Starting phenix.real_space_refine on Fri Mar 6 09:24:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvp_32856/03_2026/7wvp_32856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvp_32856/03_2026/7wvp_32856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wvp_32856/03_2026/7wvp_32856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvp_32856/03_2026/7wvp_32856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wvp_32856/03_2026/7wvp_32856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvp_32856/03_2026/7wvp_32856.map" } resolution = 3.7 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= 0.002 sd= 0.033 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 143 5.16 5 C 18942 2.51 5 N 4926 2.21 5 O 5590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'TRANS': 1002} Chain breaks: 7 Chain: "D" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Time building chain proxies: 6.50, per 1000 atoms: 0.22 Number of scatterers: 29601 At special positions: 0 Unit cell: (149.741, 134.439, 234.995, 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 143 16.00 O 5590 8.00 N 4926 7.00 C 18942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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: 2.22 Conformation dependent library (CDL) restraints added in 1.3 seconds 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 47 sheets defined 24.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.640A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.023A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.992A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.474A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 155' Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.842A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.644A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 removed outlier: 3.878A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 removed outlier: 3.503A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 3.731A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.568A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 279' Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.621A pdb=" N LYS A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.719A pdb=" N PHE A 327 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 removed outlier: 3.504A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 removed outlier: 3.732A pdb=" N ASP A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.623A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.716A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 422' Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.859A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.503A pdb=" N TYR A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.594A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.648A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 508' Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.847A pdb=" N TYR A 515 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 533 removed outlier: 3.942A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 550 removed outlier: 3.504A pdb=" N ALA A 550 " --> pdb=" O SER A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 551 through 559 removed outlier: 4.147A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.608A pdb=" N LEU A 570 " --> pdb=" O TRP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.908A pdb=" N ASN A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.758A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.694A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.798A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.551A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 782 removed outlier: 3.570A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 removed outlier: 3.709A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.537A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.582A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.860A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.649A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.564A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.659A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.654A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.883A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.038A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 4.104A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.869A pdb=" N SER C 637 " --> pdb=" O ARG C 634 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.782A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.637A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 751' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.791A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 removed outlier: 3.705A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.648A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.622A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 removed outlier: 3.586A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.626A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.606A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.543A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.645A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.708A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 4.128A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.506A pdb=" N LYS D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 404 through 408 removed outlier: 3.823A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 408' Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.647A pdb=" N HIS D 505 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 506 " --> pdb=" O VAL D 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 502 through 506' Processing helix chain 'D' and resid 737 through 742 removed outlier: 3.781A pdb=" N TYR D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 737 through 742' Processing helix chain 'D' and resid 753 through 757 removed outlier: 3.603A pdb=" N TYR D 756 " --> pdb=" O LEU D 753 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 757 " --> pdb=" O LEU D 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 753 through 757' Processing helix chain 'D' and resid 758 through 782 removed outlier: 3.969A pdb=" N GLN D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 773 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 776 " --> pdb=" O VAL D 772 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.782A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 825 " --> pdb=" O LEU D 821 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.647A pdb=" N ILE D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.657A pdb=" N MET D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.728A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 918' Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.508A pdb=" N GLY D 932 " --> pdb=" O ASN D 928 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER D 939 " --> pdb=" O GLN D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.197A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.564A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 1032 removed outlier: 4.216A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.486A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.662A pdb=" N THR B 22 " --> pdb=" O PHE B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.538A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.741A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.816A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.658A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.479A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.007A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.683A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.689A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 453 removed outlier: 4.027A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.607A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.347A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B1065 " --> pdb=" O MET B1050 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.347A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.556A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.466A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.750A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.596A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.598A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.578A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.159A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.935A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.551A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.551A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.551A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.019A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.606A pdb=" N THR D 22 " --> pdb=" O PHE D 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 28 through 30 removed outlier: 3.507A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 206 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 204 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 202 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.651A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.530A pdb=" N GLN D 239 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 311 through 319 removed outlier: 3.702A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR D 612 " --> pdb=" O CYS D 649 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.636A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.636A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.536A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.646A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AE9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.978A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 734 through 736 removed outlier: 3.521A pdb=" N THR D 859 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 5.451A pdb=" N VAL D1122 " --> pdb=" O PHE D1089 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE D1089 " --> pdb=" O VAL D1122 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY D1124 " --> pdb=" O ALA D1087 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2412 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: 6.95 Time building geometry restraints manager: 2.88 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: 9366 1.34 - 1.47: 7598 1.47 - 1.59: 13156 1.59 - 1.72: 0 1.72 - 1.85: 194 Bond restraints: 30314 Sorted by residual: bond pdb=" CA ILE C 584 " pdb=" C ILE C 584 " ideal model delta sigma weight residual 1.526 1.474 0.051 1.01e-02 9.80e+03 2.59e+01 bond pdb=" N GLU C 583 " pdb=" CA GLU C 583 " ideal model delta sigma weight residual 1.456 1.397 0.059 1.21e-02 6.83e+03 2.40e+01 bond pdb=" CA ASN B 331 " pdb=" C ASN B 331 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.35e-02 5.49e+03 1.97e+01 bond pdb=" CA PHE B 490 " pdb=" C PHE B 490 " ideal model delta sigma weight residual 1.520 1.564 -0.044 1.02e-02 9.61e+03 1.84e+01 bond pdb=" CA ILE C 584 " pdb=" CB ILE C 584 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.11e-02 8.12e+03 1.25e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 40391 2.60 - 5.21: 708 5.21 - 7.81: 82 7.81 - 10.41: 26 10.41 - 13.02: 6 Bond angle restraints: 41213 Sorted by residual: angle pdb=" N GLY B 526 " pdb=" CA GLY B 526 " pdb=" C GLY B 526 " ideal model delta sigma weight residual 112.10 122.07 -9.97 1.23e+00 6.61e-01 6.57e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 112.90 105.56 7.34 9.60e-01 1.09e+00 5.85e+01 angle pdb=" N SER C 155 " pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 108.60 119.47 -10.87 1.46e+00 4.69e-01 5.54e+01 angle pdb=" C VAL C 159 " pdb=" CA VAL C 159 " pdb=" CB VAL C 159 " ideal model delta sigma weight residual 111.29 100.84 10.45 1.64e+00 3.72e-01 4.06e+01 angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 108.19 100.22 7.97 1.29e+00 6.01e-01 3.82e+01 ... (remaining 41208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16466 