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 292 removed outlier: 3.633A pdb=" N LEU A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.676A pdb=" N MET A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 445 through 458 removed outlier: 3.511A pdb=" N ASP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.666A pdb=" N LYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 566 Processing helix chain 'A' and resid 615 through 648 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 674 through 680 Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 696 through 700 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 715 removed outlier: 3.624A pdb=" N SER A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 758 through 772 removed outlier: 3.694A pdb=" N THR A 763 " --> pdb=" O ARG A 759 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 772 " --> pdb=" O GLN A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 781 removed outlier: 3.831A pdb=" N ILE A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 829 removed outlier: 4.092A pdb=" N GLY A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.768A pdb=" N VAL B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.743A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.683A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.021A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.746A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.681A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.870A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 474 removed outlier: 3.771A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.548A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 661 Processing helix chain 'B' and resid 671 through 676 removed outlier: 3.991A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.906A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.694A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.664A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.730A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.727A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.826A pdb=" N MET B 793 " --> pdb=" O GLY B 789 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 845 Processing helix chain 'C' and resid 39 through 53 Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.726A pdb=" N GLN C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 86 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.655A pdb=" N SER C 104 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 removed outlier: 3.643A pdb=" N VAL C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.652A pdb=" N LEU C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 292 removed outlier: 3.632A pdb=" N LEU C 284 " --> pdb=" O PHE C 280 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU C 290 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C 291 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 322 removed outlier: 3.676A pdb=" N MET C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 445 through 458 removed outlier: 3.512A pdb=" N ASP C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 490 Processing helix chain 'C' and resid 503 through 510 removed outlier: 3.666A pdb=" N LYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 509 " --> pdb=" O GLU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 566 Processing helix chain 'C' and resid 615 through 648 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 674 through 680 Processing helix chain 'C' and resid 683 through 694 Processing helix chain 'C' and resid 696 through 700 Processing helix chain 'C' and resid 704 through 709 Processing helix chain 'C' and resid 710 through 715 removed outlier: 3.623A pdb=" N SER C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 733 Processing helix chain 'C' and resid 758 through 772 removed outlier: 3.695A pdb=" N THR C 763 " --> pdb=" O ARG C 759 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU C 764 " --> pdb=" O ASP C 760 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 772 " --> pdb=" O GLN C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 781 removed outlier: 3.831A pdb=" N ILE C 777 " --> pdb=" O ASN C 773 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 779 " --> pdb=" O LEU C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 829 removed outlier: 4.092A pdb=" N GLY C 806 " --> pdb=" O GLU C 802 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 807 " --> pdb=" O ASN C 803 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE C 808 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL C 809 " --> pdb=" O GLY C 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.768A pdb=" N VAL D 61 " --> pdb=" O PHE D 57 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 102 removed outlier: 3.743A pdb=" N ALA D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.683A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 4.021A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.746A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 297 Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.682A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.870A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 474 removed outlier: 3.771A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 560 through 583 removed outlier: 3.548A pdb=" N TRP D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 661 Processing helix chain 'D' and resid 671 through 676 removed outlier: 3.990A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.906A pdb=" N THR D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.694A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.664A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.730A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 788 removed outlier: 3.726A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.826A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 845 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 69 removed outlier: 5.882A pdb=" N LEU A 24 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP A 66 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET A 26 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE A 68 " --> pdb=" O MET A 26 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 28 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N SER A 92 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG A 25 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LEU A 94 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 27 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 93 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.725A pdb=" N SER A 189 