Starting phenix.real_space_refine on Fri Mar 6 09:24:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk5_32559/03_2026/7wk5_32559.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk5_32559/03_2026/7wk5_32559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wk5_32559/03_2026/7wk5_32559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk5_32559/03_2026/7wk5_32559.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wk5_32559/03_2026/7wk5_32559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk5_32559/03_2026/7wk5_32559.map" } resolution = 3.66 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= 0.006 sd= 0.108 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 37 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: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} 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: 6.68, per 1000 atoms: 0.23 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=2.04 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: 2.08 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: 1.14 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: 6.49 Time building geometry restraints manager: 2.93 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: 9365 1.34 - 1.47: 7599 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 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 bond pdb=" CA LEU D 585 " pdb=" C LEU D 585 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" CA GLU C 583 " pdb=" C GLU C 583 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.20e-02 6.94e+03 1.23e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 40412 2.60 - 5.21: 693 5.21 - 7.81: 82 7.81 - 10.41: 22 10.41 - 13.02: 4 Bond angle restraints: 41213 Sorted by residual: 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=" C ALA A 413 " pdb=" N THR A 414 " pdb=" CA THR A 414 " ideal model delta sigma weight residual 120.94 132.27 -11.33 1.90e+00 2.77e-01 3.55e+01 angle pdb=" N ILE D 584 " pdb=" CA ILE D 584 " pdb=" C ILE D 584 " ideal model delta sigma weight residual 109.30 102.36 6.94 1.25e+00 6.40e-01 3.08e+01 angle pdb=" C CYS B 480 " pdb=" N ASN B 481 " pdb=" CA ASN B 481 " ideal model delta sigma weight residual 122.46 130.11 -7.65 1.41e+00 5.03e-01 2.94e+01 angle pdb=" N VAL A 293 " pdb=" CA VAL A 293 " pdb=" C VAL A 293 " ideal model delta sigma weight residual 113.43 107.59 5.84 1.09e+00 8.42e-01 2.87e+01 ... (remaining 41208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16470 17.96 - 35.92: 1294 35.92 - 53.88: 227 53.88 - 71.85: 63 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: 4108 0.091 - 0.182: 445 0.182 - 0.273: 47 0.273 - 0.364: 2 0.364 - 0.455: 1 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 GLN B1142 " pdb=" N GLN B1142 " pdb=" C GLN B1142 " pdb=" CB GLN B1142 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN C 481 " pdb=" N ASN C 481 " pdb=" C ASN C 481 " pdb=" CB ASN C 481 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+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: 1.65 - 2.30: 2 2.30 - 2.95: 12301 2.95 - 3.60: 38552 3.60 - 4.25: 67877 4.25 - 4.90: 110158 Nonbonded interactions: 228890 Sorted by model distance: nonbonded pdb=" CD1 ILE B 472 " pdb=" CE2 PHE B 490 " model vdw 1.646 3.760 nonbonded pdb=" CD1 ILE B 472 " pdb=" CZ PHE B 490 " model vdw 2.225 3.760 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 ... (remaining 228885 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.150 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 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= 0.248 Angle : 0.839 13.017 41297 Z= 0.486 Chirality : 0.054 0.455 4603 Planarity : 0.007 0.095 5332 Dihedral : 13.401 87.356 10901 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 0.27 % Allowed : 5.81 % Favored : 93.