17.96 - 35.92: 1293 35.92 - 53.88: 229 53.88 - 71.85: 66 71.85 - 89.81: 23 Dihedral angle restraints: 18077 sinusoidal: 7135 harmonic: 10942 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 -177.19 -89.81 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.16 -87.16 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -170.65 84.65 1 1.00e+01 1.00e-02 8.70e+01 ... (remaining 18074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4098 0.091 - 0.182: 448 0.182 - 0.273: 51 0.273 - 0.364: 3 0.364 - 0.455: 3 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA SER C 155 " pdb=" N SER C 155 " pdb=" C SER C 155 " pdb=" CB SER C 155 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA VAL C 159 " pdb=" N VAL C 159 " pdb=" C VAL C 159 " pdb=" CB VAL C 159 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 4600 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.064 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO C 987 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.064 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO B 987 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " -0.064 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO D 987 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " -0.053 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 9941 2.85 - 3.36: 22207 3.36 - 3.87: 49860 3.87 - 4.39: 53417 4.39 - 4.90: 93562 Nonbonded interactions: 228987 Sorted by model distance: nonbonded pdb=" O SER C 758 " pdb=" OG SER C 758 " model vdw 2.335 3.040 nonbonded pdb=" O SER B 446 " pdb=" OG SER B 446 " model vdw 2.339 3.040 nonbonded pdb=" O ALA D 879 " pdb=" OG1 THR D 883 " model vdw 2.346 3.040 nonbonded pdb=" O LEU D 966 " pdb=" OG SER D 975 " model vdw 2.352 3.040 nonbonded pdb=" O GLN B1002 " pdb=" OG1 THR B1006 " model vdw 2.354 3.040 ... (remaining 228982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) 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: 4.780 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 27.410 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30356 Z= 0.255 Angle : 0.851 13.017 41297 Z= 0.496 Chirality : 0.055 0.455 4603 Planarity : 0.007 0.095 5332 Dihedral : 13.448 87.356 10901 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 0.40 % Allowed : 5.93 % Favored : 93.68 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.59 (0.10), residues: 3700 helix: -5.13 (0.04), residues: 806 sheet: -1.55 (0.19), residues: 567 loop : -2.78 (0.10), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 493 TYR 0.022 0.001 TYR A 385 PHE 0.018 0.001 PHE B 347 TRP 0.028 0.001 TRP A 302 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00483 (30314) covalent geometry : angle 0.84893 (41213) SS BOND : bond 0.00513 ( 42) SS BOND : angle 1.47139 ( 84) hydrogen bonds : bond 0.31755 ( 834) hydrogen bonds : angle 11.54427 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 868 time to evaluate : 1.055 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.4306 (t80) cc_final: 0.3993 (t80) REVERT: A 48 TRP cc_start: 0.1316 (t60) cc_final: 0.0582 (t60) REVERT: A 82 MET cc_start: 0.4902 (mtm) cc_final: 0.4684 (ptp) REVERT: A 249 MET cc_start: 0.0110 (mmt) cc_final: -0.0171 (mpp) REVERT: A 360 MET cc_start: 0.1903 (mmm) cc_final: 0.0979 (tpt) REVERT: A 383 MET cc_start: 0.6268 (tpt) cc_final: 0.5951 (tpt) REVERT: A 480 MET cc_start: -0.4374 (mtt) cc_final: -0.5286 (tpp) REVERT: A 586 ASN cc_start: 0.6374 (p0) cc_final: 0.5986 (p0) REVERT: A 589 GLU cc_start: 0.7449 (pm20) cc_final: 0.7125 (pm20) REVERT: B 43 PHE cc_start: 0.7100 (t80) cc_final: 0.6819 (t80) REVERT: B 78 ARG cc_start: 0.8864 (mtt180) cc_final: 0.8638 (mpt180) REVERT: B 99 ASN cc_start: 0.6992 (m-40) cc_final: 0.6675 (t0) REVERT: B 157 PHE cc_start: 0.6347 (t80) cc_final: 0.5826 (p90) REVERT: B 192 PHE cc_start: 0.7748 (m-80) cc_final: 0.7517 (m-10) REVERT: B 237 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7555 (ptp-170) REVERT: B 307 THR cc_start: 0.8332 (m) cc_final: 0.7250 (p) REVERT: B 313 TYR cc_start: 0.6919 (m-80) cc_final: 0.6235 (m-80) REVERT: B 340 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6584 (mp0) REVERT: B 437 ASN cc_start: 0.8147 (t0) cc_final: 0.7702 (t0) REVERT: B 535 LYS cc_start: 0.8730 (mttt) cc_final: 0.8352 (mmtt) REVERT: B 695 TYR cc_start: 0.7983 (p90) cc_final: 0.7600 (p90) REVERT: B 698 SER cc_start: 0.8401 (t) cc_final: 0.7627 (p) REVERT: B 725 GLU cc_start: 0.6429 (mt-10) cc_final: 0.5747 (mt-10) REVERT: B 727 LEU cc_start: 0.7770 (mt) cc_final: 0.7526 (mp) REVERT: B 752 LEU cc_start: 0.8781 (mp) cc_final: 0.8502 (mp) REVERT: B 776 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8000 (ptpp) REVERT: B 780 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 819 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7123 (mt-10) REVERT: B 822 LEU cc_start: 0.8016 (mt) cc_final: 0.7793 (mt) REVERT: B 856 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8215 (mmmt) REVERT: B 868 GLU cc_start: 0.7663 (mp0) cc_final: 0.7432 (mm-30) REVERT: B 869 MET cc_start: 0.8279 (mtp) cc_final: 0.8015 (mtp) REVERT: B 873 TYR cc_start: 0.7784 (m-80) cc_final: 0.7469 (m-80) REVERT: B 933 LYS cc_start: 0.8540 (mttt) cc_final: 0.8172 (mttm) REVERT: B 954 HIS cc_start: 0.7471 (m170) cc_final: 0.7010 (m170) REVERT: B 980 ILE cc_start: 0.9181 (mm) cc_final: 0.8834 (tp) REVERT: B 981 PHE cc_start: 0.7994 (t80) cc_final: 0.7724 (t80) REVERT: B 997 ILE cc_start: 0.9410 (tt) cc_final: 0.9165 (mm) REVERT: B 1010 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7645 (mm110) REVERT: B 1017 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 1018 ILE cc_start: 0.8970 (tp) cc_final: 0.8751 (mm) REVERT: B 1019 ARG cc_start: 0.7972 (mtp180) cc_final: 0.7772 (mtp180) REVERT: B 1040 VAL cc_start: 0.8785 (t) cc_final: 0.8244 (t) REVERT: B 1050 MET cc_start: 0.6237 (ptp) cc_final: 0.5679 (ptp) REVERT: B 1091 ARG cc_start: 0.6787 (ttp80) cc_final: 0.6396 (ttp80) REVERT: B 1092 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7227 (pm20) REVERT: C 37 TYR cc_start: 0.6813 (p90) cc_final: 0.6168 (p90) REVERT: C 43 PHE cc_start: 0.7307 (t80) cc_final: 0.7004 (t80) REVERT: C 128 ILE cc_start: 0.8845 (mt) cc_final: 0.8433 (mm) REVERT: C 133 PHE cc_start: 0.6974 (m-80) cc_final: 0.6276 (m-10) REVERT: C 135 PHE cc_start: 0.6753 (m-80) cc_final: 0.5766 (m-10) REVERT: C 186 PHE cc_start: 0.4878 (m-80) cc_final: 0.4670 (m-80) REVERT: C 221 SER cc_start: 0.7998 (t) cc_final: 0.7427 (p) REVERT: C 229 LEU cc_start: 0.8877 (mt) cc_final: 0.8585 (pt) REVERT: C 293 LEU cc_start: 0.7436 (tp) cc_final: 0.7150 (tp) REVERT: C 304 LYS cc_start: 0.8473 (tppp) cc_final: 0.8087 (mmmt) REVERT: C 339 ASP cc_start: 0.7808 (m-30) cc_final: 0.6976 (m-30) REVERT: C 358 ILE cc_start: 0.6452 (mt) cc_final: 0.6029 (tt) REVERT: C 368 LEU cc_start: 0.8875 (mm) cc_final: 0.8642 (mt) REVERT: C 396 TYR cc_start: 0.7172 (m-10) cc_final: 0.6831 (m-80) REVERT: C 421 TYR cc_start: 0.7744 (m-80) cc_final: 0.7124 (m-10) REVERT: C 453 TYR cc_start: 0.3218 (p90) cc_final: 0.2967 (p90) REVERT: C 495 TYR cc_start: 0.5417 (m-80) cc_final: 0.4150 (m-80) REVERT: C 505 HIS cc_start: 0.6375 (m-70) cc_final: 0.5081 (m-70) REVERT: C 532 ASN cc_start: 0.8447 (t0) cc_final: 0.7909 (t0) REVERT: C 546 LEU cc_start: 0.6049 (mt) cc_final: 0.5815 (mt) REVERT: C 658 ASN cc_start: 0.6124 (m-40) cc_final: 0.5807 (t0) REVERT: C 695 TYR cc_start: 0.7385 (p90) cc_final: 0.6907 (p90) REVERT: C 717 ASN cc_start: 0.5964 (m-40) cc_final: 0.5416 (t0) REVERT: C 762 GLN cc_start: 0.8638 (mt0) cc_final: 0.8183 (mp10) REVERT: C 773 GLU cc_start: 0.7711 (pt0) cc_final: 0.6915 (pt0) REVERT: C 775 ASP cc_start: 0.8263 (m-30) cc_final: 0.7968 (m-30) REVERT: C 776 LYS cc_start: 0.8489 (mtmm) cc_final: 0.7976 (mtmm) REVERT: C 869 MET cc_start: 0.8367 (mtp) cc_final: 0.7813 (mtp) REVERT: C 872 GLN cc_start: 0.8478 (mt0) cc_final: 0.8211 (mt0) REVERT: C 873 TYR cc_start: 0.7937 (m-80) cc_final: 0.7467 (m-80) REVERT: C 902 MET cc_start: 0.7522 (ttp) cc_final: 0.7115 (ttm) REVERT: C 950 ASP cc_start: 0.8036 (t0) cc_final: 0.7583 (p0) REVERT: C 954 HIS cc_start: 0.7790 (m-70) cc_final: 0.7350 (m90) REVERT: C 957 GLN cc_start: 0.8194 (mt0) cc_final: 0.7638 (tm-30) REVERT: C 964 LYS cc_start: 0.8548 (mttt) cc_final: 0.7985 (mtmm) REVERT: C 1014 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7666 (tpp80) REVERT: C 1028 LYS cc_start: 0.8869 (mttt) cc_final: 0.8572 (mttp) REVERT: C 1050 MET cc_start: 0.4899 (ptp) cc_final: 0.4681 (ptp) REVERT: C 1109 PHE cc_start: 0.5997 (p90) cc_final: 0.5276 (p90) REVERT: C 1115 ILE cc_start: 0.7563 (mt) cc_final: 0.7342 (mm) REVERT: D 49 HIS cc_start: 0.8014 (t70) cc_final: 0.7733 (t-90) REVERT: D 53 ASP cc_start: 0.7200 (t0) cc_final: 0.6738 (t0) REVERT: D 168 PHE cc_start: 0.7713 (t80) cc_final: 0.7290 (t80) REVERT: D 170 TYR cc_start: 0.8125 (t80) cc_final: 0.7145 (t80) REVERT: D 204 TYR cc_start: 0.6707 (m-80) cc_final: 0.5984 (m-80) REVERT: D 205 SER cc_start: 0.7839 (t) cc_final: 0.7616 (p) REVERT: D 206 LYS cc_start: 0.8630 (tptt) cc_final: 0.8405 (tptp) REVERT: D 287 ASP cc_start: 0.8234 (t0) cc_final: 0.7671 (t70) REVERT: D 300 LYS cc_start: 0.8182 (mttt) cc_final: 0.7766 (mtpt) REVERT: D 310 LYS cc_start: 0.8068 (tttt) cc_final: 0.7759 (ttmm) REVERT: D 314 GLN cc_start: 0.8208 (tt0) cc_final: 0.7884 (tm-30) REVERT: D 318 PHE cc_start: 0.6924 (t80) cc_final: 0.6678 (t80) REVERT: D 320 VAL cc_start: 0.7867 (t) cc_final: 0.7382 (t) REVERT: D 533 LEU cc_start: 0.8810 (tt) cc_final: 0.8527 (mm) REVERT: D 557 LYS cc_start: 0.8109 (mttt) cc_final: 0.7901 (mmtt) REVERT: D 654 GLU cc_start: 0.7000 (tt0) cc_final: 0.6678 (tp30) REVERT: D 719 THR cc_start: 0.6808 (t) cc_final: 0.6119 (t) REVERT: D 725 GLU cc_start: 0.6241 (mt-10) cc_final: 0.5955 (mt-10) REVERT: D 746 SER cc_start: 0.7230 (t) cc_final: 0.6837 (t) REVERT: D 759 PHE cc_start: 0.7060 (m-10) cc_final: 0.6678 (m-80) REVERT: D 762 GLN cc_start: 0.8579 (mt0) cc_final: 0.8340 (mt0) REVERT: D 765 ARG cc_start: 0.8257 (mtt180) cc_final: 0.8033 (ttm110) REVERT: D 773 GLU cc_start: 0.8213 (tp30) cc_final: 0.7901 (tp30) REVERT: D 776 LYS cc_start: 0.7734 (tptm) cc_final: 0.7336 (tptm) REVERT: D 780 GLU cc_start: 0.6489 (mt-10) cc_final: 0.5688 (mt-10) REVERT: D 864 LEU cc_start: 0.8221 (tp) cc_final: 0.8015 (tt) REVERT: D 872 GLN cc_start: 0.8469 (mt0) cc_final: 0.7891 (tm-30) REVERT: D 873 TYR cc_start: 0.7464 (m-10) cc_final: 0.7225 (m-80) REVERT: D 887 THR cc_start: 0.7280 (p) cc_final: 0.6915 (p) REVERT: D 888 PHE cc_start: 0.7527 (p90) cc_final: 0.6464 (p90) REVERT: D 907 ASN cc_start: 0.8490 (m-40) cc_final: 0.8274 (m-40) REVERT: D 933 LYS cc_start: 0.8728 (mttt) cc_final: 0.8411 (tppt) REVERT: D 945 LEU cc_start: 0.7818 (mt) cc_final: 0.7502 (mt) REVERT: D 969 LYS cc_start: 0.8532 (mttt) cc_final: 0.8228 (mmmt) REVERT: D 992 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8566 (mm-40) REVERT: D 1000 ARG cc_start: 0.7407 (mtt180) cc_final: 0.6512 (mtp85) REVERT: D 1001 LEU cc_start: 0.8890 (mt) cc_final: 0.8672 (mt) REVERT: D 1017 GLU cc_start: 0.7657 (pt0) cc_final: 0.7229 (tm-30) REVERT: D 1018 ILE cc_start: 0.8834 (tp) cc_final: 0.8434 (mt) REVERT: D 1019 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7513 (tpp-160) REVERT: D 1075 PHE cc_start: 0.7765 (m-80) cc_final: 0.7121 (m-80) REVERT: D 1104 VAL cc_start: 0.7055 (t) cc_final: 0.6665 (p) REVERT: D 1120 THR cc_start: 0.8369 (p) cc_final: 0.8150 (p) outliers start: 13 outliers final: 3 residues processed: 878 average time/residue: 0.1931 time to fit residues: 266.5681 Evaluate side-chains 648 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 645 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 583 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 63 ASN A 81 GLN A 98 GLN A 159 ASN A 210 ASN A 277 ASN A 338 ASN A 378 HIS ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 578 ASN A 586 ASN A 598 GLN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 606 ASN B 751 ASN B 762 GLN B 895 GLN B1005 GLN B1011 GLN C 437 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 949 GLN C1064 HIS C1101 HIS D 99 ASN D 196 ASN D 334 ASN D 477 ASN D 658 ASN D 751 ASN D 895 GLN D 913 GLN D1088 HIS ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.182907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.144487 restraints weight = 86461.