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER A 162 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP A 217 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 164 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 214 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N PHE A 267 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU A 244 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 266 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 389 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.855A pdb=" N GLU A 363 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA5, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AA6, first strand: chain 'A' and resid 701 through 702 removed outlier: 8.278A pdb=" N VAL A 702 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 668 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 665 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU A 720 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLY A 667 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N GLU A 722 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ILE A 669 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N TYR A 717 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ARG A 526 " --> pdb=" O TYR A 717 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 719 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 523 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 83 removed outlier: 6.742A pdb=" N HIS B 34 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR B 77 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N PHE B 107 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY B 39 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 203 removed outlier: 5.016A pdb=" N HIS B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.698A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 435 removed outlier: 6.658A pdb=" N LEU B 433 " --> pdb=" O GLU B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 444 through 446 Processing sheet with id=AB3, first strand: chain 'B' and resid 490 through 492 removed outlier: 3.737A pdb=" N ALA B 490 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 517 through 518 removed outlier: 4.259A pdb=" N LEU B 517 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 735 through 738 removed outlier: 3.745A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 69 removed outlier: 5.882A pdb=" N LEU C 24 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP C 66 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET C 26 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE C 68 " --> pdb=" O MET C 26 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA C 28 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N SER C 92 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG C 25 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LEU C 94 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C 27 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 93 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.725A pdb=" N SER C 189 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER C 162 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP C 217 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE C 164 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 214 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR C 242 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N PHE C 267 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU C 244 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 266 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY C 389 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.855A pdb=" N GLU C 363 " --> pdb=" O THR C 371 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AC1, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AC2, first strand: chain 'C' and resid 701 through 702 removed outlier: 8.278A pdb=" N VAL C 702 " --> pdb=" O TYR C 666 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C 668 " --> pdb=" O VAL C 702 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU C 665 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU C 720 " --> pdb=" O GLU C 665 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLY C 667 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N GLU C 722 " --> pdb=" O GLY C 667 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ILE C 669 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N TYR C 717 " --> pdb=" O ARG C 526 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG C 526 " --> pdb=" O TYR C 717 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 719 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE C 523 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 74 through 83 removed outlier: 6.741A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 198 through 203 removed outlier: 5.016A pdb=" N HIS D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.698A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 433 through 435 removed outlier: 6.657A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 444 through 446 Processing sheet with id=AC8, first strand: chain 'D' and resid 490 through 492 removed outlier: 3.737A pdb=" N ALA D 490 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 517 through 518 removed outlier: 4.258A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 735 through 738 removed outlier: 3.745A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6951 1.34 - 1.46: 5398 1.46 - 1.58: 11723 1.58 - 1.71: 0 1.71 - 1.83: 226 Bond restraints: 24298 Sorted by residual: bond pdb=" N ILE C 804 " pdb=" CA ILE C 804 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.07e-02 8.73e+03 1.19e+01 bond pdb=" N ILE A 804 " pdb=" CA ILE A 804 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.07e-02 8.73e+03 1.16e+01 bond pdb=" N GLN C 697 " pdb=" CA GLN C 697 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N VAL C 702 " pdb=" CA VAL C 702 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N VAL A 702 " pdb=" CA VAL A 702 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.81e+00 ... (remaining 24293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 30577 1.73 - 3.47: 1994 3.47 - 5.20: 258 5.20 - 6.93: 49 6.93 - 8.67: 22 Bond angle restraints: 32900 Sorted by residual: angle pdb=" N ASN B 819 " pdb=" CA ASN B 819 " pdb=" C ASN B 819 " ideal model delta sigma weight residual 113.43 107.93 5.50 1.26e+00 6.30e-01 1.90e+01 angle pdb=" N ASN D 819 " pdb=" CA ASN D 819 " pdb=" C ASN D 819 " ideal model delta sigma weight residual 113.43 107.97 5.46 1.26e+00 6.30e-01 1.88e+01 angle pdb=" CA VAL B 817 " pdb=" C VAL B 817 " pdb=" O