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 : -2.77 (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 0.00477 (30314) covalent geometry : angle 0.83669 (41213) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.49335 ( 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 750 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 741 time to evaluate : 1.025 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: A 62 MET cc_start: -0.2111 (tpt) cc_final: -0.3053 (ptp) REVERT: A 171 GLU cc_start: 0.5789 (tt0) cc_final: 0.5419 (mm-30) REVERT: A 190 MET cc_start: -0.0018 (ppp) cc_final: -0.1119 (ptt) REVERT: A 223 ILE cc_start: 0.3571 (mm) cc_final: 0.2478 (mm) REVERT: A 249 MET cc_start: 0.1231 (mmt) cc_final: 0.0043 (mtt) REVERT: A 431 ASP cc_start: 0.5078 (p0) cc_final: 0.4233 (p0) REVERT: A 566 TRP cc_start: -0.1016 (p-90) cc_final: -0.1594 (p-90) REVERT: B 41 LYS cc_start: 0.6654 (mttt) cc_final: 0.5902 (mmmt) REVERT: B 54 LEU cc_start: 0.7411 (tp) cc_final: 0.6348 (pp) REVERT: B 296 LEU cc_start: 0.7432 (tp) cc_final: 0.7076 (tp) REVERT: B 309 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8512 (tp30) REVERT: B 731 MET cc_start: 0.8178 (mtp) cc_final: 0.7725 (mtt) REVERT: B 751 ASN cc_start: 0.9134 (m-40) cc_final: 0.8932 (m-40) REVERT: B 755 GLN cc_start: 0.8254 (mt0) cc_final: 0.7835 (mp10) REVERT: B 770 ILE cc_start: 0.9044 (pt) cc_final: 0.8693 (pt) REVERT: B 868 GLU cc_start: 0.8351 (mp0) cc_final: 0.7946 (mm-30) REVERT: B 869 MET cc_start: 0.8371 (mtp) cc_final: 0.7956 (mtp) REVERT: B 896 ILE cc_start: 0.7059 (mm) cc_final: 0.6740 (tp) REVERT: B 921 LYS cc_start: 0.8199 (mttt) cc_final: 0.7719 (tptt) REVERT: B 925 ASN cc_start: 0.7714 (m-40) cc_final: 0.7450 (m-40) REVERT: B 931 ILE cc_start: 0.7997 (mm) cc_final: 0.7627 (mm) REVERT: B 964 LYS cc_start: 0.8709 (ptpp) cc_final: 0.8504 (mtmm) REVERT: B 1001 LEU cc_start: 0.9342 (mt) cc_final: 0.9073 (tt) REVERT: B 1009 THR cc_start: 0.9129 (p) cc_final: 0.8862 (t) REVERT: B 1013 ILE cc_start: 0.8813 (pt) cc_final: 0.8588 (mt) REVERT: B 1038 LYS cc_start: 0.8283 (mttt) cc_final: 0.7978 (mtpp) REVERT: B 1103 PHE cc_start: 0.6579 (m-80) cc_final: 0.6167 (m-80) REVERT: C 293 LEU cc_start: 0.8333 (tp) cc_final: 0.7333 (tp) REVERT: C 298 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: C 314 GLN cc_start: 0.8187 (tt0) cc_final: 0.7886 (mm-40) REVERT: C 458 LYS cc_start: 0.4085 (mttt) cc_final: 0.3767 (mmtm) REVERT: C 462 LYS cc_start: 0.8156 (mttt) cc_final: 0.7897 (mmtm) REVERT: C 695 TYR cc_start: 0.7120 (p90) cc_final: 0.6524 (p90) REVERT: C 712 ILE cc_start: 0.6556 (tt) cc_final: 0.6324 (tt) REVERT: C 732 THR cc_start: 0.8622 (m) cc_final: 0.8331 (p) REVERT: C 814 LYS cc_start: 0.7793 (mttt) cc_final: 0.7091 (mmmt) REVERT: C 864 LEU cc_start: 0.7847 (tp) cc_final: 0.7580 (tt) REVERT: C 902 MET cc_start: 0.7461 (ttp) cc_final: 0.6935 (ttm) REVERT: C 933 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8457 (tptp) REVERT: C 962 LEU cc_start: 0.8973 (tp) cc_final: 0.8697 (tp) REVERT: C 1014 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8162 (mmm160) REVERT: C 1043 CYS cc_start: 0.1639 (m) cc_final: 0.1132 (m) REVERT: C 1071 GLN cc_start: 0.7327 (mt0) cc_final: 0.6974 (mp10) REVERT: C 1139 ASP cc_start: 0.6697 (t0) cc_final: 0.6136 (m-30) REVERT: D 40 