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.147978 restraints weight = 49729.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.150267 restraints weight = 32368.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.151716 restraints weight = 23936.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.153026 restraints weight = 19092.788| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30356 Z= 0.154 Angle : 0.649 17.147 41297 Z= 0.336 Chirality : 0.045 0.252 4603 Planarity : 0.005 0.067 5332 Dihedral : 4.724 68.434 4028 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 2.43 % Allowed : 12.92 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.16 (0.11), residues: 3700 helix: -2.87 (0.12), residues: 821 sheet: -0.82 (0.21), residues: 536 loop : -2.22 (0.11), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 983 TYR 0.023 0.002 TYR D 660 PHE 0.026 0.002 PHE D1109 TRP 0.026 0.002 TRP D 104 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00325 (30314) covalent geometry : angle 0.64583 (41213) SS BOND : bond 0.00497 ( 42) SS BOND : angle 1.53924 ( 84) hydrogen bonds : bond 0.04900 ( 834) hydrogen bonds : angle 6.58473 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 716 time to evaluate : 1.051 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: 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 82 MET cc_start: 0.5216 (mtm) cc_final: 0.4985 (ptp) REVERT: A 190 MET cc_start: 0.4432 (ppp) cc_final: 0.3536 (pmm) REVERT: A 360 MET cc_start: 0.1491 (mmm) cc_final: 0.0856 (mmm) REVERT: A 368 ASP cc_start: 0.1994 (t0) cc_final: 0.1728 (t0) REVERT: A 417 HIS cc_start: 0.1071 (t70) cc_final: 0.0832 (t-170) REVERT: A 455 MET cc_start: 0.7125 (ttt) cc_final: 0.6315 (ttt) REVERT: A 480 MET cc_start: -0.4819 (mtt) cc_final: -0.5185 (mmt) REVERT: B 83 VAL cc_start: 0.7990 (t) cc_final: 0.7719 (p) REVERT: B 157 PHE cc_start: 0.5895 (t80) cc_final: 0.5543 (p90) REVERT: B 298 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 307 THR cc_start: 0.8370 (m) cc_final: 0.7926 (p) REVERT: B 313 TYR cc_start: 0.7051 (m-80) cc_final: 0.6811 (m-80) REVERT: B 347 PHE cc_start: 0.3948 (p90) cc_final: 0.2970 (p90) REVERT: B 595 VAL cc_start: 0.7050 (t) cc_final: 0.6652 (m) REVERT: B 698 SER cc_start: 0.8580 (t) cc_final: 0.7825 (p) REVERT: B 723 THR cc_start: 0.7621 (t) cc_final: 0.7180 (p) REVERT: B 727 LEU cc_start: 0.7776 (mt) cc_final: 0.7569 (mp) REVERT: B 752 LEU cc_start: 0.8751 (mp) cc_final: 0.8515 (mp) REVERT: B 820 ASP cc_start: 0.7518 (m-30) cc_final: 0.7270 (m-30) REVERT: B 821 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8215 (mm) REVERT: B 822 LEU cc_start: 0.8308 (mt) cc_final: 0.8042 (mt) REVERT: B 856 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8286 (mmmm) REVERT: B 872 GLN cc_start: 0.7617 (mt0) cc_final: 0.7406 (tm-30) REVERT: B 933 LYS cc_start: 0.8871 (mttt) cc_final: 0.8424 (mmtm) REVERT: B 960 ASN cc_start: 0.8317 (p0) cc_final: 0.7865 (p0) REVERT: B 964 LYS cc_start: 0.8344 (ptpp) cc_final: 0.7843 (ptpp) REVERT: B 980 ILE cc_start: 0.9013 (mm) cc_final: 0.8806 (tp) REVERT: B 996 LEU cc_start: 0.9194 (tp) cc_final: 0.8827 (tt) REVERT: B 997 ILE cc_start: 0.9231 (tt) cc_final: 0.8879 (mm) REVERT: B 1002 GLN cc_start: 0.7943 (tp40) cc_final: 0.7343 (tp40) REVERT: B 1010 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7973 (mm-40) REVERT: B 1029 MET cc_start: 0.8222 (mmm) cc_final: 0.7827 (mmm) REVERT: C 54 LEU cc_start: 0.8271 (mt) cc_final: 0.7879 (pt) REVERT: C 133 PHE cc_start: 0.6799 (m-80) cc_final: 0.6269 (m-80) REVERT: C 309 GLU cc_start: 0.7647 (tp30) cc_final: 0.7227 (tp30) REVERT: C 314 GLN cc_start: 0.8050 (mp10) cc_final: 0.7836 (mp10) REVERT: C 358 ILE cc_start: 0.6726 (mt) cc_final: 0.6030 (tt) REVERT: C 421 TYR cc_start: 0.7457 (m-80) cc_final: 0.6657 (m-10) REVERT: C 696 THR cc_start: 0.7702 (m) cc_final: 0.7421 (p) REVERT: C 733 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7965 (mtpt) REVERT: C 739 THR cc_start: 0.7897 (p) cc_final: 0.7507 (p) REVERT: C 759 PHE cc_start: 0.6476 (t80) cc_final: 0.5308 (t80) REVERT: C 765 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8063 (ptp90) REVERT: C 773 GLU cc_start: 0.7687 (pt0) cc_final: 0.7045 (pt0) REVERT: C 775 ASP cc_start: 0.7930 (m-30) cc_final: 0.7477 (m-30) REVERT: C 776 LYS cc_start: 0.8677 (mtmm) cc_final: 0.7916 (mtmm) REVERT: C 869 MET cc_start: 0.8229 (mtp) cc_final: 0.7842 (mtp) REVERT: C 902 MET cc_start: 0.7245 (ttp) cc_final: 0.6977 (ttm) REVERT: C 921 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8178 (mmmt) REVERT: C 949 GLN cc_start: 0.7182 (tp40) cc_final: 0.6646 (tp-100) REVERT: C 954 HIS cc_start: 0.7640 (m-70) cc_final: 0.7158 (m90) REVERT: C 957 GLN cc_start: 0.8155 (mt0) cc_final: 0.7929 (tm-30) REVERT: C 964 LYS cc_start: 0.8662 (mttt) cc_final: 0.8224 (mtpp) REVERT: C 979 ASP cc_start: 0.7904 (t0) cc_final: 0.7691 (t0) REVERT: C 1005 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8553 (tp40) REVERT: C 1013 ILE cc_start: 0.8868 (pt) cc_final: 0.8645 (mt) REVERT: C 1014 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7972 (tpp80) REVERT: C 1023 ASN cc_start: 0.8543 (m-40) cc_final: 0.8321 (m110) REVERT: C 1028 LYS cc_start: 0.8754 (mttt) cc_final: 0.8475 (mttp) REVERT: C 1050 MET cc_start: 0.5053 (ptp) cc_final: 0.4772 (ptp) REVERT: D 55 PHE cc_start: 0.6675 (m-10) cc_final: 0.6284 (m-10) REVERT: D 196 ASN cc_start: 0.7540 (t0) cc_final: 0.7334 (t0) REVERT: D 206 LYS cc_start: 0.8540 (tptt) cc_final: 0.8304 (tptp) REVERT: D 287 ASP cc_start: 0.8307 (t0) cc_final: 0.8096 (t70) REVERT: D 298 GLU cc_start: 0.8267 (tp30) cc_final: 0.8038 (tp30) REVERT: D 300 LYS cc_start: 0.8540 (mttt) cc_final: 0.8242 (mtpp) REVERT: D 306 PHE cc_start: 0.7602 (m-80) cc_final: 0.7284 (m-80) REVERT: D 320 VAL cc_start: 0.8132 (t) cc_final: 0.7623 (t) REVERT: D 533 LEU cc_start: 0.8835 (tt) cc_final: 0.8272 (mm) REVERT: D 583 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: D 762 GLN cc_start: 0.8343 (mt0) cc_final: 0.8103 (mt0) REVERT: D 773 GLU cc_start: 0.7932 (tp30) cc_final: 0.7046 (tp30) REVERT: D 888 PHE cc_start: 0.7640 (p90) cc_final: 0.6952 (p90) REVERT: D 919 ASN cc_start: 0.6484 (m-40) cc_final: 0.6231 (t0) REVERT: D 933 LYS cc_start: 0.8744 (mttt) cc_final: 0.8470 (tppt) REVERT: D 966 LEU cc_start: 0.8851 (mt) cc_final: 0.8609 (mt) REVERT: D 969 LYS cc_start: 0.8576 (mttt) cc_final: 0.8295 (mppt) REVERT: D 992 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8502 (mm-40) REVERT: D 1010 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7737 (tm-30) REVERT: D 1018 ILE cc_start: 0.8869 (tp) cc_final: 0.8331 (mt) REVERT: D 1110 TYR cc_start: 0.7880 (t80) cc_final: 0.7475 (t80) outliers start: 80 outliers final: 57 residues processed: 765 average time/residue: 0.1810 time to fit residues: 222.9148 Evaluate side-chains 688 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 629 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 95 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 250 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 341 optimal weight: 0.8980 chunk 351 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 305 GLN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN B 49 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 343 ASN B 448 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 613 GLN B 751 ASN B 824 ASN B1005 GLN B1088 HIS B1119 ASN C 134 GLN C 394 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 641 ASN C 703 ASN C 895 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C 978 ASN C1011 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 99 ASN D 207 HIS D 613 GLN D 658 ASN D 913 GLN D 965 GLN D1074 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.172598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.134816 restraints weight = 84271.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.137447 restraints weight = 47927.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.139612 restraints weight = 30937.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.141247 restraints weight = 22242.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.142116 restraints weight = 17277.710| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 30356 Z= 0.269 Angle : 0.764 13.915 41297 Z= 0.402 Chirality : 0.048 0.257 4603 Planarity : 0.005 0.066 5332 Dihedral : 5.275 73.674 4028 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.56 % Allowed : 16.33 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.12), residues: 3700 helix: -1.56 (0.16), residues: 893 sheet: -0.79 (0.20), residues: 598 loop : -1.97 (0.12), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1091 TYR 0.021 0.002 TYR C 266 PHE 0.030 0.003 PHE D 643 TRP 0.030 0.003 TRP D 64 HIS 0.009 0.002 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00552 (30314) covalent geometry : angle 0.76002 (41213) SS BOND : bond 0.00750 ( 42) SS BOND : angle 1.96066 ( 84) hydrogen bonds : bond 0.05112 ( 834) hydrogen bonds : angle 6.33493 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 684 time to evaluate : 0.827 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5402 (ppp) cc_final: 0.4452 (pmm) REVERT: A 360 MET cc_start: 0.2205 (mmm) cc_final: 0.1162 (mmm) REVERT: A 455 MET cc_start: 0.7087 (ttt) cc_final: 0.6519 (ttp) REVERT: A 578 ASN cc_start: 0.7645 (m110) cc_final: 0.7135 (t0) REVERT: A 579 MET cc_start: 0.4437 (mpp) cc_final: 0.3896 (mpp) REVERT: B 78 ARG cc_start: 0.7042 (mpt180) cc_final: 0.6543 (mmt-90) REVERT: B 157 PHE cc_start: 0.6357 (t80) cc_final: 0.6022 (p90) REVERT: B 294 ASP cc_start: 0.7840 (t70) cc_final: 0.7623 (t0) REVERT: B 307 THR cc_start: 0.8364 (m) cc_final: 0.7782 (p) REVERT: B 313 TYR cc_start: 0.7152 (m-80) cc_final: 0.6811 (m-80) REVERT: B 448 ASN cc_start: -0.1536 (OUTLIER) cc_final: -0.1844 (t0) REVERT: B 569 ILE cc_start: 0.8383 (pt) cc_final: 0.7982 (mp) REVERT: B 595 VAL cc_start: 0.7414 (t) cc_final: 0.6940 (m) REVERT: B 695 TYR cc_start: 0.7922 (p90) cc_final: 0.7592 (p90) REVERT: B 698 SER cc_start: 0.8760 (t) cc_final: 0.7805 (p) REVERT: B 727 LEU cc_start: 0.7681 (mt) cc_final: 0.7463 (mt) REVERT: B 752 LEU cc_start: 0.8875 (mp) cc_final: 0.8642 (mp) REVERT: B 820 ASP cc_start: 0.8307 (m-30) cc_final: 0.7812 (m-30) REVERT: B 822 LEU cc_start: 0.8537 (mt) cc_final: 0.8196 (mt) REVERT: B 856 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8447 (mmmm) REVERT: B 872 GLN cc_start: 0.8008 (mt0) cc_final: 0.7456 (tt0) REVERT: B 933 LYS cc_start: 0.9020 (mttt) cc_final: 0.8609 (mmtm) REVERT: B 955 ASN cc_start: 0.8453 (m110) cc_final: 0.8252 (m-40) REVERT: B 960 ASN cc_start: 0.8627 (p0) cc_final: 0.8301 (p0) REVERT: B 964 LYS cc_start: 0.8682 (ptpp) cc_final: 0.8094 (ptpp) REVERT: B 966 LEU cc_start: 0.8602 (mt) cc_final: 0.8344 (mm) REVERT: B 980 ILE cc_start: 0.9243 (mm) cc_final: 0.8924 (tp) REVERT: B 996 LEU cc_start: 0.9436 (tp) cc_final: 0.9208 (tt) REVERT: B 997 ILE cc_start: 0.9434 (tt) cc_final: 0.9233 (mm) REVERT: B 1002 GLN cc_start: 0.8111 (tp40) cc_final: 0.7763 (tp40) REVERT: B 1006 THR cc_start: 0.8893 (m) cc_final: 0.8264 (p) REVERT: B 1010 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8157 (mm-40) REVERT: B 1017 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 1019 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.7763 (ttp-110) REVERT: B 1031 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6853 (mm-30) REVERT: B 1101 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.5847 (m170) REVERT: C 49 HIS cc_start: 0.8056 (t-170) cc_final: 0.7757 (t-170) REVERT: C 108 THR cc_start: 0.7912 (m) cc_final: 0.7655 (p) REVERT: C 135 PHE cc_start: 0.6616 (m-10) cc_final: 0.5910 (m-10) REVERT: C 314 GLN cc_start: 0.8052 (mp10) cc_final: 0.7787 (mp10) REVERT: C 421 TYR cc_start: 0.7313 (m-80) cc_final: 0.6518 (m-10) REVERT: C 733 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8188 (mtpt) REVERT: C 773 GLU cc_start: 0.7994 (pt0) cc_final: 0.7452 (pt0) REVERT: C 775 ASP cc_start: 0.7960 (m-30) cc_final: 