VAL B 817 " ideal model delta sigma weight residual 122.13 117.35 4.78 1.11e+00 8.12e-01 1.85e+01 angle pdb=" CA VAL D 817 " pdb=" C VAL D 817 " pdb=" O VAL D 817 " ideal model delta sigma weight residual 122.13 117.36 4.77 1.11e+00 8.12e-01 1.84e+01 angle pdb=" N LEU C 799 " pdb=" CA LEU C 799 " pdb=" C LEU C 799 " ideal model delta sigma weight residual 113.17 108.24 4.93 1.26e+00 6.30e-01 1.53e+01 ... (remaining 32895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 12936 17.83 - 35.66: 1345 35.66 - 53.49: 236 53.49 - 71.32: 45 71.32 - 89.15: 32 Dihedral angle restraints: 14594 sinusoidal: 5874 harmonic: 8720 Sorted by residual: dihedral pdb=" CB CYS C 36 " pdb=" SG CYS C 36 " pdb=" SG CYS C 292 " pdb=" CB CYS C 292 " ideal model delta sinusoidal sigma weight residual 93.00 14.85 78.15 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS A 36 " pdb=" SG CYS A 36 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual 93.00 14.88 78.12 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS A 83 " pdb=" SG CYS A 83 " pdb=" SG CYS A 334 " pdb=" CB CYS A 334 " ideal model delta sinusoidal sigma weight residual 93.00 29.00 64.00 1 1.00e+01 1.00e-02 5.39e+01 ... (remaining 14591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3090 0.077 - 0.153: 556 0.153 - 0.230: 70 0.230 - 0.307: 0 0.307 - 0.384: 2 Chirality restraints: 3718 Sorted by residual: chirality pdb=" CB ILE D 434 " pdb=" CA ILE D 434 " pdb=" CG1 ILE D 434 " pdb=" CG2 ILE D 434 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE B 434 " pdb=" CA ILE B 434 " pdb=" CG1 ILE B 434 " pdb=" CG2 ILE B 434 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA LEU C 799 " pdb=" N LEU C 799 " pdb=" C LEU C 799 " pdb=" CB LEU C 799 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3715 not shown) Planarity restraints: 4176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 795 " -0.248 9.50e-02 1.11e+02 1.11e-01 7.59e+00 pdb=" NE ARG A 795 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 795 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 795 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 795 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 795 " -0.247 9.50e-02 1.11e+02 1.11e-01 7.57e+00 pdb=" NE ARG C 795 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 795 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 795 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 795 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 86 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO C 87 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " -0.038 5.00e-02 4.00e+02 ... (remaining 4173 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2062 2.74 - 3.28: 21544 3.28 - 3.82: 36607 3.82 - 4.36: 42702 4.36 - 4.90: 76208 Nonbonded interactions: 179123 Sorted by model distance: nonbonded pdb=" OG SER A 616 " pdb=" OG SER B 834 " model vdw 2.203 3.040 nonbonded pdb=" OG SER C 616 " pdb=" OG SER D 834 " model vdw 2.209 3.040 nonbonded pdb=" O LEU D 674 " pdb=" OH TYR D 682 " model vdw 2.245 3.040 nonbonded pdb=" O LEU B 674 " pdb=" OH TYR B 682 " model vdw 2.245 3.040 nonbonded pdb=" OG SER C 654 " pdb=" OD1 ASP C 656 " model vdw 2.299 3.040 ... (remaining 179118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.860 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.850 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 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 : 0.006 0.064 24308 Z= 0.372 Angle : 0.950 8.667 32920 Z= 0.597 Chirality : 0.058 0.384 3718 Planarity : 0.007 0.111 4176 Dihedral : 15.049 89.148 8948 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.26 % Rotamer: Outliers : 0.69 % Allowed : 8.73 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -4.00 (0.12), residues: 2980 helix: -2.34 (0.11), residues: 1250 sheet: -2.07 (0.23), residues: 430 loop : -3.11 (0.13), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 458 TYR 0.026 0.002 TYR B 488 PHE 0.025 0.002 PHE A 516 TRP 0.014 0.002 TRP B 296 HIS 0.006 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.37 (24298) covalent geometry : angle 0.94965 / 0.60 (32900) SS BOND : bond 0.00631 / 0.29 ( 10) SS BOND : angle 1.30373 / 0.72 ( 20) hydrogen bonds : bond 0.17367 / 12.06 ( 902) hydrogen bonds : angle 6.14886 / 4.27 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 483 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.8874 (m) cc_final: 0.8544 (t) REVERT: B 360 MET cc_start: 0.7697 (tpt) cc_final: 0.7301 (tpp) REVERT: B 736 LEU cc_start: 0.6137 (mm) cc_final: 0.5811 (mp) REVERT: C 82 MET cc_start: 0.7540 (tpt) cc_final: 0.7239 (tpp) REVERT: C 820 PHE cc_start: 0.6295 (t80) cc_final: 0.6090 (t80) REVERT: D 248 MET cc_start: 0.8924 (mmm) cc_final: 0.8581 (mmm) outliers start: 18 outliers final: 7 residues processed: 497 average time/residue: 0.1811 time to fit residues: 138.3113 Evaluate side-chains 256 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 249 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain D residue 272 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 687 GLN A 714 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 203 GLN B 499 ASN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 GLN C 108 HIS C 342 HIS C 687 GLN C 694 GLN C 714 ASN C 726 ASN C 738 GLN C 803 ASN D 98 GLN D 111 HIS D 119 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN D 253 HIS ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 557 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.150679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102185 restraints weight = 51626.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094970 restraints weight = 45680.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096637 restraints weight = 42973.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097211 restraints weight = 33814.