ASP cc_start: 0.6422 (p0) cc_final: 0.6173 (t70) REVERT: D 287 ASP cc_start: 0.8149 (t0) cc_final: 0.7678 (t0) REVERT: D 310 LYS cc_start: 0.7937 (tttt) cc_final: 0.7391 (tppt) REVERT: D 503 VAL cc_start: 0.2409 (OUTLIER) cc_final: 0.2000 (p) REVERT: D 660 TYR cc_start: 0.7114 (m-80) cc_final: 0.6766 (m-10) REVERT: D 725 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6195 (tm-30) REVERT: D 790 LYS cc_start: 0.8349 (mttt) cc_final: 0.7854 (mmmt) REVERT: D 887 THR cc_start: 0.7089 (p) cc_final: 0.6854 (p) REVERT: D 888 PHE cc_start: 0.6255 (p90) cc_final: 0.6013 (p90) REVERT: D 978 ASN cc_start: 0.8628 (m-40) cc_final: 0.8346 (m110) outliers start: 9 outliers final: 2 residues processed: 749 average time/residue: 0.2007 time to fit residues: 233.9949 Evaluate side-chains 417 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 413 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 63 ASN A 98 GLN A 159 ASN A 221 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 378 HIS A 522 GLN A 572 ASN A 578 ASN A 586 ASN A 598 GLN B 121 ASN B 234 ASN B 536 ASN B 564 GLN B 606 ASN B 613 GLN B 955 ASN B 965 GLN B 992 GLN B1023 ASN B1101 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 394 ASN C 505 HIS C 519 HIS C 606 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 926 GLN C 955 ASN C1023 ASN C1101 HIS D 87 ASN D 334 ASN D 477 ASN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN D 777 ASN D 787 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN D 953 ASN D 954 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.149487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.123911 restraints weight = 118456.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.122705 restraints weight = 83085.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.122676 restraints weight = 68328.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.123085 restraints weight = 65942.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.123377 restraints weight = 51295.944| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30356 Z= 0.269 Angle : 0.793 16.749 41297 Z= 0.417 Chirality : 0.049 0.250 4603 Planarity : 0.006 0.065 5332 Dihedral : 5.107 62.940 4029 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 3.16 % Allowed : 13.23 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -3.25 (0.12), residues: 3700 helix: -2.90 (0.12), residues: 826 sheet: -1.24 (0.20), residues: 610 loop : -2.20 (0.11), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 246 TYR 0.028 0.003 TYR C 612 PHE 0.041 0.003 PHE D 541 TRP 0.019 0.002 TRP D1102 HIS 0.009 0.002 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00580 (30314) covalent geometry : angle 0.78867 (41213) SS BOND : bond 0.00481 ( 42) SS BOND : angle 1.96426 ( 84) hydrogen bonds : bond 0.04909 ( 834) hydrogen bonds : angle 6.86319 ( 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 516 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 412 time to evaluate : 1.177 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: A 62 MET cc_start: -0.2743 (tpt) cc_final: -0.4545 (ptm) REVERT: A 67 ASP cc_start: 0.6532 (m-30) cc_final: 0.6266 (m-30) REVERT: A 190 MET cc_start: -0.0682 (ppp) cc_final: -0.0917 (ptt) REVERT: A 221 GLN cc_start: 0.1319 (OUTLIER) cc_final: 0.0733 (tm130) REVERT: A 249 MET cc_start: 0.1129 (mmt) cc_final: -0.0831 (ttm) REVERT: A 288 LYS cc_start: 0.2302 (ptpp) cc_final: 0.1684 (tppp) REVERT: A 408 MET cc_start: 0.1031 (mtm) cc_final: 0.0688 (mpp) REVERT: A 455 MET cc_start: -0.0989 (ppp) cc_final: -0.1492 (ppp) REVERT: A 480 MET cc_start: 0.2738 (mtt) cc_final: 0.2171 (mtp) REVERT: A 554 LEU cc_start: -0.0977 (mt) cc_final: -0.1573 (pp) REVERT: A 566 TRP cc_start: -0.0753 (p-90) cc_final: -0.1572 (p-90) REVERT: A 579 MET cc_start: 0.0729 (mmp) cc_final: -0.0283 (mmt) REVERT: A 585 LEU cc_start: 0.3899 (mt) cc_final: 0.3483 (mt) REVERT: A 586 ASN cc_start: 0.4892 (p0) cc_final: 0.3951 (m-40) REVERT: A 589 GLU cc_start: 0.7097 (pm20) cc_final: 0.6883 (mm-30) REVERT: B 755 GLN cc_start: 0.8132 (mt0) cc_final: 0.7920 (mp10) REVERT: B 964 LYS cc_start: 0.8333 (ptpp) cc_final: 0.8133 (mtmm) REVERT: C 458 LYS cc_start: 0.3851 (mttt) cc_final: 0.3567 (mmtm) REVERT: C 462 LYS cc_start: 0.8005 (mttt) cc_final: 0.7692 (mmtm) REVERT: C 732 THR cc_start: 0.8868 (m) cc_final: 0.8656 (p) REVERT: C 754 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8270 (tp) REVERT: C 955 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7663 (m110) REVERT: C 1014 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8106 (mmm160) REVERT: C 1018 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8449 (mm) REVERT: C 1139 ASP cc_start: 0.6916 (t0) cc_final: 0.6221 (m-30) REVERT: D 84 LEU cc_start: 0.8033 (mp) cc_final: 0.7666 (tp) REVERT: D 177 MET cc_start: -0.1771 (mmp) cc_final: -0.3316 (mtt) REVERT: D 334 ASN cc_start: 0.8167 (t0) cc_final: 0.7246 (m110) REVERT: D 802 PHE cc_start: 0.5627 (m-80) cc_final: 0.5354 (m-80) REVERT: D 949 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6821 (mm-40) outliers start: 104 outliers final: 50 residues processed: 489 average time/residue: 0.1834 time to fit residues: 145.5209 Evaluate side-chains 365 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 95 optimal weight: 0.7980 chunk 205 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 143 optimal weight: 0.0000 chunk 292 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 341 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 236 optimal weight: 2.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 81 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN B 234 ASN B 321 GLN B 606 ASN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1135 ASN C 606 ASN C 907 ASN C1002 GLN C1023 ASN D 218 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.151744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.125208 restraints weight = 117482.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.125994 restraints weight = 82918.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.126137 restraints weight = 52266.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.126385 restraints weight = 47598.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.126708 restraints weight = 43335.219| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30356 Z= 0.106 Angle : 0.591 11.605 41297 Z= 0.296 Chirality : 0.044 0.182 4603 Planarity : 0.004 0.061 5332 Dihedral : 4.381 57.296 4025 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.92 % Allowed : 16.08 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.42 (0.12), residues: 3700 helix: -1.42 (0.17), residues: 819 sheet: -0.85 (0.20), residues: 614 loop : -1.97 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.023 0.001 TYR B 91 PHE 0.032 0.001 PHE D1109 TRP 0.013 0.001 TRP B1102 HIS 0.006 0.001 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00230 (30314) covalent geometry : angle 0.58935 (41213) SS BOND : bond 0.00279 ( 42) SS BOND : angle 1.17313 ( 84) hydrogen bonds : bond 0.04016 ( 834) hydrogen bonds : angle 5.99600 ( 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 