0.7568 (m-30) REVERT: C 776 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8174 (mtmm) REVERT: C 821 LEU cc_start: 0.8707 (mt) cc_final: 0.8451 (mt) REVERT: C 868 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7741 (mm-30) REVERT: C 873 TYR cc_start: 0.8058 (m-80) cc_final: 0.7662 (m-80) REVERT: C 902 MET cc_start: 0.7554 (ttp) cc_final: 0.7220 (ttm) REVERT: C 921 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8539 (mmmt) REVERT: C 949 GLN cc_start: 0.7804 (tp40) cc_final: 0.7277 (tp-100) REVERT: C 954 HIS cc_start: 0.7897 (m-70) cc_final: 0.7067 (m90) REVERT: C 957 GLN cc_start: 0.8423 (mt0) cc_final: 0.8091 (tp40) REVERT: C 964 LYS cc_start: 0.8978 (mttt) cc_final: 0.8749 (mttt) REVERT: C 983 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.8105 (ptm-80) REVERT: C 993 ILE cc_start: 0.8469 (tt) cc_final: 0.8261 (tp) REVERT: C 1005 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8149 (tp-100) REVERT: C 1014 ARG cc_start: 0.8471 (mtt180) cc_final: 0.8103 (tpp80) REVERT: C 1028 LYS cc_start: 0.8816 (mttt) cc_final: 0.8526 (mttp) REVERT: C 1031 GLU cc_start: 0.7365 (tt0) cc_final: 0.7027 (tt0) REVERT: D 55 PHE cc_start: 0.6989 (m-10) cc_final: 0.6467 (m-10) REVERT: D 196 ASN cc_start: 0.7658 (t0) cc_final: 0.7166 (t0) REVERT: D 287 ASP cc_start: 0.8477 (t0) cc_final: 0.8257 (t70) REVERT: D 300 LYS cc_start: 0.8551 (mttt) cc_final: 0.8195 (mtpp) REVERT: D 317 ASN cc_start: 0.8562 (m-40) cc_final: 0.8362 (m-40) REVERT: D 320 VAL cc_start: 0.8334 (t) cc_final: 0.7796 (m) REVERT: D 533 LEU cc_start: 0.8964 (tt) cc_final: 0.8418 (mm) REVERT: D 731 MET cc_start: 0.7659 (ptm) cc_final: 0.7348 (ptm) REVERT: D 765 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8425 (ttp-110) REVERT: D 772 VAL cc_start: 0.8934 (t) cc_final: 0.8620 (p) REVERT: D 775 ASP cc_start: 0.7700 (p0) cc_final: 0.7431 (p0) REVERT: D 776 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8035 (mtmm) REVERT: D 861 LEU cc_start: 0.8634 (mm) cc_final: 0.8409 (mt) REVERT: D 888 PHE cc_start: 0.7952 (p90) cc_final: 0.7336 (p90) REVERT: D 933 LYS cc_start: 0.8966 (mttt) cc_final: 0.8632 (tppt) REVERT: D 964 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8377 (ttmm) REVERT: D 992 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8759 (mm-40) REVERT: D 1010 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7923 (tm-30) REVERT: D 1018 ILE cc_start: 0.8763 (tp) cc_final: 0.8359 (mt) REVERT: D 1019 ARG cc_start: 0.8447 (ttt90) cc_final: 0.7849 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8730 (m110) cc_final: 0.8193 (m110) outliers start: 150 outliers final: 92 residues processed: 772 average time/residue: 0.1749 time to fit residues: 219.6058 Evaluate side-chains 731 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 636 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 157 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 188 optimal weight: 0.1980 chunk 200 optimal weight: 0.0040 chunk 194 optimal weight: 0.9990 chunk 314 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 61 ASN A 98 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 546 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 207 HIS C 271 GLN C 519 HIS C 606 ASN C 703 ASN C 779 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 606 ASN D 613 GLN D 957 GLN D 965 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.176121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.137385 restraints weight = 81740.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.139937 restraints weight = 46110.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.142473 restraints weight = 30305.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.144212 restraints weight = 22231.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.145065 restraints weight = 17761.329| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30356 Z= 0.126 Angle : 0.622 14.442 41297 Z= 0.315 Chirality : 0.045 0.179 4603 Planarity : 0.004 0.058 5332 Dihedral : 4.823 69.330 4028 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.71 % Allowed : 20.16 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 3700 helix: -0.98 (0.17), residues: 862 sheet: -0.67 (0.20), residues: 582 loop : -1.74 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 765 TYR 0.028 0.002 TYR B 655 PHE 0.029 0.002 PHE D 759 TRP 0.027 0.002 TRP C 104 HIS 0.008 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00280 (30314) covalent geometry : angle 0.61951 (41213) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.40840 ( 84) hydrogen bonds : bond 0.03909 ( 834) hydrogen bonds : angle 5.83564 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 660 time to evaluate : 0.972 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5276 (ppp) cc_final: 0.4547 (pmm) REVERT: A 360 MET cc_start: 0.1869 (mmm) cc_final: 0.1008 (mmm) REVERT: A 455 MET cc_start: 0.6931 (ttt) cc_final: 0.6494 (ttp) REVERT: A 578 ASN cc_start: 0.7729 (m110) cc_final: 0.7380 (t0) REVERT: A 579 MET cc_start: 0.5423 (mpp) cc_final: 0.4880 (mpp) REVERT: B 78 ARG cc_start: 0.7160 (mpt180) cc_final: 0.6696 (mmt-90) REVERT: B 157 PHE cc_start: 0.6667 (t80) cc_final: 0.6451 (p90) REVERT: B 294 ASP cc_start: 0.7881 (t70) cc_final: 0.7650 (t0) REVERT: B 307 THR cc_start: 0.8325 (m) cc_final: 0.7941 (p) REVERT: B 347 PHE cc_start: 0.3926 (p90) cc_final: 0.2841 (p90) REVERT: B 569 ILE cc_start: 0.8396 (pt) cc_final: 0.8023 (mp) REVERT: B 595 VAL cc_start: 0.7217 (t) cc_final: 0.6754 (m) REVERT: B 698 SER cc_start: 0.8529 (t) cc_final: 0.7504 (p) REVERT: B 727 LEU cc_start: 0.7572 (mt) cc_final: 0.7352 (mt) REVERT: B 752 LEU cc_start: 0.8963 (mp) cc_final: 0.8736 (mp) REVERT: B 776 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7901 (ptpp) REVERT: B 814 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8064 (mmmt) REVERT: B 820 ASP cc_start: 0.8385 (m-30) cc_final: 0.7880 (m-30) REVERT: B 822 LEU cc_start: 0.8507 (mt) cc_final: 0.8095 (mt) REVERT: B 856 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8426 (mmmm) REVERT: B 933 LYS cc_start: 0.9039 (mttt) cc_final: 0.8605 (mmtm) REVERT: B 955 ASN cc_start: 0.8584 (m110) cc_final: 0.8235 (m-40) REVERT: B 960 ASN cc_start: 0.8611 (p0) cc_final: 0.8364 (p0) REVERT: B 964 LYS cc_start: 0.8635 (ptpp) cc_final: 0.8021 (ptpp) REVERT: B 966 LEU cc_start: 0.8582 (mt) cc_final: 0.8293 (mm) REVERT: B 980 ILE cc_start: 0.9143 (mm) cc_final: 0.8799 (tp) REVERT: B 995 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7872 (mtp-110) REVERT: B 996 LEU cc_start: 0.9400 (tp) cc_final: 0.9125 (tt) REVERT: B 997 ILE cc_start: 0.9384 (tt) cc_final: 0.9118 (mm) REVERT: B 1001 LEU cc_start: 0.9192 (mt) cc_final: 0.8281 (tt) REVERT: B 1002 GLN cc_start: 0.8039 (tp40) cc_final: 0.7560 (tp40) REVERT: B 1005 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: B 1010 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8143 (mm-40) REVERT: B 1017 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 1019 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.7729 (ttp-110) REVERT: B 1029 MET cc_start: 0.8390 (mmm) cc_final: 0.8039 (mmm) REVERT: B 1031 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6702 (mm-30) REVERT: B 1101 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.5863 (m170) REVERT: C 108 THR cc_start: 0.8006 (m) cc_final: 0.7771 (p) REVERT: C 135 PHE cc_start: 0.6610 (m-80) cc_final: 0.5989 (m-10) REVERT: C 223 LEU cc_start: 0.8264 (mp) cc_final: 0.7871 (tp) REVERT: C 290 ASP cc_start: 0.7468 (t0) cc_final: 0.6735 (t0) REVERT: C 294 ASP cc_start: 0.7122 (t0) cc_final: 0.6295 (t0) REVERT: C 314 GLN cc_start: 0.7938 (mp10) cc_final: 0.7644 (mp10) REVERT: C 378 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7744 (ptpp) REVERT: C 421 TYR cc_start: 0.7372 (m-80) cc_final: 0.6606 (m-10) REVERT: C 697 MET cc_start: 0.7770 (ppp) cc_final: 0.7487 (ppp) REVERT: C 733 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8099 (mtpt) REVERT: C 740 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6914 (tpp) REVERT: C 773 GLU cc_start: 0.8006 (pt0) cc_final: 0.7451 (pt0) REVERT: C 775 ASP cc_start: 0.7889 (m-30) cc_final: 0.7453 (m-30) REVERT: C 776 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8103 (mtmm) REVERT: C 821 LEU cc_start: 0.8698 (mt) cc_final: 0.8400 (mt) REVERT: C 858 LEU cc_start: 0.8873 (mm) cc_final: 0.8651 (mt) REVERT: C 868 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7920 (mm-30) REVERT: C 873 TYR cc_start: 0.8026 (m-80) cc_final: 0.7669 (m-80) REVERT: C 902 MET cc_start: 0.7633 (ttp) cc_final: 0.7108 (ttm) REVERT: C 921 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8529 (mmmt) REVERT: C 949 GLN cc_start: 0.7813 (tp40) cc_final: 0.7205 (tp-100) REVERT: C 953 ASN cc_start: 0.8231 (p0) cc_final: 0.7627 (p0) REVERT: C 954 HIS cc_start: 0.7907 (m-70) cc_final: 0.7123 (m-70) REVERT: C 957 GLN cc_start: 0.8493 (mt0) cc_final: 0.8236 (mt0) REVERT: C 983 ARG cc_start: 0.8308 (ptm-80) cc_final: 0.8102 (ptm-80) REVERT: C 1005 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8037 (tp-100) REVERT: C 1014 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8207 (tpp80) REVERT: C 1028 LYS cc_start: 0.8829 (mttt) cc_final: 0.8565 (mttp) REVERT: C 1031 GLU cc_start: 0.7464 (tt0) cc_final: 0.7060 (tt0) REVERT: C 1050 MET cc_start: 0.5130 (ptp) cc_final: 0.4069 (ptp) REVERT: D 55 PHE cc_start: 0.6915 (m-10) cc_final: 0.6372 (m-10) REVERT: D 101 ILE cc_start: 0.8648 (mp) cc_final: 0.8377 (tp) REVERT: D 196 ASN cc_start: 0.7774 (t0) cc_final: 0.7196 (t0) REVERT: D 206 LYS cc_start: 0.8249 (tppt) cc_final: 0.7937 (tptp) REVERT: D 234 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.7132 (p0) REVERT: D 273 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7645 (ttm110) REVERT: D 287 ASP cc_start: 0.8451 (t0) cc_final: 0.8176 (t70) REVERT: D 300 LYS cc_start: 0.8394 (mttt) cc_final: 0.8034 (mtpt) REVERT: D 320 VAL cc_start: 0.8295 (t) cc_final: 0.7853 (m) REVERT: D 543 PHE cc_start: 0.8034 (m-10) cc_final: 0.7789 (m-80) REVERT: D 557 LYS cc_start: 0.6285 (mmtt) cc_final: 0.6058 (mmtm) REVERT: D 731 MET cc_start: 0.7746 (ptm) cc_final: 0.7332 (ptm) REVERT: D 762 GLN cc_start: 0.8504 (mt0) cc_final: 0.8261 (mt0) REVERT: D 765 ARG cc_start: 0.8653 (ttm110) cc_final: 0.8277 (ttm110) REVERT: D 772 VAL cc_start: 0.8859 (t) cc_final: 0.8543 (p) REVERT: D 775 ASP cc_start: 0.7750 (p0) cc_final: 0.7432 (p0) REVERT: D 776 LYS cc_start: 0.8276 (mtmm) cc_final: 0.7957 (mtmm) REVERT: D 819 GLU cc_start: 0.8244 (tp30) cc_final: 0.8036 (tp30) REVERT: D 859 THR cc_start: 0.7814 (m) cc_final: 0.7337 (p) REVERT: D 861 LEU cc_start: 0.8643 (mm) cc_final: 0.8414 (mt) REVERT: D 873 TYR cc_start: 0.7553 (m-80) cc_final: 0.7305 (m-80) REVERT: D 888 PHE cc_start: 0.7928 (p90) cc_final: 0.7136 (p90) REVERT: D 919 ASN cc_start: 0.6993 (m110) cc_final: 0.6498 (p0) REVERT: D 933 LYS cc_start: 0.8914 (mttt) cc_final: 0.8551 (tppt) REVERT: D 969 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8204 (mmmt) REVERT: D 992 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8743 (mm-40) REVERT: D 1010 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 1018 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8419 (mt) REVERT: D 1019 ARG cc_start: 0.8497 (ttt90) cc_final: 0.7746 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8680 (m110) cc_final: 0.7998 (m110) REVERT: D 1107 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7135 (mtt90) outliers start: 122 outliers final: 83 residues processed: 735 average time/residue: 0.1807 time to fit residues: 214.4579 Evaluate side-chains 711 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 622 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 227 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 363 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 315 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 240 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 188 ASN C 207 HIS C 271 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 613 GLN D 965 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.175212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.136638 restraints weight = 82359.