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097379 restraints weight = 31558.689| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 24308 Z= 0.282 Angle : 0.769 11.595 32920 Z= 0.398 Chirality : 0.046 0.171 3718 Planarity : 0.006 0.060 4176 Dihedral : 5.483 55.619 3289 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.31 % Allowed : 15.58 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.75 (0.14), residues: 2980 helix: -0.77 (0.14), residues: 1278 sheet: -2.28 (0.23), residues: 450 loop : -2.73 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 800 TYR 0.034 0.002 TYR B 86 PHE 0.030 0.003 PHE B 145 TRP 0.027 0.003 TRP A 391 HIS 0.008 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.28 (24298) covalent geometry : angle 0.76847 / 0.40 (32900) SS BOND : bond 0.01093 / 0.45 ( 10) SS BOND : angle 1.54421 / 0.89 ( 20) hydrogen bonds : bond 0.05441 / 3.70 ( 902) hydrogen bonds : angle 4.58895 / 3.17 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 284 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9615 (m) cc_final: 0.9208 (t) REVERT: A 286 MET cc_start: 0.8229 (tpt) cc_final: 0.7958 (tpt) REVERT: A 347 MET cc_start: 0.7972 (tpp) cc_final: 0.7661 (tpp) REVERT: A 352 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7766 (mpp) REVERT: A 484 MET cc_start: 0.7247 (ttp) cc_final: 0.7019 (ttm) REVERT: A 561 LEU cc_start: 0.8727 (pp) cc_final: 0.8369 (tp) REVERT: A 562 PHE cc_start: 0.7796 (t80) cc_final: 0.7576 (t80) REVERT: A 648 MET cc_start: 0.7625 (tmm) cc_final: 0.7375 (tmm) REVERT: A 678 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8494 (t80) REVERT: A 689 MET cc_start: 0.9107 (mmm) cc_final: 0.8900 (mmm) REVERT: A 824 MET cc_start: 0.7731 (tmm) cc_final: 0.6950 (ptt) REVERT: B 153 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: B 234 MET cc_start: 0.8276 (tpp) cc_final: 0.7895 (ttp) REVERT: B 308 ASP cc_start: 0.7443 (m-30) cc_final: 0.6982 (p0) REVERT: B 346 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8285 (pt0) REVERT: B 664 MET cc_start: 0.8183 (tmm) cc_final: 0.7612 (tmm) REVERT: B 705 MET cc_start: 0.8538 (mmm) cc_final: 0.8312 (tpp) REVERT: B 735 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5411 (t80) REVERT: B 737 MET cc_start: 0.6020 (mmm) cc_final: 0.4934 (mmm) REVERT: B 790 LYS cc_start: 0.9092 (tppt) cc_final: 0.8876 (mmmt) REVERT: B 794 MET cc_start: 0.8553 (mtp) cc_final: 0.8327 (tpt) REVERT: C 94 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8524 (pp) REVERT: C 307 MET cc_start: 0.7877 (mmt) cc_final: 0.7643 (tpp) REVERT: C 523 ILE cc_start: 0.8925 (mp) cc_final: 0.8569 (mm) REVERT: C 535 TYR cc_start: 0.6204 (p90) cc_final: 0.5974 (p90) REVERT: C 752 MET cc_start: 0.5687 (mmm) cc_final: 0.5405 (mmm) REVERT: D 152 ASP cc_start: 0.8164 (t0) cc_final: 0.7812 (t70) REVERT: D 153 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8677 (m-80) REVERT: D 501 MET cc_start: 0.6997 (tpp) cc_final: 0.6731 (tpt) REVERT: D 696 LYS cc_start: 0.8734 (pttt) cc_final: 0.8488 (tmtt) REVERT: D 706 TRP cc_start: 0.8217 (t-100) cc_final: 0.7966 (t-100) REVERT: D 747 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8954 (tp40) outliers start: 86 outliers final: 54 residues processed: 349 average time/residue: 0.1643 time to fit residues: 91.5030 Evaluate side-chains 282 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 221 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 753 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 108 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 179 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 269 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 733 ASN B 129 HIS B 253 HIS B 754 GLN C 108 HIS C 679 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.152248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104090 restraints weight = 51534.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.097423 restraints weight = 45952.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099154 restraints weight = 42397.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100238 restraints weight = 32870.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100271 restraints weight = 30108.410| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24308 Z= 0.145 Angle : 0.612 12.633 32920 Z= 0.311 Chirality : 0.041 0.196 3718 Planarity : 0.004 0.046 4176 Dihedral : 4.839 55.372 3289 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.04 % Allowed : 17.73 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.00 (0.15), residues: 2980 helix: 0.01 (0.15), residues: 1293 sheet: -2.13 (0.23), residues: 441 loop : -2.45 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 800 TYR 0.028 0.001 TYR D 86 PHE 0.019 0.001 PHE D 708 TRP 0.029 0.002 TRP B 798 HIS 0.018 0.001 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (24298) covalent geometry : angle 0.61065 / 0.31 (32900) SS BOND : bond 0.00450 / 0.20 ( 10) SS BOND : angle 1.46354 / 0.85 ( 20) hydrogen bonds : bond 0.04173 / 2.82 ( 902) hydrogen bonds : angle 4.10329 / 2.85 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 247 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9573 (m) cc_final: 0.9203 (t) REVERT: A 235 MET cc_start: 0.5813 (tpp) cc_final: 0.5487 (tpp) REVERT: A 286 MET cc_start: 0.8236 (tpt) cc_final: 0.7949 (tpt) REVERT: A 562 PHE cc_start: 0.7777 (t80) cc_final: 0.7576 (t80) REVERT: A 648 MET cc_start: 0.7586 (tmm) cc_final: 0.7179 (tmm) REVERT: A 678 PHE cc_start: 0.8749 (m-80) cc_final: 0.8393 (t80) REVERT: A 689 MET cc_start: 0.9012 (mmm) cc_final: 0.8751 (mmm) REVERT: B 234 MET cc_start: 0.8237 (tpp) cc_final: 0.7676 (ttm) REVERT: B 288 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: B 308 ASP cc_start: 0.7665 (m-30) cc_final: 0.7273 (p0) REVERT: B 691 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6473 (ptm) REVERT: B 709 MET cc_start: 0.6799 (ppp) cc_final: 0.6598 (ppp) REVERT: B 798 TRP cc_start: 0.7601 (m100) cc_final: 0.7198 (m-10) REVERT: C 235 MET cc_start: 0.6728 (mmt) cc_final: 0.6470 (tpp) REVERT: C 429 MET cc_start: 0.6613 (mpp) cc_final: 0.6412 (mpp) REVERT: C 535 TYR cc_start: 0.6240 (p90) cc_final: 0.6022 (p90) REVERT: C 689 MET cc_start: 0.8198 (mmm) cc_final: 0.7892 (mmm) REVERT: D 152 ASP cc_start: 0.8073 (t0) cc_final: 0.7556 (t0) REVERT: D 415 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: D 696 LYS cc_start: 0.8744 (pttt) cc_final: 0.8521 (tmtt) REVERT: D 750 CYS cc_start: 0.8579 (p) cc_final: 0.7255 (t) REVERT: D 783 LEU cc_start: 0.8646 (mt) cc_final: 0.7764 (tt) outliers start: 79 outliers final: 43 residues processed: 310 average time/residue: 0.1597 time to fit residues: 79.6944 Evaluate side-chains 264 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 753 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 194 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 chunk 170 optimal weight: 0.5980 chunk 291 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 204 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 346 GLN B 726 GLN B 754 GLN C 803 ASN D 119 GLN D 747 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.150990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101772 restraints weight = 51553.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095123 restraints weight = 46522.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096599 restraints weight = 42015.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097182 restraints weight = 34225.