450 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 387 time to evaluate : 1.223 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: A 67 ASP cc_start: 0.6943 (m-30) cc_final: 0.6714 (m-30) REVERT: A 171 GLU cc_start: 0.5025 (tt0) cc_final: 0.4450 (mm-30) REVERT: A 249 MET cc_start: 0.1091 (mmt) cc_final: -0.0873 (ttm) REVERT: A 288 LYS cc_start: 0.2476 (ptpp) cc_final: 0.1756 (tppp) REVERT: A 408 MET cc_start: 0.1052 (mtm) cc_final: 0.0712 (mpp) REVERT: A 480 MET cc_start: 0.2433 (mtt) cc_final: 0.1792 (mtp) REVERT: A 554 LEU cc_start: -0.1037 (mt) cc_final: -0.1623 (pp) REVERT: A 566 TRP cc_start: -0.0783 (p-90) cc_final: -0.1447 (p-90) REVERT: A 579 MET cc_start: 0.0778 (mmp) cc_final: -0.0027 (mmt) REVERT: A 586 ASN cc_start: 0.4562 (p0) cc_final: 0.4194 (p0) REVERT: A 589 GLU cc_start: 0.7108 (pm20) cc_final: 0.6884 (mm-30) REVERT: B 54 LEU cc_start: 0.8008 (tp) cc_final: 0.6841 (pp) REVERT: B 237 ARG cc_start: 0.7376 (tpt-90) cc_final: 0.7126 (tpt-90) REVERT: B 577 ARG cc_start: 0.5252 (mpt180) cc_final: 0.4546 (mmt90) REVERT: B 736 VAL cc_start: 0.8908 (p) cc_final: 0.8618 (m) REVERT: B 773 GLU cc_start: 0.7015 (tt0) cc_final: 0.6792 (tt0) REVERT: B 776 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8271 (ptmm) REVERT: B 803 SER cc_start: 0.7755 (OUTLIER) cc_final: 0.7501 (t) REVERT: B 964 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8134 (mtmm) REVERT: B 1001 LEU cc_start: 0.8976 (mt) cc_final: 0.8613 (mt) REVERT: B 1028 LYS cc_start: 0.7555 (mttt) cc_final: 0.7287 (mtpp) REVERT: C 141 LEU cc_start: 0.7985 (tp) cc_final: 0.7726 (tp) REVERT: C 340 GLU cc_start: 0.7124 (pp20) cc_final: 0.6501 (tp30) REVERT: C 458 LYS cc_start: 0.3838 (mttt) cc_final: 0.3596 (mmtm) REVERT: C 462 LYS cc_start: 0.7938 (mttt) cc_final: 0.7619 (mmtm) REVERT: C 719 THR cc_start: 0.7812 (t) cc_final: 0.7580 (p) REVERT: C 754 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8245 (tp) REVERT: C 759 PHE cc_start: 0.6837 (t80) cc_final: 0.6602 (t80) REVERT: C 814 LYS cc_start: 0.7321 (mttt) cc_final: 0.6864 (mmmt) REVERT: C 906 PHE cc_start: 0.4954 (m-10) cc_final: 0.4579 (m-10) REVERT: C 955 ASN cc_start: 0.7810 (m110) cc_final: 0.7096 (t0) REVERT: C 1014 ARG cc_start: 0.8417 (mtt180) cc_final: 0.8167 (mmm160) REVERT: C 1139 ASP cc_start: 0.6874 (t0) cc_final: 0.6198 (m-30) REVERT: D 177 MET cc_start: -0.1456 (mmp) cc_final: -0.2946 (mtt) REVERT: D 334 ASN cc_start: 0.8103 (t0) cc_final: 0.7097 (m110) REVERT: D 790 LYS cc_start: 0.8374 (mtpt) cc_final: 0.8141 (tppt) REVERT: D 949 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6758 (mm-40) REVERT: D 1002 GLN cc_start: 0.7797 (tp40) cc_final: 0.7442 (tm-30) REVERT: D 1090 PRO cc_start: 0.6764 (Cg_endo) cc_final: 0.6538 (Cg_exo) outliers start: 63 outliers final: 38 residues processed: 431 average time/residue: 0.1824 time to fit residues: 128.7272 Evaluate side-chains 367 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1106 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 157 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 216 optimal weight: 0.0030 chunk 109 optimal weight: 5.9990 chunk 188 optimal weight: 0.1980 chunk 200 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 314 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.0394 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 751 ASN B 777 ASN B 872 GLN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 137 ASN C 437 ASN C 606 ASN ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1023 ASN C1108 ASN D 23 GLN D 30 ASN D 414 GLN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 690 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 953 ASN D 955 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.148163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.120338 restraints weight = 116295.