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.139797 restraints weight = 46469.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.142020 restraints weight = 30158.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.143585 restraints weight = 22077.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.144855 restraints weight = 17765.537| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30356 Z= 0.139 Angle : 0.627 13.579 41297 Z= 0.318 Chirality : 0.045 0.182 4603 Planarity : 0.004 0.056 5332 Dihedral : 4.549 55.968 4025 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.23 % Allowed : 20.37 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 3700 helix: -0.71 (0.18), residues: 853 sheet: -0.56 (0.20), residues: 589 loop : -1.64 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 765 TYR 0.022 0.002 TYR B 655 PHE 0.038 0.002 PHE D 92 TRP 0.027 0.001 TRP C 104 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00306 (30314) covalent geometry : angle 0.62512 (41213) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.35577 ( 84) hydrogen bonds : bond 0.03838 ( 834) hydrogen bonds : angle 5.69047 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 654 time to evaluate : 1.048 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: symmetry clash REVERT: A 190 MET cc_start: 0.5442 (ppp) cc_final: 0.4681 (pmm) REVERT: A 360 MET cc_start: 0.1933 (mmm) cc_final: 0.1155 (mmm) REVERT: A 368 ASP cc_start: 0.2141 (t0) cc_final: 0.1761 (t0) REVERT: A 455 MET cc_start: 0.6852 (ttt) cc_final: 0.5955 (ttt) REVERT: A 480 MET cc_start: -0.5130 (mtm) cc_final: -0.5531 (mmt) REVERT: A 578 ASN cc_start: 0.7836 (m110) cc_final: 0.7452 (t0) REVERT: A 579 MET cc_start: 0.5004 (mpp) cc_final: 0.4640 (mpp) REVERT: B 78 ARG cc_start: 0.7098 (mpt180) cc_final: 0.6578 (mmt-90) REVERT: B 278 LYS cc_start: 0.7989 (tptt) cc_final: 0.7762 (tptt) REVERT: B 294 ASP cc_start: 0.7979 (t70) cc_final: 0.7751 (t0) REVERT: B 307 THR cc_start: 0.8357 (m) cc_final: 0.7845 (p) REVERT: B 347 PHE cc_start: 0.4373 (p90) cc_final: 0.3303 (p90) REVERT: B 438 SER cc_start: 0.5811 (OUTLIER) cc_final: 0.4918 (p) REVERT: B 569 ILE cc_start: 0.8481 (pt) cc_final: 0.8153 (mp) REVERT: B 595 VAL cc_start: 0.7260 (t) cc_final: 0.6814 (m) REVERT: B 698 SER cc_start: 0.8457 (t) cc_final: 0.7538 (p) REVERT: B 752 LEU cc_start: 0.8981 (mp) cc_final: 0.8714 (mp) REVERT: B 820 ASP cc_start: 0.8505 (m-30) cc_final: 0.8028 (m-30) REVERT: B 822 LEU cc_start: 0.8527 (mt) cc_final: 0.8135 (mt) REVERT: B 856 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8251 (mmmm) REVERT: B 933 LYS cc_start: 0.9055 (mttt) cc_final: 0.8680 (mttm) REVERT: B 955 ASN cc_start: 0.8559 (m110) cc_final: 0.8344 (m-40) REVERT: B 964 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8025 (ptpp) REVERT: B 966 LEU cc_start: 0.8596 (mt) cc_final: 0.8333 (mm) REVERT: B 980 ILE cc_start: 0.9179 (mm) cc_final: 0.8791 (tp) REVERT: B 996 LEU cc_start: 0.9395 (tp) cc_final: 0.9158 (tt) REVERT: B 1002 GLN cc_start: 0.8045 (tp40) cc_final: 0.7450 (tp40) REVERT: B 1010 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8104 (mm-40) REVERT: B 1017 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8068 (tm-30) REVERT: B 1019 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.7733 (ttp-110) REVERT: B 1029 MET cc_start: 0.8375 (mmm) cc_final: 0.8051 (mmm) REVERT: C 108 THR cc_start: 0.8025 (m) cc_final: 0.7807 (p) REVERT: C 135 PHE cc_start: 0.6846 (m-80) cc_final: 0.6300 (m-10) REVERT: C 191 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7681 (mt-10) REVERT: C 314 GLN cc_start: 0.7929 (mp10) cc_final: 0.7588 (mp10) REVERT: C 421 TYR cc_start: 0.7375 (m-80) cc_final: 0.6611 (m-10) REVERT: C 516 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: C 697 MET cc_start: 0.7883 (ppp) cc_final: 0.7556 (ppp) REVERT: C 698 SER cc_start: 0.8154 (t) cc_final: 0.7754 (p) REVERT: C 733 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8250 (mtpt) REVERT: C 740 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6760 (tpp) REVERT: C 773 GLU cc_start: 0.8037 (pt0) cc_final: 0.7563 (pt0) REVERT: C 775 ASP cc_start: 0.7942 (m-30) cc_final: 0.7433 (m-30) REVERT: C 776 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8125 (mtmm) REVERT: C 821 LEU cc_start: 0.8655 (mt) cc_final: 0.8354 (mt) REVERT: C 858 LEU cc_start: 0.8870 (mm) cc_final: 0.8643 (mt) REVERT: C 868 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 902 MET cc_start: 0.7562 (ttp) cc_final: 0.7167 (ttm) REVERT: C 916 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6161 (tt) REVERT: C 921 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8530 (mmmt) REVERT: C 949 GLN cc_start: 0.7819 (tp40) cc_final: 0.7103 (tp-100) REVERT: C 953 ASN cc_start: 0.8225 (p0) cc_final: 0.7776 (p0) REVERT: C 954 HIS cc_start: 0.7894 (m-70) cc_final: 0.7191 (m-70) REVERT: C 1005 GLN cc_start: 0.8561 (tp-100) cc_final: 0.7999 (tp-100) REVERT: C 1014 ARG cc_start: 0.8470 (mtt180) cc_final: 0.8167 (tpp80) REVERT: C 1028 LYS cc_start: 0.8820 (mttt) cc_final: 0.8606 (mttp) REVERT: C 1031 GLU cc_start: 0.7565 (tt0) cc_final: 0.7118 (tt0) REVERT: D 55 PHE cc_start: 0.6848 (m-10) cc_final: 0.6371 (m-10) REVERT: D 100 ILE cc_start: 0.8027 (mt) cc_final: 0.7794 (mt) REVERT: D 196 ASN cc_start: 0.7727 (t0) cc_final: 0.7331 (t0) REVERT: D 273 ARG cc_start: 0.7959 (mmt90) cc_final: 0.7717 (ttm110) REVERT: D 287 ASP cc_start: 0.8480 (t0) cc_final: 0.8219 (t70) REVERT: D 300 LYS cc_start: 0.8390 (mttt) cc_final: 0.8028 (mtpt) REVERT: D 320 VAL cc_start: 0.8348 (t) cc_final: 0.7880 (m) REVERT: D 557 LYS cc_start: 0.5992 (mmtt) cc_final: 0.5599 (mmtt) REVERT: D 731 MET cc_start: 0.7730 (ptm) cc_final: 0.7359 (ptm) REVERT: D 762 GLN cc_start: 0.8478 (mt0) cc_final: 0.8237 (mt0) REVERT: D 765 ARG cc_start: 0.8636 (ttm110) cc_final: 0.8224 (ttm110) REVERT: D 772 VAL cc_start: 0.8869 (t) cc_final: 0.8640 (p) REVERT: D 775 ASP cc_start: 0.7803 (p0) cc_final: 0.7578 (p0) REVERT: D 776 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8167 (mtmm) REVERT: D 787 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7725 (mm-40) REVERT: D 819 GLU cc_start: 0.8198 (tp30) cc_final: 0.7970 (tp30) REVERT: D 859 THR cc_start: 0.7962 (m) cc_final: 0.7548 (p) REVERT: D 888 PHE cc_start: 0.7937 (p90) cc_final: 0.7144 (p90) REVERT: D 919 ASN cc_start: 0.7013 (m110) cc_final: 0.6541 (p0) REVERT: D 933 LYS cc_start: 0.8931 (mttt) cc_final: 0.8574 (tppt) REVERT: D 965 GLN cc_start: 0.8332 (mm110) cc_final: 0.8107 (mm110) REVERT: D 1010 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7767 (tm-30) REVERT: D 1019 ARG cc_start: 0.8517 (ttt90) cc_final: 0.7755 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8683 (m110) cc_final: 0.8005 (m110) REVERT: D 1075 PHE cc_start: 0.6970 (m-80) cc_final: 0.6684 (m-80) outliers start: 139 outliers final: 100 residues processed: 732 average time/residue: 0.1727 time to fit residues: 206.0639 Evaluate side-chains 730 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 626 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 340 optimal weight: 0.5980 chunk 287 optimal weight: 0.7980 chunk 324 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1088 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 872 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 606 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.173966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.134446 restraints weight = 82815.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.137904 restraints weight = 46789.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.140155 restraints weight = 30842.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.141649 restraints weight = 22827.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.142761 restraints weight = 18292.594| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30356 Z= 0.145 Angle : 0.645 13.569 41297 Z= 0.324 Chirality : 0.045 0.194 4603 Planarity : 0.004 0.053 5332 Dihedral : 4.525 56.735 4024 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.56 % Allowed : 21.65 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 3700 helix: -0.49 (0.18), residues: 847 sheet: -0.60 (0.20), residues: 615 loop : -1.57 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 765 TYR 0.023 0.002 TYR C 674 PHE 0.047 0.002 PHE D 92 TRP 0.028 0.002 TRP C 104 HIS 0.019 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00319 (30314) covalent geometry : angle 0.64165 (41213) SS BOND : bond 0.00364 ( 42) SS BOND : angle 1.49539 ( 84) hydrogen bonds : bond 0.03800 ( 834) hydrogen bonds : angle 5.64949 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 641 time to evaluate : 1.007 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5742 (ppp) cc_final: 0.5151 (pmm) REVERT: A 360 MET cc_start: 0.1888 (mmm) cc_final: 0.1079 (mmm) REVERT: A 455 MET cc_start: 0.6861 (ttt) cc_final: 0.6014 (ttt) REVERT: A 480 MET cc_start: -0.5165 (mtm) cc_final: -0.5487 (mmt) REVERT: A 578 ASN cc_start: 0.7860 (m110) cc_final: 0.7468 (t0) REVERT: A 579 MET cc_start: 0.5406 (mpp) cc_final: 0.4906 (mpp) REVERT: B 278 LYS cc_start: 0.8093 (tptt) cc_final: 0.7841 (tptt) REVERT: B 307 THR cc_start: 0.8357 (m) cc_final: 0.7987 (p) REVERT: B 347 PHE cc_start: 0.4424 (p90) cc_final: 0.3340 (p90) REVERT: B 349 SER cc_start: -0.0441 (OUTLIER) cc_final: -0.1259 (t) REVERT: B 438 SER cc_start: 0.6115 (OUTLIER) cc_final: 0.5200 (p) REVERT: B 569 ILE cc_start: 0.8539 (pt) cc_final: 0.8231 (mp) REVERT: B 595 VAL cc_start: 0.7452 (t) cc_final: 0.7049 (m) REVERT: B 698 SER cc_start: 0.8506 (t) cc_final: 0.7630 (p) REVERT: B 748 GLU cc_start: 0.8294 (pm20) cc_final: 0.7923 (pm20) REVERT: B 752 LEU cc_start: 0.8852 (mp) cc_final: 0.8636 (mp) REVERT: B 776 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7929 (ptpp) REVERT: B 820 ASP cc_start: 0.8548 (m-30) cc_final: 0.8169 (m-30) REVERT: B 822 LEU cc_start: 0.8522 (mt) cc_final: 0.8228 (mt) REVERT: B 856 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8243 (mmmm) REVERT: B 933 LYS cc_start: 0.9020 (mttt) cc_final: 0.8647 (mttm) REVERT: B 964 LYS cc_start: 0.8693 (ptpp) cc_final: 0.8136 (ptpp) REVERT: B 981 PHE cc_start: 0.7585 (t80) cc_final: 0.6788 (t80) REVERT: B 996 LEU cc_start: 0.9390 (tp) cc_final: 0.9172 (tt) REVERT: B 1002 GLN cc_start: 0.7987 (tp40) cc_final: 0.7411 (tp40) REVERT: B 1010 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8058 (mm-40) REVERT: B 1017 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8022 (tm-30) REVERT: B 1019 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.7661 (ttp-110) REVERT: B 1029 MET cc_start: 0.8488 (mmm) cc_final: 0.8193 (mmm) REVERT: B 1101 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.5763 (m90) REVERT: C 135 PHE cc_start: 0.6951 (m-80) cc_final: 0.6430 (m-10) REVERT: C 314 GLN cc_start: 0.7944 (mp10) cc_final: 0.7585 (mp10) REVERT: C 421 TYR cc_start: 0.7326 (m-80) cc_final: 0.6562 (m-10) REVERT: C 495 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.4784 (m-10) REVERT: C 516 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: C 697 MET cc_start: 0.7919 (ppp) cc_final: 0.7566 (ppp) REVERT: C 698 SER cc_start: 0.8149 (t) cc_final: 0.7792 (p) REVERT: C 733 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8193 (mtpt) REVERT: C 737 ASP cc_start: 0.7365 (p0) cc_final: 0.6282 (p0) REVERT: C 773 GLU cc_start: 0.7956 (pt0) cc_final: 0.7464 (pt0) REVERT: C 775 ASP cc_start: 0.7963 (m-30) cc_final: 0.7422 (m-30) REVERT: C 776 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8133 (mtmm) REVERT: C 821 LEU cc_start: 0.8613 (mt) cc_final: 0.8333 (mt) REVERT: C 858 LEU cc_start: 0.8882 (mm) cc_final: 0.8659 (mt) REVERT: C 868 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7754 (mm-30) REVERT: C 902 MET cc_start: 0.7540 (ttp) cc_final: 0.7190 (ttm) REVERT: C 921 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8508 (mmmt) REVERT: C 949 GLN cc_start: 0.7776 (tp40) cc_final: 0.7014 (tp-100) REVERT: C 953 ASN cc_start: 0.8145 (p0) cc_final: 0.7797 (p0) REVERT: C 954 HIS cc_start: 0.7746 (m-70) cc_final: 0.7091 (m-70) REVERT: C 983 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7904 (ptm-80) REVERT: C 1005 GLN cc_start: 0.8474 (tp-100) cc_final: 0.7896 (tp40) REVERT: C 1014 ARG cc_start: 0.8328 (mtt180) cc_final: 0.8057 (tpp80) REVERT: C 1031 GLU cc_start: 0.7465 (tt0) cc_final: 0.7153 (tt0) REVERT: C 1050 MET cc_start: 0.5253 (ptp) cc_final: 0.4667 (ptp) REVERT: D 55 PHE cc_start: 0.6838 (m-10) cc_final: 0.6452 (m-10) REVERT: D 100 ILE cc_start: 0.8036 (mt) cc_final: 0.7765 (mt) REVERT: D 131 CYS cc_start: 0.4343 (OUTLIER) cc_final: 0.2543 (m) REVERT: D 196 ASN cc_start: 0.7653 (t0) cc_final: 0.7275 (t0) REVERT: D 287 ASP cc_start: 0.8497 (t0) cc_final: 0.8260 (t70) REVERT: D 300 LYS cc_start: 0.8334 (mttt) cc_final: 0.8023 (mtpt) REVERT: D 304 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8249 (mmmm) REVERT: D 326 ILE cc_start: 0.4456 (OUTLIER) cc_final: 0.4104 (tp) REVERT: D 557 LYS cc_start: 0.6010 (mmtt) cc_final: 0.5571 (mmtt) REVERT: D 731 MET cc_start: 0.7670 (ptm) cc_final: 0.7320 (ptm) REVERT: D 762 GLN cc_start: 0.8388 (mt0) cc_final: 0.8168 (mt0) REVERT: D 765 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8156 (ttm110) REVERT: D 772 VAL cc_start: 0.8815 (t) cc_final: 0.8600 (p) REVERT: D 775 ASP cc_start: 0.7804 (p0) cc_final: 0.7516 (p0) REVERT: D 776 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8145 (mtmm) REVERT: D 819 GLU cc_start: 0.8071 (tp30) cc_final: 0.7862 (tp30) REVERT: D 888 PHE cc_start: 0.7873 (p90) cc_final: 0.7271 (p90) REVERT: D 919 ASN cc_start: 0.6851 (m110) cc_final: 0.6467 (p0) REVERT: D 933 LYS cc_start: 0.8896 (mttt) cc_final: 0.8551 (tppt) REVERT: D 969 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8388 (mmmt) REVERT: D 1010 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 1019 ARG cc_start: 0.8478 (ttt90) cc_final: 0.7734 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8681 (m110) cc_final: 0.8018 (m110) REVERT: D 1075 PHE cc_start: 0.6793 (m-80) cc_final: 0.6546 (m-80) REVERT: D 1107 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7084 (mtt90) REVERT: D 1111 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5951 (tm-30) REVERT: D 1113 GLN cc_start: 0.7245 (mp10) cc_final: 0.5998 (mp10) outliers start: 150 outliers final: 108 residues processed: 727 average time/residue: 0.1754 time to fit residues: 208.0837 Evaluate side-chains 733 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 617 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1111 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 358 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 368 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 354 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN A 572 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 872 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.172112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.131981 restraints weight = 81213.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.135410 restraints weight = 46244.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.137627 restraints weight = 30704.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.139422 restraints weight = 23021.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.140390 restraints weight = 18470.960| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30356 Z= 0.183 Angle : 0.694 14.986 41297 Z= 0.353 Chirality : 0.047 0.285 4603 Planarity : 0.004 0.059 5332 Dihedral : 4.762 58.548 4024 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.83 % Allowed : 22.44 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.13), residues: 3700 helix: -0.48 (0.18), residues: 863 sheet: -0.72 (0.19), residues: 640 loop : -1.57 (0.12), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 34 TYR 0.024 0.002 TYR C 674 PHE 0.042 0.002 PHE D 759 TRP 0.030 0.002 TRP C 104 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00398 (30314) covalent geometry : angle 0.68886 (41213) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.95416 ( 84) hydrogen bonds : bond 0.04028 ( 834) hydrogen bonds : angle 5.81929 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 647 time to evaluate : 0.842 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5828 (ppp) cc_final: 0.5046 (pmm) REVERT: A 341 LYS cc_start: 0.4753 (tppt) cc_final: 0.4478 (ttpp) REVERT: A 358 ILE cc_start: 0.6788 (mm) cc_final: 0.6409 (mm) REVERT: A 360 MET cc_start: 0.1966 (mmm) cc_final: 0.1317 (mmm) REVERT: A 368 ASP cc_start: 0.2361 (t0) cc_final: 0.1885 (t0) REVERT: A 455 MET cc_start: 0.6783 (ttt) cc_final: 0.5995 (ttt) REVERT: A 480 MET cc_start: -0.5251 (mtm) cc_final: -0.5726 (mmt) REVERT: A 526 GLN cc_start: -0.3574 (OUTLIER) cc_final: -0.4322 (tt0) REVERT: A 578 ASN cc_start: 0.7963 (m110) cc_final: 0.7572 (t0) REVERT: A 579 MET cc_start: 0.5614 (mpp) cc_final: 0.5186 (mpp) REVERT: B 78 ARG cc_start: 0.7234 (mpt180) cc_final: 0.6685 (mmt-90) REVERT: B 99 ASN cc_start: 0.5130 (t0) cc_final: 0.4862 (m110) REVERT: B 278 LYS cc_start: 0.8049 (tptt) cc_final: 0.7823 (tptt) REVERT: B 307 THR cc_start: 0.8438 (m) cc_final: 0.7955 (p) REVERT: B 347 PHE cc_start: 0.4389 (p90) cc_final: 0.3217 (p90) REVERT: B 349 SER cc_start: -0.0024 (OUTLIER) cc_final: -0.1132 (t) REVERT: B 438 SER cc_start: 0.5900 (OUTLIER) cc_final: 0.5125 (p) REVERT: B 559 PHE cc_start: 0.5331 (OUTLIER) cc_final: 0.4356 (m-80) REVERT: B 565 PHE cc_start: 0.7303 (p90) cc_final: 0.6833 (p90) REVERT: B 569 ILE cc_start: 0.8654 (pt) cc_final: 0.8353 (mp) REVERT: B 656 VAL cc_start: 0.8543 (m) cc_final: 0.8332 (t) REVERT: B 698 SER cc_start: 0.8507 (t) cc_final: 0.7661 (p) REVERT: B 748 GLU cc_start: 0.8374 (pm20) cc_final: 0.8012 (pm20) REVERT: B 752 LEU cc_start: 0.8897 (mp) cc_final: 0.8649 (mp) REVERT: B 776 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7910 (ptpp) REVERT: B 779 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7639 (mm-40) REVERT: B 820 ASP cc_start: 0.8651 (m-30) cc_final: 0.8289 (m-30) REVERT: B 822 LEU cc_start: 0.8590 (mt) cc_final: 0.8360 (mt) REVERT: B 856 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8299 (mmmm) REVERT: B 872 GLN cc_start: 0.7853 (tp40) cc_final: 0.7057 (tm-30) REVERT: B 933 LYS cc_start: 0.9115 (mttt) cc_final: 0.8685 (mmtm) REVERT: B 964 LYS cc_start: 0.8809 (ptpp) cc_final: 0.8161 (ptpp) REVERT: B 966 LEU cc_start: 0.8714 (mt) cc_final: 0.8485 (mm) REVERT: B 981 PHE cc_start: 0.7756 (t80) cc_final: 0.7053 (t80) REVERT: B 1002 GLN cc_start: 0.8163 (tp40) cc_final: 0.7753 (tp40) REVERT: B 1010 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8150 (mm-40) REVERT: B 1017 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8134 (tm-30) REVERT: B 1019 ARG cc_start: 0.8367 (ttp-170) cc_final: 0.7718 (ttp-110) REVERT: B 1029 MET cc_start: 0.8445 (mmm) cc_final: 0.8161 (mmm) REVERT: B 1031 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6369 (mm-30) REVERT: B 1101 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.5730 (m90) REVERT: C 135 PHE cc_start: 0.7084 (m-80) cc_final: 0.6512 (m-10) REVERT: C 221 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 223 LEU cc_start: 0.8580 (mp) cc_final: 0.8293 (tp) REVERT: C 421 TYR cc_start: 0.7229 (m-80) cc_final: 0.6390 (m-10) REVERT: C 516 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: C 572 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.7964 (p) REVERT: C 697 MET cc_start: 0.7957 (ppp) cc_final: 0.7495 (ppp) REVERT: C 698 SER cc_start: 0.7687 (t) cc_final: 0.7418 (p) REVERT: C 733 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8201 (mtpt) REVERT: C 737 ASP cc_start: 0.7391 (p0) cc_final: 0.6420 (p0) REVERT: C 759 PHE cc_start: 0.7325 (t80) cc_final: 0.6764 (t80) REVERT: C 765 ARG cc_start: 0.8553 (ptp-110) cc_final: 0.8336 (ptp90) REVERT: C 773 GLU cc_start: 0.8063 (pt0) cc_final: 0.7735 (pt0) REVERT: C 775 ASP cc_start: 0.8070 (m-30) cc_final: 0.7395 (m-30) REVERT: C 776 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8197 (mtmm) REVERT: C 821 LEU cc_start: 0.8722 (mt) cc_final: 0.8367 (mt) REVERT: C 868 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7827 (mm-30) REVERT: C 921 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8532 (mmmt) REVERT: C 949 GLN cc_start: 0.7988 (tp40) cc_final: 0.7189 (tp-100) REVERT: C 953 ASN cc_start: 0.8215 (p0) cc_final: 0.7888 (p0) REVERT: C 954 HIS cc_start: 0.7853 (m-70) cc_final: 0.7195 (m-70) REVERT: C 983 ARG cc_start: 0.8191 (ptm-80) cc_final: 0.7842 (ptm-80) REVERT: C 990 GLU cc_start: 0.8197 (tp30) cc_final: 0.7844 (tp30) REVERT: C 1005 GLN cc_start: 0.8484 (tp-100) cc_final: 0.7886 (tp40) REVERT: C 1014 ARG cc_start: 0.8416 (mtt180) cc_final: 0.8089 (tpp80) REVERT: C 1019 ARG cc_start: 0.8443 (tpp-160) cc_final: 0.7825 (tpp-160) REVERT: C 1031 GLU cc_start: 0.7710 (tt0) cc_final: 0.7457 (tt0) REVERT: C 1050 MET cc_start: 0.5307 (ptp) cc_final: 0.4742 (ptp) REVERT: C 1118 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: D 55 PHE cc_start: 0.6901 (m-10) cc_final: 0.6625 (m-10) REVERT: D 131 CYS cc_start: 0.4613 (OUTLIER) cc_final: 0.3470 (m) REVERT: D 196 ASN cc_start: 0.7665 (t0) cc_final: 0.7232 (t0) REVERT: D 300 LYS cc_start: 0.8315 (mttt) cc_final: 0.7988 (mtpt) REVERT: D 731 MET cc_start: 0.7789 (ptm) cc_final: 0.7471 (ptm) REVERT: D 765 ARG cc_start: 0.8670 (ttm110) cc_final: 0.8221 (ttm110) REVERT: D 772 VAL cc_start: 0.8792 (t) cc_final: 0.8588 (p) REVERT: D 775 ASP cc_start: 0.7860 (p0) cc_final: 0.7609 (p0) REVERT: D 776 LYS cc_start: 0.8505 (mtmm) cc_final: 0.7741 (mtmm) REVERT: D 780 GLU cc_start: 0.6456 (mt-10) cc_final: 0.6036 (mt-10) REVERT: D 790 LYS cc_start: 0.8461 (mttt) cc_final: 0.8217 (tppt) REVERT: D 819 GLU cc_start: 0.8173 (tp30) cc_final: 0.7811 (tp30) REVERT: D 859 THR cc_start: 0.8226 (m) cc_final: 0.7810 (p) REVERT: D 888 PHE cc_start: 0.7888 (p90) cc_final: 0.7261 (p90) REVERT: D 916 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5685 (tt) REVERT: D 919 ASN cc_start: 0.7156 (m110) cc_final: 0.6854 (p0) REVERT: D 933 LYS cc_start: 0.9013 (mttt) cc_final: 0.8655 (tppt) REVERT: D 969 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8456 (mmmt) REVERT: D 1010 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 1019 ARG cc_start: 0.8524 (ttt90) cc_final: 0.7768 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8704 (m110) cc_final: 0.8031 (m110) REVERT: D 1107 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7260 (mtt90) REVERT: D 1111 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: D 1113 GLN cc_start: 0.7349 (mp10) cc_final: 0.6240 (mp10) outliers start: 159 outliers final: 117 residues processed: 736 average time/residue: 0.1801 time to fit residues: 214.1206 Evaluate side-chains 764 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 634 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 978 ASN Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1111 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 181 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 336 optimal weight: 0.9990 chunk 364 optimal weight: 0.6980 chunk 244 optimal weight: 0.5980 chunk 217 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 207 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 926 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN ** D 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.172308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.132779 restraints weight = 83253.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.136125 restraints weight = 46906.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.138428 restraints weight = 30807.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.140147 restraints weight = 22666.