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097431 restraints weight = 31960.277| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24308 Z= 0.143 Angle : 0.602 12.936 32920 Z= 0.303 Chirality : 0.041 0.165 3718 Planarity : 0.004 0.043 4176 Dihedral : 4.615 54.791 3288 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.96 % Allowed : 19.38 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.60 (0.15), residues: 2980 helix: 0.42 (0.15), residues: 1286 sheet: -1.96 (0.23), residues: 458 loop : -2.30 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 463 TYR 0.026 0.001 TYR D 86 PHE 0.022 0.001 PHE C 538 TRP 0.020 0.002 TRP C 690 HIS 0.005 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (24298) covalent geometry : angle 0.60162 / 0.30 (32900) SS BOND : bond 0.00532 / 0.25 ( 10) SS BOND : angle 1.21712 / 0.70 ( 20) hydrogen bonds : bond 0.03926 / 2.64 ( 902) hydrogen bonds : angle 4.00762 / 2.78 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 240 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9546 (m) cc_final: 0.9189 (t) REVERT: A 108 HIS cc_start: 0.8023 (t70) cc_final: 0.7688 (m-70) REVERT: A 235 MET cc_start: 0.5903 (tpp) cc_final: 0.5470 (tpp) REVERT: A 286 MET cc_start: 0.8241 (tpt) cc_final: 0.7964 (tpt) REVERT: A 352 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7419 (mpp) REVERT: A 561 LEU cc_start: 0.8615 (pp) cc_final: 0.8339 (tp) REVERT: A 678 PHE cc_start: 0.8730 (m-80) cc_final: 0.8450 (t80) REVERT: A 689 MET cc_start: 0.8994 (mmm) cc_final: 0.8751 (mmm) REVERT: A 824 MET cc_start: 0.7614 (tmm) cc_final: 0.6780 (ptt) REVERT: B 234 MET cc_start: 0.8174 (tpp) cc_final: 0.7608 (ttm) REVERT: B 288 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: B 308 ASP cc_start: 0.7879 (m-30) cc_final: 0.7459 (p0) REVERT: B 709 MET cc_start: 0.6805 (ppp) cc_final: 0.6494 (ppp) REVERT: B 735 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.5908 (t80) REVERT: B 737 MET cc_start: 0.5808 (mmm) cc_final: 0.5146 (mmm) REVERT: B 755 ILE cc_start: 0.8256 (mp) cc_final: 0.7660 (tp) REVERT: C 235 MET cc_start: 0.6770 (mmt) cc_final: 0.6525 (tpp) REVERT: C 429 MET cc_start: 0.6635 (mpp) cc_final: 0.6432 (mpp) REVERT: C 535 TYR cc_start: 0.6357 (p90) cc_final: 0.6052 (p90) REVERT: D 152 ASP cc_start: 0.8139 (t0) cc_final: 0.7599 (t0) REVERT: D 317 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8662 (p) REVERT: D 415 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: D 750 CYS cc_start: 0.8616 (p) cc_final: 0.7460 (t) REVERT: D 770 MET cc_start: 0.7777 (tpt) cc_final: 0.7029 (mtt) REVERT: D 793 MET cc_start: 0.8761 (ppp) cc_final: 0.7396 (ppp) outliers start: 77 outliers final: 54 residues processed: 303 average time/residue: 0.1518 time to fit residues: 75.7302 Evaluate side-chains 278 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 753 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 82 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.152193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104198 restraints weight = 51928.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099219 restraints weight = 49076.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.100760 restraints weight = 42891.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101096 restraints weight = 33067.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104197 restraints weight = 31707.880| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24308 Z= 0.122 Angle : 0.584 13.462 32920 Z= 0.292 Chirality : 0.041 0.149 3718 Planarity : 0.004 0.054 4176 Dihedral : 4.336 54.339 3285 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.08 % Allowed : 19.69 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.34 (0.15), residues: 2980 helix: 0.62 (0.15), residues: 1290 sheet: -1.78 (0.24), residues: 444 loop : -2.18 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 800 TYR 0.023 0.001 TYR D 86 PHE 0.026 0.001 PHE C 538 TRP 0.042 0.002 TRP B 798 HIS 0.004 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (24298) covalent geometry : angle 0.58357 / 0.29 (32900) SS BOND : bond 0.00393 / 0.16 ( 10) SS BOND : angle 1.16308 / 0.66 ( 20) hydrogen bonds : bond 0.03637 / 2.44 ( 902) hydrogen bonds : angle 3.87861 / 2.69 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 234 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9565 (m) cc_final: 0.9187 (t) REVERT: A 108 HIS cc_start: 0.8078 (t70) cc_final: 0.7690 (m-70) REVERT: A 235 MET cc_start: 0.5891 (tpp) cc_final: 0.5620 (tpp) REVERT: A 286 MET cc_start: 0.8135 (tpt) cc_final: 0.7904 (tpt) REVERT: A 352 MET cc_start: 0.7412 (mpp) cc_final: 0.7207 (mpp) REVERT: A 429 MET cc_start: 0.7758 (mpp) cc_final: 0.7404 (mpp) REVERT: A 648 MET cc_start: 0.7600 (tmm) cc_final: 0.7379 (tmm) REVERT: A 675 MET cc_start: 0.8234 (ptm) cc_final: 0.7949 (ptp) REVERT: A 689 MET cc_start: 0.8873 (mmm) cc_final: 0.8639 (mmm) REVERT: B 234 MET cc_start: 0.7950 (tpp) cc_final: 0.7409 (ttm) REVERT: B 288 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: B 308 ASP cc_start: 0.7913 (m-30) cc_final: 0.7594 (p0) REVERT: B 345 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5534 (mt) REVERT: B 534 MET cc_start: 0.6246 (tpp) cc_final: 0.5773 (tpp) REVERT: B 664 MET cc_start: 0.7354 (tmm) cc_final: 0.7030 (tmm) REVERT: B 691 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6692 (ptm) REVERT: B 709 MET cc_start: 0.6877 (ppp) cc_final: 0.6375 (ppp) REVERT: B 735 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6060 (t80) REVERT: B 737 MET cc_start: 0.6014 (mmm) cc_final: 0.5416 (mmm) REVERT: C 235 MET cc_start: 0.6704 (mmt) cc_final: 0.6499 (tpp) REVERT: C 286 MET cc_start: 0.8557 (ttp) cc_final: 0.8335 (ttp) REVERT: C 429 MET cc_start: 0.6550 (mpp) cc_final: 0.6335 (mpp) REVERT: C 519 LEU cc_start: 0.8245 (tp) cc_final: 0.7546 (mt) REVERT: D 152 ASP cc_start: 0.8129 (t0) cc_final: 0.7562 (t0) REVERT: D 234 MET cc_start: 0.7647 (tpp) cc_final: 0.7276 (ttm) REVERT: D 415 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: D 536 LEU cc_start: 0.7712 (mm) cc_final: 0.7339 (mm) REVERT: D 750 CYS cc_start: 0.8545 (p) cc_final: 0.7525 (t) REVERT: D 770 MET cc_start: 0.7743 (tpt) cc_final: 0.6953 (mtt) REVERT: D 794 MET cc_start: 0.7756 (mmt) cc_final: 0.7433 (mmm) outliers start: 80 outliers final: 55 residues processed: 297 average time/residue: 0.1517 time to fit residues: 74.3585 Evaluate side-chains 274 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 214 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 235 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 chunk 112 optimal weight: 0.0170 overall best weight: 2.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 HIS A 803 ASN C 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.149608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.101461 restraints weight = 52474.