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.121134 restraints weight = 81963.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.121118 restraints weight = 55662.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.121437 restraints weight = 49984.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.121844 restraints weight = 44569.506| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30356 Z= 0.168 Angle : 0.628 11.852 41297 Z= 0.318 Chirality : 0.045 0.199 4603 Planarity : 0.004 0.051 5332 Dihedral : 4.497 50.662 4025 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.10 % Allowed : 16.81 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.11 (0.13), residues: 3700 helix: -0.97 (0.17), residues: 849 sheet: -0.75 (0.20), residues: 590 loop : -1.81 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 983 TYR 0.014 0.002 TYR B 707 PHE 0.021 0.002 PHE B 888 TRP 0.013 0.001 TRP C 633 HIS 0.007 0.001 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00377 (30314) covalent geometry : angle 0.62461 (41213) SS BOND : bond 0.00444 ( 42) SS BOND : angle 1.57160 ( 84) hydrogen bonds : bond 0.03945 ( 834) hydrogen bonds : angle 5.90404 ( 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 454 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 352 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: A 62 MET cc_start: -0.3008 (tpt) cc_final: -0.4655 (ptm) REVERT: A 67 ASP cc_start: 0.7003 (m-30) cc_final: 0.6774 (m-30) REVERT: A 171 GLU cc_start: 0.4990 (tt0) cc_final: 0.4384 (mm-30) REVERT: A 249 MET cc_start: 0.0500 (mmt) cc_final: -0.1336 (mtm) REVERT: A 288 LYS cc_start: 0.2312 (ptpp) cc_final: 0.1606 (tppp) REVERT: A 408 MET cc_start: 0.1581 (mtm) cc_final: 0.1357 (mpp) REVERT: A 480 MET cc_start: 0.2739 (mtt) cc_final: 0.2112 (mtp) REVERT: A 554 LEU cc_start: -0.0810 (mt) cc_final: -0.1479 (pp) REVERT: A 566 TRP cc_start: -0.0588 (p-90) cc_final: -0.1143 (p-90) REVERT: A 579 MET cc_start: 0.0586 (mmp) cc_final: -0.0104 (mmt) REVERT: B 1001 LEU cc_start: 0.9039 (mt) cc_final: 0.8713 (mt) REVERT: B 1028 LYS cc_start: 0.7682 (mttt) cc_final: 0.7443 (mttt) REVERT: C 141 LEU cc_start: 0.7981 (tp) cc_final: 0.7704 (tp) REVERT: C 340 GLU cc_start: 0.7232 (pp20) cc_final: 0.6662 (tp30) REVERT: C 458 LYS cc_start: 0.3822 (mttt) cc_final: 0.3496 (mmtm) REVERT: C 462 LYS cc_start: 0.7898 (mttt) cc_final: 0.7495 (mmtm) REVERT: C 754 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8229 (tp) REVERT: C 814 LYS cc_start: 0.7568 (mttt) cc_final: 0.6924 (mmmt) REVERT: C 983 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7755 (ttm110) REVERT: C 1014 ARG cc_start: 0.8515 (mtt180) cc_final: 0.8240 (mmm160) REVERT: C 1139 ASP cc_start: 0.7002 (t0) cc_final: 0.6342 (m-30) REVERT: D 177 MET cc_start: -0.1613 (mmp) cc_final: -0.3075 (mtt) REVERT: D 334 ASN cc_start: 0.8296 (t0) cc_final: 0.7427 (m110) REVERT: D 720 ILE cc_start: 0.7673 (mt) cc_final: 0.7377 (pt) REVERT: D 790 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8379 (mtpp) REVERT: D 1002 GLN cc_start: 0.7797 (tp40) cc_final: 0.7389 (tm-30) REVERT: D 1090 PRO cc_start: 0.7168 (Cg_endo) cc_final: 0.6924 (Cg_exo) REVERT: D 1107 ARG cc_start: 0.7006 (mtt90) cc_final: 0.6729 (mtm-85) outliers start: 102 outliers final: 