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.141104 restraints weight = 18169.918| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30356 Z= 0.141 Angle : 0.681 14.230 41297 Z= 0.343 Chirality : 0.046 0.181 4603 Planarity : 0.004 0.051 5332 Dihedral : 4.651 59.047 4024 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.89 % Allowed : 23.99 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3700 helix: -0.43 (0.18), residues: 856 sheet: -0.69 (0.19), residues: 652 loop : -1.52 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1000 TYR 0.026 0.002 TYR C 265 PHE 0.044 0.002 PHE B 490 TRP 0.043 0.002 TRP C 104 HIS 0.026 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00316 (30314) covalent geometry : angle 0.67617 (41213) SS BOND : bond 0.00371 ( 42) SS BOND : angle 1.90670 ( 84) hydrogen bonds : bond 0.03808 ( 834) hydrogen bonds : angle 5.67264 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 637 time to evaluate : 1.048 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: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: -0.1175 (OUTLIER) cc_final: -0.2884 (t60) REVERT: A 190 MET cc_start: 0.6160 (ppp) cc_final: 0.5416 (pmm) REVERT: A 323 MET cc_start: 0.1006 (ttp) cc_final: 0.0784 (tmm) REVERT: A 358 ILE cc_start: 0.6774 (mm) cc_final: 0.6458 (mm) REVERT: A 360 MET cc_start: 0.2022 (mmm) cc_final: 0.1436 (mmm) REVERT: A 368 ASP cc_start: 0.2265 (t0) cc_final: 0.1787 (t0) REVERT: A 455 MET cc_start: 0.6774 (ttt) cc_final: 0.6424 (ttt) REVERT: A 578 ASN cc_start: 0.7994 (m110) cc_final: 0.7667 (t0) REVERT: B 78 ARG cc_start: 0.7225 (mpt180) cc_final: 0.6686 (mmt-90) REVERT: B 99 ASN cc_start: 0.5360 (t0) cc_final: 0.4994 (m110) REVERT: B 307 THR cc_start: 0.8509 (m) cc_final: 0.8138 (p) REVERT: B 347 PHE cc_start: 0.4436 (p90) cc_final: 0.3302 (p90) REVERT: B 349 SER cc_start: 0.0282 (OUTLIER) cc_final: -0.0882 (t) REVERT: B 438 SER cc_start: 0.5966 (OUTLIER) cc_final: 0.5028 (p) REVERT: B 559 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.4356 (m-80) REVERT: B 565 PHE cc_start: 0.7289 (p90) cc_final: 0.6830 (p90) REVERT: B 569 ILE cc_start: 0.8634 (pt) cc_final: 0.8332 (mp) REVERT: B 595 VAL cc_start: 0.7453 (t) cc_final: 0.6911 (m) REVERT: B 698 SER cc_start: 0.8416 (t) cc_final: 0.7489 (p) REVERT: B 748 GLU cc_start: 0.8311 (pm20) cc_final: 0.7976 (pm20) REVERT: B 752 LEU cc_start: 0.8871 (mp) cc_final: 0.8480 (mp) REVERT: B 776 LYS cc_start: 0.8337 (mtpp) cc_final: 0.7869 (ptpp) REVERT: B 808 ASP cc_start: 0.7713 (t0) cc_final: 0.7463 (t0) REVERT: B 820 ASP cc_start: 0.8645 (m-30) cc_final: 0.8270 (m-30) REVERT: B 822 LEU cc_start: 0.8583 (mt) cc_final: 0.8270 (mt) REVERT: B 856 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8358 (mmmm) REVERT: B 921 LYS cc_start: 0.8321 (tppt) cc_final: 0.7726 (tptp) REVERT: B 925 ASN cc_start: 0.7954 (m-40) cc_final: 0.7358 (m110) REVERT: B 933 LYS cc_start: 0.9086 (mttt) cc_final: 0.8657 (mmtm) REVERT: B 964 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8102 (ptpp) REVERT: B 981 PHE cc_start: 0.7632 (t80) cc_final: 0.6972 (t80) REVERT: B 1002 GLN cc_start: 0.8139 (tp40) cc_final: 0.7462 (tp40) REVERT: B 1010 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8117 (mm-40) REVERT: B 1017 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8098 (tm-30) REVERT: B 1019 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7705 (ttp-110) REVERT: B 1029 MET cc_start: 0.8443 (mmm) cc_final: 0.8178 (mmm) REVERT: B 1031 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6298 (mm-30) REVERT: B 1101 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.5626 (m90) REVERT: C 135 PHE cc_start: 0.6967 (m-80) cc_final: 0.6519 (m-10) REVERT: C 193 VAL cc_start: 0.6942 (t) cc_final: 0.6604 (m) REVERT: C 221 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7816 (p) REVERT: C 314 GLN cc_start: 0.7917 (mp10) cc_final: 0.7598 (mp10) REVERT: C 421 TYR cc_start: 0.7266 (m-80) cc_final: 0.6521 (m-10) REVERT: C 516 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: C 572 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7880 (p) REVERT: C 697 MET cc_start: 0.7866 (ppp) cc_final: 0.7509 (ppp) REVERT: C 733 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8179 (mtpt) REVERT: C 765 ARG cc_start: 0.8514 (ptp-110) cc_final: 0.8300 (ptp90) REVERT: C 773 GLU cc_start: 0.7980 (pt0) cc_final: 0.7650 (pt0) REVERT: C 775 ASP cc_start: 0.7998 (m-30) cc_final: 0.7374 (m-30) REVERT: C 776 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8182 (mtmm) REVERT: C 821 LEU cc_start: 0.8686 (mt) cc_final: 0.8316 (mt) REVERT: C 868 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7848 (mm-30) REVERT: C 921 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8487 (mmmt) REVERT: C 949 GLN cc_start: 0.7909 (tp40) cc_final: 0.7095 (tp-100) REVERT: C 953 ASN cc_start: 0.8096 (p0) cc_final: 0.7847 (p0) REVERT: C 954 HIS cc_start: 0.7717 (m-70) cc_final: 0.7056 (m-70) REVERT: C 990 GLU cc_start: 0.8053 (tp30) cc_final: 0.7690 (tp30) REVERT: C 1005 GLN cc_start: 0.8457 (tp-100) cc_final: 0.7820 (tp40) REVERT: C 1014 ARG cc_start: 0.8338 (mtt180) cc_final: 0.8012 (tpp80) REVERT: C 1019 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.7816 (tpp-160) REVERT: C 1031 GLU cc_start: 0.7643 (tt0) cc_final: 0.7365 (tt0) REVERT: C 1050 MET cc_start: 0.5351 (ptp) cc_final: 0.4944 (ptp) REVERT: D 55 PHE cc_start: 0.6796 (m-10) cc_final: 0.6472 (m-10) REVERT: D 131 CYS cc_start: 0.4666 (OUTLIER) cc_final: 0.2922 (m) REVERT: D 169 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7142 (mp0) REVERT: D 196 ASN cc_start: 0.7734 (t0) cc_final: 0.7291 (t0) REVERT: D 287 ASP cc_start: 0.8530 (t0) cc_final: 0.8069 (t70) REVERT: D 300 LYS cc_start: 0.8318 (mttt) cc_final: 0.7931 (mtpp) REVERT: D 304 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8177 (mmmm) REVERT: D 557 LYS cc_start: 0.6290 (mmtt) cc_final: 0.5740 (mmtt) REVERT: D 731 MET cc_start: 0.7734 (ptm) cc_final: 0.7254 (ptm) REVERT: D 765 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8175 (ttm110) REVERT: D 772 VAL cc_start: 0.8754 (t) cc_final: 0.8548 (p) REVERT: D 775 ASP cc_start: 0.7870 (p0) cc_final: 0.7519 (p0) REVERT: D 776 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7656 (mtmm) REVERT: D 780 GLU cc_start: 0.6399 (mt-10) cc_final: 0.5988 (mt-10) REVERT: D 787 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7823 (mm-40) REVERT: D 790 LYS cc_start: 0.8308 (mttt) cc_final: 0.8101 (tppt) REVERT: D 859 THR cc_start: 0.8178 (m) cc_final: 0.7777 (p) REVERT: D 888 PHE cc_start: 0.7854 (p90) cc_final: 0.7316 (p90) REVERT: D 916 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5534 (tt) REVERT: D 919 ASN cc_start: 0.7057 (m110) cc_final: 0.6620 (p0) REVERT: D 933 LYS cc_start: 0.8993 (mttt) cc_final: 0.8551 (mmmm) REVERT: D 969 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8409 (mmmt) REVERT: D 1010 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 1019 ARG cc_start: 0.8485 (ttt90) cc_final: 0.7728 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8662 (m110) cc_final: 0.8013 (m110) outliers start: 128 outliers final: 93 residues processed: 713 average time/residue: 0.1796 time to fit residues: 206.9071 Evaluate side-chains 724 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 620 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 337 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 354 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 207 HIS C 872 GLN C 926 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.171911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.133233 restraints weight = 81981.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.135645 restraints weight = 46265.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.137831 restraints weight = 30415.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.139703 restraints weight = 22514.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.140720 restraints weight = 18101.327| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30356 Z= 0.147 Angle : 0.694 14.128 41297 Z= 0.350 Chirality : 0.046 0.200 4603 Planarity : 0.004 0.051 5332 Dihedral : 4.666 55.958 4024 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.01 % Allowed : 24.23 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 3700 helix: -0.34 (0.18), residues: 842 sheet: -0.66 (0.19), residues: 638 loop : -1.50 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1107 TYR 0.022 0.001 TYR C 674 PHE 0.052 0.002 PHE D 515 TRP 0.055 0.002 TRP C 104 HIS 0.035 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00329 (30314) covalent geometry : angle 0.68841 (41213) SS BOND : bond 0.00402 ( 42) SS BOND : angle 2.10126 ( 84) hydrogen bonds : bond 0.03838 ( 834) hydrogen bonds : angle 5.66348 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 623 time to evaluate : 1.140 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: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: -0.1045 (OUTLIER) cc_final: -0.2890 (t60) REVERT: A 190 MET cc_start: 0.6300 (ppp) cc_final: 0.5459 (pmm) REVERT: A 323 MET cc_start: 0.0649 (ttp) cc_final: 0.0417 (tmm) REVERT: A 358 ILE cc_start: 0.6759 (mm) cc_final: 0.6436 (mm) REVERT: A 455 MET cc_start: 0.6869 (ttt) cc_final: 0.6569 (ttt) REVERT: A 578 ASN cc_start: 0.7946 (m110) cc_final: 0.7577 (t0) REVERT: B 78 ARG cc_start: 0.7233 (mpt180) cc_final: 0.6853 (mmt-90) REVERT: B 96 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: B 307 THR cc_start: 0.8504 (m) cc_final: 0.8092 (p) REVERT: B 347 PHE cc_start: 0.4426 (p90) cc_final: 0.3683 (p90) REVERT: B 349 SER cc_start: 0.0445 (OUTLIER) cc_final: -0.0678 (t) REVERT: B 438 SER cc_start: 0.5822 (OUTLIER) cc_final: 0.4916 (p) REVERT: B 451 TYR cc_start: 0.6018 (m-80) cc_final: 0.5460 (m-80) REVERT: B 559 PHE cc_start: 0.5422 (OUTLIER) cc_final: 0.4377 (m-80) REVERT: B 565 PHE cc_start: 0.7274 (p90) cc_final: 0.6822 (p90) REVERT: B 569 ILE cc_start: 0.8657 (pt) cc_final: 0.8374 (mp) REVERT: B 595 VAL cc_start: 0.7501 (t) cc_final: 0.7103 (m) REVERT: B 698 SER cc_start: 0.8350 (t) cc_final: 0.7506 (p) REVERT: B 752 LEU cc_start: 0.8889 (mp) cc_final: 0.8614 (mp) REVERT: B 776 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7835 (ptpp) REVERT: B 808 ASP cc_start: 0.7793 (t0) cc_final: 0.7520 (t0) REVERT: B 820 ASP cc_start: 0.8668 (m-30) cc_final: 0.8227 (m-30) REVERT: B 822 LEU cc_start: 0.8605 (mt) cc_final: 0.8299 (mt) REVERT: B 856 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8260 (mmmm) REVERT: B 872 GLN cc_start: 0.7884 (tp40) cc_final: 0.6943 (tm-30) REVERT: B 933 LYS cc_start: 0.9122 (mttt) cc_final: 0.8614 (mmtt) REVERT: B 964 LYS cc_start: 0.8721 (ptpp) cc_final: 0.8040 (ptpp) REVERT: B 995 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8318 (ttp80) REVERT: B 1002 GLN cc_start: 0.7976 (tp40) cc_final: 0.7429 (tp40) REVERT: B 1010 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8143 (mm-40) REVERT: B 1017 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 1019 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.7689 (ttp-110) REVERT: B 1029 MET cc_start: 0.8393 (mmm) cc_final: 0.8089 (mmm) REVERT: B 1101 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.5717 (m90) REVERT: C 135 PHE cc_start: 0.7086 (m-80) cc_final: 0.6741 (m-10) REVERT: C 193 VAL cc_start: 0.7073 (t) cc_final: 0.6667 (m) REVERT: C 221 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7789 (p) REVERT: C 223 LEU cc_start: 0.8653 (mp) cc_final: 0.8386 (tp) REVERT: C 421 TYR cc_start: 0.7220 (m-80) cc_final: 0.6428 (m-10) REVERT: C 516 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: C 697 MET cc_start: 0.7860 (ppp) cc_final: 0.7354 (ppp) REVERT: C 733 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8226 (mtpt) REVERT: C 765 ARG cc_start: 0.8566 (ptp-110) cc_final: 0.8250 (ptp90) REVERT: C 773 GLU cc_start: 0.8028 (pt0) cc_final: 0.7799 (pt0) REVERT: C 775 ASP cc_start: 0.7968 (m-30) cc_final: 0.7414 (m-30) REVERT: C 776 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8194 (mtmm) REVERT: C 821 LEU cc_start: 0.8682 (mt) cc_final: 0.8307 (mt) REVERT: C 856 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8828 (mmmm) REVERT: C 868 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 921 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8490 (mmmt) REVERT: C 949 GLN cc_start: 0.7968 (tp40) cc_final: 0.7143 (tp-100) REVERT: C 953 ASN cc_start: 0.8075 (p0) cc_final: 0.7827 (p0) REVERT: C 954 HIS cc_start: 0.7775 (m-70) cc_final: 0.7106 (m-70) REVERT: C 990 GLU cc_start: 0.8108 (tp30) cc_final: 0.7747 (tp30) REVERT: C 1005 GLN cc_start: 0.8483 (tp-100) cc_final: 0.7882 (tp40) REVERT: C 1014 ARG cc_start: 0.8345 (mtt180) cc_final: 0.7990 (tpp80) REVERT: C 1018 ILE cc_start: 0.8920 (tp) cc_final: 0.8623 (mt) REVERT: C 1019 