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094729 restraints weight = 48920.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096048 restraints weight = 45616.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097114 restraints weight = 35871.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097220 restraints weight = 32275.759| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24308 Z= 0.204 Angle : 0.648 11.937 32920 Z= 0.325 Chirality : 0.043 0.152 3718 Planarity : 0.004 0.042 4176 Dihedral : 4.643 59.713 3285 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.80 % Rotamer: Outliers : 3.54 % Allowed : 20.00 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.41 (0.15), residues: 2980 helix: 0.55 (0.15), residues: 1301 sheet: -1.86 (0.23), residues: 484 loop : -2.18 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.026 0.002 TYR C 692 PHE 0.029 0.002 PHE C 538 TRP 0.045 0.002 TRP B 798 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (24298) covalent geometry : angle 0.64768 / 0.33 (32900) SS BOND : bond 0.00808 / 0.38 ( 10) SS BOND : angle 1.17091 / 0.67 ( 20) hydrogen bonds : bond 0.04420 / 3.00 ( 902) hydrogen bonds : angle 4.17120 / 2.87 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 225 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9621 (m) cc_final: 0.9250 (t) REVERT: A 286 MET cc_start: 0.8206 (tpt) cc_final: 0.7915 (tpt) REVERT: A 352 MET cc_start: 0.7681 (mpp) cc_final: 0.7441 (mpp) REVERT: A 429 MET cc_start: 0.7991 (mpp) cc_final: 0.7721 (mpp) REVERT: A 648 MET cc_start: 0.7658 (tmm) cc_final: 0.7265 (tmm) REVERT: A 675 MET cc_start: 0.8224 (ptm) cc_final: 0.7967 (ptp) REVERT: A 824 MET cc_start: 0.7551 (tmm) cc_final: 0.6702 (ptt) REVERT: B 234 MET cc_start: 0.8261 (tpp) cc_final: 0.7734 (ttm) REVERT: B 288 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: B 296 TRP cc_start: 0.7781 (t60) cc_final: 0.7126 (t60) REVERT: B 308 ASP cc_start: 0.8040 (m-30) cc_final: 0.7754 (p0) REVERT: B 534 MET cc_start: 0.6269 (tpp) cc_final: 0.5928 (tpp) REVERT: B 664 MET cc_start: 0.7320 (tmm) cc_final: 0.6948 (tmm) REVERT: B 691 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6710 (ptm) REVERT: B 735 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.6326 (t80) REVERT: B 737 MET cc_start: 0.6290 (mmm) cc_final: 0.5785 (mmm) REVERT: C 235 MET cc_start: 0.6903 (mmt) cc_final: 0.6358 (tpp) REVERT: C 286 MET cc_start: 0.8671 (ttp) cc_final: 0.8464 (ttp) REVERT: C 352 MET cc_start: 0.7363 (ppp) cc_final: 0.6974 (ppp) REVERT: C 429 MET cc_start: 0.6641 (mpp) cc_final: 0.6417 (mpp) REVERT: C 529 MET cc_start: 0.7465 (mmm) cc_final: 0.6780 (mpp) REVERT: C 670 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7869 (t-170) REVERT: C 689 MET cc_start: 0.8216 (mmm) cc_final: 0.7848 (mmm) REVERT: D 152 ASP cc_start: 0.8244 (t0) cc_final: 0.7634 (t70) REVERT: D 234 MET cc_start: 0.7837 (tpp) cc_final: 0.7422 (ttm) REVERT: D 415 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: D 445 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8689 (tt) REVERT: D 536 LEU cc_start: 0.7719 (mm) cc_final: 0.7245 (mm) REVERT: D 750 CYS cc_start: 0.8572 (p) cc_final: 0.7578 (t) REVERT: D 758 LEU cc_start: 0.8277 (tp) cc_final: 0.7913 (tp) outliers start: 92 outliers final: 73 residues processed: 299 average time/residue: 0.1435 time to fit residues: 71.7479 Evaluate side-chains 284 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 205 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 670 HIS Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 242 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 250 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 39 optimal weight: 8.9990 chunk 117 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.151352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104930 restraints weight = 52282.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098029 restraints weight = 46135.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099124 restraints weight = 47117.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099815 restraints weight = 37575.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100000 restraints weight = 33911.287| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24308 Z= 0.126 Angle : 0.605 13.142 32920 Z= 0.299 Chirality : 0.041 0.153 3718 Planarity : 0.003 0.045 4176 Dihedral : 4.354 50.815 3285 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 3.27 % Allowed : 20.50 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.18 (0.16), residues: 2980 helix: 0.72 (0.15), residues: 1299 sheet: -1.73 (0.23), residues: 471 loop : -2.05 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.025 0.001 TYR C 692 PHE 0.035 0.001 PHE C 538 TRP 0.045 0.002 TRP C 690 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (24298) covalent geometry : angle 0.60473 / 0.30 (32900) SS BOND : bond 0.00504 / 0.25 ( 10) SS BOND : angle 1.09502 / 0.65 ( 20) hydrogen bonds : bond 0.03786 / 2.55 ( 902) hydrogen bonds : angle 3.94750 / 2.73 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 222 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9536 (m) cc_final: 0.9170 (t) REVERT: A 286 MET cc_start: 0.8248 (tpt) cc_final: 0.7978 (tpt) REVERT: A 352 MET cc_start: 0.7736 (mpp) cc_final: 0.7508 (mpp) REVERT: A 429 MET cc_start: 0.8037 (mpp) cc_final: 0.7578 (mpp) REVERT: A 484 MET cc_start: 0.6683 (ttm) cc_final: 0.6259 (tpt) REVERT: A 648 MET cc_start: 0.7711 (tmm) cc_final: 0.7268 (tmm) REVERT: A 666 TYR cc_start: 0.5140 (OUTLIER) cc_final: 0.4814 (p90) REVERT: A 675 MET cc_start: 0.8128 (ptm) cc_final: 0.7860 (ptp) REVERT: A 795 ARG cc_start: 0.6515 (ttt90) cc_final: 0.6276 (ttt-90) REVERT: A 824 MET cc_start: 0.7412 (tmm) cc_final: 0.6727 (ptt) REVERT: B 234 MET cc_start: 0.8083 (tpp) cc_final: 0.7678 (ttm) REVERT: B 288 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: B 296 TRP cc_start: 0.7657 (t60) cc_final: 0.7086 (t60) REVERT: B 308 ASP cc_start: 0.8137 (m-30) cc_final: 0.7844 (p0) REVERT: B 316 MET cc_start: 0.7756 (tpt) cc_final: 0.7466 (tpt) REVERT: B 534 MET cc_start: 0.6289 (tpp) cc_final: 0.6034 (tpp) REVERT: B 664 MET cc_start: 0.7328 (tmm) cc_final: 0.6962 (tmm) REVERT: B 691 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6921 (ptm) REVERT: B 735 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6299 (t80) REVERT: B 737 MET cc_start: 0.6486 (mmm) cc_final: 0.6102 (mmm) REVERT: C 286 MET cc_start: 0.8713 (ttp) cc_final: 0.8513 (ttp) REVERT: C 352 MET cc_start: 0.7336 (ppp) cc_final: 0.7012 (ppp) REVERT: C 529 MET cc_start: 0.7524 (mmm) cc_final: 0.6864 (mpp) REVERT: C 535 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.6419 (p90) REVERT: C 689 MET cc_start: 0.8274 (mmm) cc_final: 0.7845 (mmm) REVERT: D 234 MET cc_start: 0.7622 (tpp) cc_final: 0.7221 (ttm) REVERT: D 415 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: D 536 LEU cc_start: 0.7665 (mm) cc_final: 0.7209 (mm) REVERT: D 705 MET cc_start: 0.8834 (tpp) cc_final: 0.8477 (tpt) REVERT: D 717 LEU cc_start: 0.6265 (mm) cc_final: 0.5496 (mm) REVERT: D 750 CYS cc_start: 0.8626 (p) cc_final: 0.7591 (t) REVERT: D 770 MET cc_start: 0.7741 (tpt) cc_final: 0.7345 (mmt) outliers start: 85 outliers final: 61 residues processed: 288 average time/residue: 0.1468 time to fit residues: 71.0166 Evaluate side-chains 273 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 206 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 535 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 210 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS ** B 350 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 = 0.4229 r_free = 0.4229 target = 0.150307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.106516 restraints weight = 51489.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.108113 restraints weight = 69461.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104998 restraints weight = 41867.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.103335 restraints weight = 46381.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.103639 restraints weight = 46055.097| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24308 Z= 0.145 Angle : 0.616 13.650 32920 Z= 0.304 Chirality : 0.042 0.150 3718 Planarity : 0.004 0.042 4176 Dihedral : 4.340 47.090 3285 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.80 % Rotamer: Outliers : 3.31 % Allowed : 20.88 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.10 (0.16), residues: 2980 helix: 0.85 (0.15), residues: 1283 sheet: -1.86 (0.23), residues: 481 loop : -1.97 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 468 TYR 0.025 0.001 TYR D 733 PHE 0.034 0.001 PHE C 538 TRP 0.043 0.002 TRP C 690 HIS 0.005 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (24298) covalent geometry : angle 0.61590 / 0.30 (32900) SS BOND : bond 0.00458 / 0.22 ( 10) SS BOND : angle 1.07577 / 0.62 ( 20) hydrogen bonds : bond 0.03901 / 2.62 ( 902) hydrogen bonds : angle 4.04498 / 2.79 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 213 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9576 (m) cc_final: 0.9204 (t) REVERT: A 429 MET cc_start: 0.7406 (mpp) cc_final: 0.6941 (mpp) REVERT: A 484 MET cc_start: 0.6493 (ttm) cc_final: 0.6237 (tpt) REVERT: A 529 MET cc_start: 0.5658 (mpp) cc_final: 0.5442 (mpp) REVERT: A 675 MET cc_start: 0.7896 (ptm) cc_final: 0.7663 (ptp) REVERT: A 795 ARG cc_start: 0.6374 (ttt90) cc_final: 0.6095 (ttt-90) REVERT: A 824 MET cc_start: 0.7127 (tmm) cc_final: 0.6668 (ptt) REVERT: B 234 MET cc_start: 0.8182 (tpp) cc_final: 0.7799 (ttm) REVERT: B 288 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: B 534 MET cc_start: 0.6280 (tpp) cc_final: 0.6030 (tpp) REVERT: B 536 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6455 (mm) REVERT: B 729 LEU cc_start: 0.8641 (tp) cc_final: 0.8153 (pp) REVERT: B 735 PHE cc_start: 0.6592 (OUTLIER) cc_final: 0.6369 (t80) REVERT: B 770 MET cc_start: 0.4780 (mmt) cc_final: 0.4339 (mmm) REVERT: C 235 MET cc_start: 0.6618 (tpp) cc_final: 0.6061 (tpp) REVERT: C 352 MET cc_start: 0.7265 (ppp) cc_final: 0.6965 (ppp) REVERT: C 387 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6079 (tm-30) REVERT: C 519 LEU cc_start: 0.7719 (tp) cc_final: 0.7282 (mt) REVERT: C 529 MET cc_start: 0.7376 (mmm) cc_final: 0.6886 (mpp) REVERT: D 234 MET cc_start: 0.7847 (tpp) cc_final: 0.7477 (ttm) REVERT: D 317 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8850 (p) REVERT: D 415 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: D 536 LEU cc_start: 0.7252 (mm) cc_final: 0.6934 (mm) REVERT: D 705 MET cc_start: 0.8410 (tpp) cc_final: 0.8153 (tpt) REVERT: D 750 CYS cc_start: 0.8356 (p) cc_final: 0.7595 (t) REVERT: D 770 MET cc_start: 0.7505 (tpt) cc_final: 0.7188 (mmt) outliers start: 86 outliers final: 72 residues processed: 282 average time/residue: 0.1472 time to fit residues: 69.3384 Evaluate side-chains 278 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 200 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 40.0000 chunk 179 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 GLN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 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 = 0.4217 r_free = 0.4217 target = 0.149410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101017 restraints weight = 51543.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093804 restraints weight = 46450.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094895 restraints weight = 44825.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095244 restraints weight = 35757.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096611 restraints weight = 34108.881| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24308 Z= 0.163 Angle : 0.640 13.621 32920 Z= 0.315 Chirality : 0.042 0.183 3718 Planarity : 0.004 0.043 4176 Dihedral : 4.386 42.121 3285 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 3.42 % Allowed : 21.08 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.06 (0.16), residues: 2980 helix: 0.89 (0.15), residues: 1278 sheet: -1.90 (0.23), residues: 479 loop : -1.90 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 800 TYR 0.022 0.001 TYR C 692 PHE 0.045 0.002 PHE B 694 TRP 0.038 0.002 TRP C 690 HIS 0.005 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (24298) covalent geometry : angle 0.63919 / 0.31 (32900) SS BOND : bond 0.00385 / 0.18 ( 10) SS BOND : angle 1.07204 / 0.61 ( 20) hydrogen bonds : bond 0.04069 / 2.73 ( 902) hydrogen bonds : angle 4.11384 / 2.84 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 203 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9589 (m) cc_final: 0.9241 (t) REVERT: A 429 MET cc_start: 0.8032 (mpp) cc_final: 0.7567 (mpp) REVERT: A 484 MET cc_start: 0.6923 (ttm) cc_final: 0.6458 (tpt) REVERT: A 529 MET cc_start: 0.5675 (mpp) cc_final: 0.5460 (mpp) REVERT: A 648 MET cc_start: 0.7699 (tmm) cc_final: 0.7487 (tmm) REVERT: A 675 MET cc_start: 0.8093 (ptm) cc_final: 0.7843 (ptp) REVERT: A 824 MET cc_start: 0.7379 (tmm) cc_final: 0.6822 (ptt) REVERT: B 234 MET cc_start: 0.8146 (tpp) cc_final: 0.7749 (ttm) REVERT: B 288 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: B 296 TRP cc_start: 0.7854 (t60) cc_final: 0.7207 (t60) REVERT: B 534 MET cc_start: 0.6220 (tpp) cc_final: 0.5896 (tpp) REVERT: B 536 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6702 (mm) REVERT: B 729 LEU cc_start: 0.8913 (tp) cc_final: 0.8387 (pp) REVERT: B 770 MET cc_start: 0.5595 (mmt) cc_final: 0.5161 (mmm) REVERT: C 235 MET cc_start: 0.6626 (tpp) cc_final: 0.6123 (tpp) REVERT: C 352 MET cc_start: 0.7501 (ppp) cc_final: 0.7213 (ppp) REVERT: C 387 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6022 (tm-30) REVERT: C 519 LEU cc_start: 0.8033 (tp) cc_final: 0.7361 (mt) REVERT: C 535 TYR cc_start: 0.6618 (p90) cc_final: 0.6256 (p90) REVERT: D 234 MET cc_start: 0.7736 (tpp) cc_final: 0.7386 (ttm) REVERT: D 317 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8878 (p) REVERT: D 415 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: D 536 LEU cc_start: 0.7669 (mm) cc_final: 0.7196 (mm) REVERT: D 705 MET cc_start: 0.8934 (tpp) cc_final: 0.8674 (tpt) REVERT: D 709 MET cc_start: 0.7026 (mmp) cc_final: 0.6814 (mmt) REVERT: D 750 CYS cc_start: 0.8665 (p) cc_final: 0.7624 (t) REVERT: D 770 MET cc_start: 0.7880 (tpt) cc_final: 0.7491 (mmt) outliers start: 89 outliers final: 75 residues processed: 278 average time/residue: 0.1484 time to fit residues: 68.6593 Evaluate side-chains 279 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 199 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 247 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 38 optimal weight: 50.0000 chunk 81 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 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 = 0.4206 r_free = 0.4206 target = 0.148293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099332 restraints weight = 51655.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093464 restraints weight = 48214.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.094788 restraints weight = 45135.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095064 restraints weight = 35367.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096201 restraints weight = 34020.197| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24308 Z= 0.198 Angle : 0.682 13.774 32920 Z= 0.337 Chirality : 0.044 0.235 3718 Planarity : 0.004 0.044 4176 Dihedral : 4.580 40.802 3285 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 3.42 % Allowed : 21.23 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.19 (0.15), residues: 2980 helix: 0.76 (0.15), residues: 1281 sheet: -2.07 (0.23), residues: 473 loop : -1.92 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 351 TYR 0.029 0.002 TYR C 666 PHE 0.038 0.002 PHE C 538 TRP 0.038 0.002 TRP C 690 HIS 0.005 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (24298) covalent geometry : angle 0.68162 / 0.34 (32900) SS BOND : bond 0.00432 / 0.21 ( 10) SS BOND : angle 1.10021 / 0.62 ( 20) hydrogen bonds : bond 0.04427 / 2.98 ( 902) hydrogen bonds : angle 4.30346 / 2.98 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 211 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9611 (m) cc_final: 0.9257 (t) REVERT: A 235 MET cc_start: 0.6157 (tpp) cc_final: 0.5676 (tpp) REVERT: A 429 MET cc_start: 0.7811 (mpp) cc_final: 0.7163 (mpp) REVERT: A 484 MET cc_start: 0.7064 (ttm) cc_final: 0.6516 (tpt) REVERT: A 529 MET cc_start: 0.5783 (mpp) cc_final: 0.5560 (mpp) REVERT: A 648 MET cc_start: 0.7613 (tmm) cc_final: 0.7330 (tmm) REVERT: A 675 MET cc_start: 0.8103 (ptm) cc_final: 0.7862 (ptp) REVERT: A 824 MET cc_start: 0.7438 (tmm) cc_final: 0.6945 (ptt) REVERT: B 234 MET cc_start: 0.8231 (tpp) cc_final: 0.7777 (ttm) REVERT: B 288 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: B 534 MET cc_start: 0.6317 (tpp) cc_final: 0.5981 (tpp) REVERT: B 536 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6407 (mm) REVERT: B 729 LEU cc_start: 0.8808 (tp) cc_final: 0.8271 (pp) REVERT: B 770 MET cc_start: 0.5473 (mmt) cc_final: 0.5087 (mmm) REVERT: B 794 MET cc_start: 0.7156 (tpp) cc_final: 0.6751 (tpp) REVERT: C 235 MET cc_start: 0.6517 (tpp) cc_final: 0.6143 (tpp) REVERT: C 352 MET cc_start: 0.7424 (ppp) cc_final: 0.7158 (ppp) REVERT: C 451 LEU cc_start: 0.8236 (pp) cc_final: 0.7838 (mt) REVERT: C 519 LEU cc_start: 0.7998 (tp) cc_final: 0.7405 (mt) REVERT: C 529 MET cc_start: 0.7530 (mmm) cc_final: 0.6962 (mpp) REVERT: C 725 MET cc_start: 0.8006 (pmm) cc_final: 0.7274 (pmm) REVERT: D 153 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: D 234 MET cc_start: 0.7693 (tpp) cc_final: 0.7403 (ttm) REVERT: D 415 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: D 536 LEU cc_start: 0.7537 (mm) cc_final: 0.7060 (mm) REVERT: D 705 MET cc_start: 0.8886 (tpp) cc_final: 0.8597 (tpt) REVERT: D 750 CYS cc_start: 0.8602 (p) cc_final: 0.7660 (t) REVERT: D 770 MET cc_start: 0.7904 (tpt) cc_final: 0.7531 (mmt) outliers start: 89 outliers final: 75 residues processed: 282 average time/residue: 0.1583 time to fit residues: 74.2476 Evaluate side-chains 284 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 205 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 729 HIS Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 198 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 291 optimal weight: 30.0000 chunk 40 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** 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 = 0.4206 r_free = 0.4206 target = 0.148346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.102366 restraints weight = 51480.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.101820 restraints weight = 64751.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101229 restraints weight = 45909.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.100649 restraints weight = 34214.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101048 restraints weight = 34616.892| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24308 Z= 0.185 Angle : 0.674 13.686 32920 Z= 0.333 Chirality : 0.043 0.256 3718 Planarity : 0.004 0.045 4176 Dihedral : 4.522 40.927 3283 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 3.12 % Allowed : 21.42 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.19 (0.15), residues: 2980 helix: 0.77 (0.15), residues: 1283 sheet: -2.12 (0.23), residues: 468 loop : -1.91 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.037 0.002 TYR C 692 PHE 0.038 0.002 PHE C 538 TRP 0.041 0.002 TRP D 498 HIS 0.005 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (24298) covalent geometry : angle 0.67359 / 0.33 (32900) SS BOND : bond 0.00398 / 0.19 ( 10) SS BOND : angle 1.16978 / 0.64 ( 20) hydrogen bonds : bond 0.04281 / 2.88 ( 902) hydrogen bonds : angle 4.29532 / 2.97 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.19 seconds wall clock time: 77 minutes 44.35 seconds (4664.35 seconds total)