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.7785 (tpp-160) REVERT: C 1031 GLU cc_start: 0.7667 (tt0) cc_final: 0.7440 (tt0) REVERT: C 1050 MET cc_start: 0.5484 (ptp) cc_final: 0.5128 (ptp) REVERT: D 55 PHE cc_start: 0.6744 (m-10) cc_final: 0.6426 (m-10) REVERT: D 131 CYS cc_start: 0.4614 (OUTLIER) cc_final: 0.3015 (m) REVERT: D 169 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7278 (mp0) REVERT: D 196 ASN cc_start: 0.7709 (t0) cc_final: 0.7263 (t0) REVERT: D 287 ASP cc_start: 0.8542 (t0) cc_final: 0.8053 (t70) REVERT: D 300 LYS cc_start: 0.8306 (mttt) cc_final: 0.7962 (mtpp) REVERT: D 304 LYS cc_start: 0.8437 (mmtm) cc_final: 0.8194 (mmmm) REVERT: D 557 LYS cc_start: 0.6283 (mmtt) cc_final: 0.5743 (mmtt) REVERT: D 731 MET cc_start: 0.7742 (ptm) cc_final: 0.7251 (ptm) REVERT: D 765 ARG cc_start: 0.8619 (ttm110) cc_final: 0.8184 (ttm110) REVERT: D 772 VAL cc_start: 0.8736 (t) cc_final: 0.8429 (p) REVERT: D 776 LYS cc_start: 0.8450 (mtmm) cc_final: 0.7729 (mtmm) REVERT: D 780 GLU cc_start: 0.6492 (mt-10) cc_final: 0.6034 (mt-10) REVERT: D 787 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7881 (mm-40) REVERT: D 790 LYS cc_start: 0.8391 (mttt) cc_final: 0.8072 (tppt) REVERT: D 859 THR cc_start: 0.8195 (m) cc_final: 0.7781 (p) REVERT: D 888 PHE cc_start: 0.7874 (p90) cc_final: 0.7288 (p90) REVERT: D 916 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5604 (tt) REVERT: D 919 ASN cc_start: 0.7102 (m110) cc_final: 0.6813 (p0) REVERT: D 933 LYS cc_start: 0.8982 (mttt) cc_final: 0.8599 (tppt) REVERT: D 969 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8418 (mmmt) REVERT: D 1010 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 1019 ARG cc_start: 0.8501 (ttt90) cc_final: 0.7719 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8676 (m110) cc_final: 0.8037 (m110) REVERT: D 1111 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.5755 (tm-30) REVERT: D 1113 GLN cc_start: 0.7635 (mp10) cc_final: 0.6403 (mp10) outliers start: 132 outliers final: 99 residues processed: 700 average time/residue: 0.1778 time to fit residues: 201.4933 Evaluate side-chains 724 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 614 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 51 optimal weight: 0.9990 chunk 257 optimal weight: 0.9980 chunk 303 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 369 optimal weight: 0.0000 chunk 27 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 210 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 872 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.172850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.134373 restraints weight = 82648.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.137126 restraints weight = 46387.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.139464 restraints weight = 30365.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.140932 restraints weight = 22401.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.142296 restraints weight = 18093.232| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30356 Z= 0.132 Angle : 0.700 13.663 41297 Z= 0.351 Chirality : 0.046 0.259 4603 Planarity : 0.004 0.052 5332 Dihedral : 4.580 51.973 4024 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.31 % Allowed : 25.21 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.13), residues: 3700 helix: -0.40 (0.18), residues: 854 sheet: -0.54 (0.20), residues: 616 loop : -1.47 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1107 TYR 0.021 0.001 TYR C 674 PHE 0.060 0.002 PHE D 515 TRP 0.064 0.002 TRP C 104 HIS 0.027 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00299 (30314) covalent geometry : angle 0.69536 (41213) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.91169 ( 84) hydrogen bonds : bond 0.03737 ( 834) hydrogen bonds : angle 5.59360 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 618 time to evaluate : 0.874 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: A 69 TRP cc_start: -0.1082 (OUTLIER) cc_final: -0.2818 (t60) REVERT: A 190 MET cc_start: 0.6157 (ppp) cc_final: 0.5425 (pmm) REVERT: A 270 MET cc_start: 0.5002 (mtp) cc_final: 0.4789 (mtp) REVERT: A 323 MET cc_start: 0.0982 (ttp) cc_final: 0.0754 (tmm) REVERT: A 358 ILE cc_start: 0.6900 (mm) cc_final: 0.6586 (mm) REVERT: A 455 MET cc_start: 0.6822 (ttt) cc_final: 0.6548 (ttt) REVERT: A 578 ASN cc_start: 0.8249 (m110) cc_final: 0.7936 (t0) REVERT: B 78 ARG cc_start: 0.7356 (mpt180) cc_final: 0.6966 (mmt-90) REVERT: B 307 THR cc_start: 0.8459 (m) cc_final: 0.8048 (p) REVERT: B 313 TYR cc_start: 0.7020 (m-80) cc_final: 0.6638 (m-80) REVERT: B 347 PHE cc_start: 0.4256 (p90) cc_final: 0.3186 (p90) REVERT: B 438 SER cc_start: 0.5784 (OUTLIER) cc_final: 0.4812 (p) REVERT: B 559 PHE cc_start: 0.5378 (OUTLIER) cc_final: 0.4263 (m-80) REVERT: B 565 PHE cc_start: 0.7225 (p90) cc_final: 0.6787 (p90) REVERT: B 569 ILE cc_start: 0.8668 (pt) cc_final: 0.8400 (mp) REVERT: B 595 VAL cc_start: 0.7519 (t) cc_final: 0.7115 (m) REVERT: B 698 SER cc_start: 0.8237 (t) cc_final: 0.7457 (p) REVERT: B 748 GLU cc_start: 0.8340 (pm20) cc_final: 0.8026 (pm20) REVERT: B 752 LEU cc_start: 0.8869 (mp) cc_final: 0.8636 (mp) REVERT: B 776 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7836 (ptpp) REVERT: B 808 ASP cc_start: 0.7705 (t0) cc_final: 0.7398 (t0) REVERT: B 820 ASP cc_start: 0.8653 (m-30) cc_final: 0.8196 (m-30) REVERT: B 822 LEU cc_start: 0.8609 (mt) cc_final: 0.8304 (mt) REVERT: B 856 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8236 (mmmm) REVERT: B 872 GLN cc_start: 0.7851 (tp40) cc_final: 0.6950 (tm-30) REVERT: B 921 LYS cc_start: 0.8437 (tptp) cc_final: 0.8146 (tptp) REVERT: B 933 LYS cc_start: 0.9115 (mttt) cc_final: 0.8601 (mmtt) REVERT: B 964 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8010 (ptpp) REVERT: B 1002 GLN cc_start: 0.8049 (tp40) cc_final: 0.7323 (tp40) REVERT: B 1010 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8111 (mm-40) REVERT: B 1017 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8036 (tm-30) REVERT: B 1019 ARG cc_start: 0.8297 (ttp-170) cc_final: 0.7642 (ttp-110) REVERT: B 1029 MET cc_start: 0.8350 (mmm) cc_final: 0.8088 (mmm) REVERT: B 1101 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.5700 (m90) REVERT: C 135 PHE cc_start: 0.7181 (m-80) cc_final: 0.6584 (m-10) REVERT: C 193 VAL cc_start: 0.7025 (t) cc_final: 0.6651 (m) REVERT: C 221 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7868 (p) REVERT: C 223 LEU cc_start: 0.8673 (mp) cc_final: 0.8358 (tp) REVERT: C 314 GLN cc_start: 0.7863 (mp10) cc_final: 0.7522 (mp10) REVERT: C 421 TYR cc_start: 0.7234 (m-80) cc_final: 0.6524 (m-10) REVERT: C 516 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: C 697 MET cc_start: 0.7831 (ppp) cc_final: 0.7492 (ppp) REVERT: C 733 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8162 (mtpt) REVERT: C 765 ARG cc_start: 0.8467 (ptp-110) cc_final: 0.8169 (ptp90) REVERT: C 773 GLU cc_start: 0.8002 (pt0) cc_final: 0.7791 (pt0) REVERT: C 775 ASP cc_start: 0.7890 (m-30) cc_final: 0.7371 (m-30) REVERT: C 776 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8221 (mtmm) REVERT: C 819 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7233 (mt-10) REVERT: C 821 LEU cc_start: 0.8562 (mt) cc_final: 0.8155 (mt) REVERT: C 868 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7877 (mm-30) REVERT: C 921 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8444 (mmmt) REVERT: C 949 GLN cc_start: 0.7962 (tp40) cc_final: 0.7144 (tp-100) REVERT: C 953 ASN cc_start: 0.7959 (p0) cc_final: 0.7737 (p0) REVERT: C 954 HIS cc_start: 0.7725 (m-70) cc_final: 0.7056 (m-70) REVERT: C 990 GLU cc_start: 0.8051 (tp30) cc_final: 0.7675 (tp30) REVERT: C 1005 GLN cc_start: 0.8502 (tp-100) cc_final: 0.7889 (tp40) REVERT: C 1014 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7969 (tpp80) REVERT: C 1018 ILE cc_start: 0.8942 (tp) cc_final: 0.8642 (mt) REVERT: C 1019 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.7793 (tpp-160) REVERT: C 1031 GLU cc_start: 0.7660 (tt0) cc_final: 0.7403 (tt0) REVERT: C 1050 MET cc_start: 0.5443 (ptp) cc_final: 0.5086 (ptp) REVERT: C 1118 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: D 55 PHE cc_start: 0.6699 (m-10) cc_final: 0.6393 (m-10) REVERT: D 131 CYS cc_start: 0.4590 (OUTLIER) cc_final: 0.2980 (m) REVERT: D 169 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7386 (mp0) REVERT: D 196 ASN cc_start: 0.7766 (t0) cc_final: 0.7327 (t0) REVERT: D 287 ASP cc_start: 0.8489 (t0) cc_final: 0.8175 (t70) REVERT: D 300 LYS cc_start: 0.8312 (mttt) cc_final: 0.7975 (mtpp) REVERT: D 304 LYS cc_start: 0.8442 (mmtm) cc_final: 0.8199 (mmmm) REVERT: D 306 PHE cc_start: 0.7837 (m-10) cc_final: 0.7582 (m-10) REVERT: D 557 LYS cc_start: 0.6306 (mmtt) cc_final: 0.5812 (mmtt) REVERT: D 573 THR cc_start: 0.7570 (m) cc_final: 0.7362 (p) REVERT: D 660 TYR cc_start: 0.5686 (m-10) cc_final: 0.5458 (m-10) REVERT: D 731 MET cc_start: 0.7666 (ptm) cc_final: 0.7309 (ptm) REVERT: D 765 ARG cc_start: 0.8601 (ttm110) cc_final: 0.8159 (ttm110) REVERT: D 772 VAL cc_start: 0.8734 (t) cc_final: 0.8428 (p) REVERT: D 776 LYS cc_start: 0.8428 (mtmm) cc_final: 0.7696 (mtmm) REVERT: D 780 GLU cc_start: 0.6475 (mt-10) cc_final: 0.5992 (mt-10) REVERT: D 787 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7771 (mm-40) REVERT: D 790 LYS cc_start: 0.8304 (mttt) cc_final: 0.8097 (tppt) REVERT: D 888 PHE cc_start: 0.7871 (p90) cc_final: 0.7264 (p90) REVERT: D 916 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5504 (tt) REVERT: D 919 ASN cc_start: 0.7057 (m110) cc_final: 0.6789 (p0) REVERT: D 921 LYS cc_start: 0.7976 (mppt) cc_final: 0.7633 (mppt) REVERT: D 933 LYS cc_start: 0.8967 (mttt) cc_final: 0.8581 (tppt) REVERT: D 969 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8420 (mmmt) REVERT: D 1010 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7656 (tm-30) REVERT: D 1019 ARG cc_start: 0.8475 (ttt90) cc_final: 0.7698 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8690 (m110) cc_final: 0.8038 (m110) REVERT: D 1111 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5599 (tm-30) REVERT: D 1113 GLN cc_start: 0.7553 (mp10) cc_final: 0.6337 (mp10) outliers start: 109 outliers final: 87 residues processed: 681 average time/residue: 0.1778 time to fit residues: 196.1065 Evaluate side-chains 702 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 605 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 44 optimal weight: 5.9990 chunk 323 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 366 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 193 optimal weight: 0.0170 chunk 139 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 872 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN ** D1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.170466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.130945 restraints weight = 82403.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.134354 restraints weight = 46175.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.136716 restraints weight = 30371.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.138379 restraints weight = 22340.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.139581 restraints weight = 18023.723| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30356 Z= 0.169 Angle : 0.727 14.418 41297 Z= 0.367 Chirality : 0.047 0.246 4603 Planarity : 0.004 0.050 5332 Dihedral : 4.750 48.424 4024 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.80 % Allowed : 24.90 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 3700 helix: -0.35 (0.18), residues: 842 sheet: -0.63 (0.19), residues: 650 loop : -1.48 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 21 TYR 0.022 0.002 TYR B 489 PHE 0.085 0.002 PHE D 392 TRP 0.068 0.002 TRP C 104 HIS 0.025 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00375 (30314) covalent geometry : angle 0.72192 (41213) SS BOND : bond 0.00402 ( 42) SS BOND : angle 2.03707 ( 84) hydrogen bonds : bond 0.03910 ( 834) hydrogen bonds : angle 5.67344 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9115.45 seconds wall clock time: 156 minutes 19.91 seconds (9379.91 seconds total)