66 residues processed: 420 average time/residue: 0.1696 time to fit residues: 116.7541 Evaluate side-chains 373 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 306 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1106 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 227 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 363 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 240 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 334 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 245 HIS ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 755 GLN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1113 GLN C 121 ASN C 606 ASN C 953 ASN C 955 ASN C1023 ASN C1106 GLN D 606 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.147584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.119629 restraints weight = 117128.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.120426 restraints weight = 81803.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.120443 restraints weight = 52450.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.120668 restraints weight = 48925.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.121242 restraints weight = 42776.605| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30356 Z= 0.149 Angle : 0.608 11.467 41297 Z= 0.307 Chirality : 0.045 0.187 4603 Planarity : 0.004 0.053 5332 Dihedral : 4.458 51.705 4025 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.19 % Allowed : 17.57 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.96 (0.13), residues: 3700 helix: -0.66 (0.18), residues: 837 sheet: -0.71 (0.20), residues: 587 loop : -1.78 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 765 TYR 0.022 0.001 TYR C1110 PHE 0.023 0.001 PHE B 888 TRP 0.009 0.001 TRP D 436 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00336 (30314) covalent geometry : angle 0.60530 (41213) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.44116 ( 84) hydrogen bonds : bond 0.03720 ( 834) hydrogen bonds : angle 5.81023 ( 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 439 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 334 time to evaluate : 1.147 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: A 63 ASN cc_start: 0.3725 (m-40) cc_final: 0.2681 (t0) REVERT: A 67 ASP cc_start: 0.7039 (m-30) cc_final: 0.6786 (m-30) REVERT: A 171 GLU cc_start: 0.5459 (tt0) cc_final: 0.4716 (mm-30) REVERT: A 249 MET cc_start: 0.0069 (mmt) cc_final: -0.1798 (mtm) REVERT: A 288 LYS cc_start: 0.2249 (ptpp) cc_final: 0.1624 (tppp) REVERT: A 480 MET cc_start: 0.2495 (mtt) cc_final: 0.1931 (mtp) REVERT: A 554 LEU cc_start: -0.0720 (mt) cc_final: -0.1464 (pp) REVERT: A 566 TRP cc_start: -0.0551 (p-90) cc_final: -0.0962 (p-90) REVERT: A 579 MET cc_start: 0.0496 (mmp) cc_final: -0.0073 (mmt) REVERT: A 586 ASN cc_start: 0.4682 (p0) cc_final: 0.4204 (p0) REVERT: A 589 GLU cc_start: 0.7099 (pm20) cc_final: 0.6851 (mm-30) REVERT: B 131 CYS cc_start: 0.5788 (OUTLIER) cc_final: 0.5586 (t) REVERT: B 418 ILE cc_start: 0.1220 (OUTLIER) cc_final: 0.0651 (pt) REVERT: B 776 LYS cc_start: 0.8845 (ptpt) cc_final: 0.8429 (ptmm) REVERT: B 1012 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9167 (tt) REVERT: C 141 LEU cc_start: 0.7977 (tp) cc_final: 0.7718 (tp) REVERT: C 458 LYS cc_start: 0.4012 (mttt) cc_final: 0.3690 (mmtm) REVERT: C 462 LYS cc_start: 0.7925 (mttt) cc_final: 0.7480 (mmtm) REVERT: C 754 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8362 (tp) REVERT: C 759 PHE cc_start: 0.7084 (t80) cc_final: 0.6823 (t80) REVERT: C 1108 ASN cc_start: 0.5943 (OUTLIER) cc_final: 0.5559 (t0) REVERT: C 1139 ASP cc_start: 0.6971 (t0) cc_final: 0.6390 (m-30) REVERT: D 177 MET cc_start: -0.1198 (mmp) cc_final: -0.1735 (mtt) REVERT: D 720 ILE cc_start: 0.7793 (mt) cc_final: 0.7561 (pt) REVERT: D 1002 GLN cc_start: 0.7891 (tp40) cc_final: 0.7321 (tm-30) REVERT: D 1090 PRO cc_start: 0.7271 (Cg_endo) cc_final: 0.6969 (Cg_exo) REVERT: D 1107 ARG cc_start: 0.7046 (mtt90) cc_final: 0.6827 (mtm-85) outliers start: 105 outliers final: 71 residues processed: 409 average time/residue: 0.1671 time to fit residues: 112.6874 Evaluate side-chains 379 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 303 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 777 ASN Chi-restraints excluded: chain D residue 915 VAL 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 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 340 optimal weight: 0.4980 chunk 287 optimal weight: 0.0570 chunk 324 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 95 optimal weight: 0.0070 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 221 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 777 ASN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 926 GLN C 953 ASN C 955 ASN C1023 ASN C1108 ASN D 690 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.149011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.121562 restraints weight = 115371.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.122008 restraints weight = 83551.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.122325 restraints weight = 55170.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.122687 restraints weight = 49277.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.122934 restraints weight = 43096.262| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 30356 Z= 0.100 Angle : 0.559 11.568 41297 Z= 0.278 Chirality : 0.044 0.360 4603 Planarity : 0.004 0.051 5332 Dihedral : 4.174 51.866 4025 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.34 % Allowed : 18.46 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.74 (0.13), residues: 3700 helix: -0.41 (0.18), residues: 833 sheet: -0.55 (0.21), residues: 586 loop : -1.67 (0.12), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.028 0.001 TYR B 91 PHE 0.020 0.001 PHE C1109 TRP 0.010 0.001 TRP D 64 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00228 (30314) covalent geometry : angle 0.55741 (41213) SS BOND : bond 0.00286 ( 42) SS BOND : angle 1.16368 ( 84) hydrogen bonds : bond 0.03333 ( 834) hydrogen bonds : angle 5.49457 ( 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 431 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 354 time to evaluate : 1.470 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 62 MET cc_start: -0.3030 (tpt) cc_final: -0.4869 (ptm) REVERT: A 63 ASN cc_start: 0.3847 (m-40) cc_final: 0.3477 (t0) REVERT: A 67 ASP cc_start: 0.7068 (m-30) cc_final: 0.6813 (m-30) REVERT: A 82 MET cc_start: 0.3633 (ptp) cc_final: 0.2910 (ptp) REVERT: A 171 GLU cc_start: 0.5701 (tt0) cc_final: 0.4999 (mm-30) REVERT: A 249 MET cc_start: -0.0037 (mmt) cc_final: -0.1862 (mtm) REVERT: A 288 LYS cc_start: 0.2261 (ptpp) cc_final: 0.1642 (tppp) REVERT: A 480 MET cc_start: 0.2156 (mtt) cc_final: 0.1544 (mtp) REVERT: A 566 TRP cc_start: -0.0663 (p-90) cc_final: -0.1034 (p-90) REVERT: A 579 MET cc_start: 0.0323 (mmp) cc_final: -0.0073 (mmt) REVERT: B 92 PHE cc_start: 0.5062 (m-80) cc_final: 0.4739 (m-10) REVERT: B 303 LEU cc_start: 0.8391 (mp) cc_final: 0.7981 (tt) REVERT: B 776 LYS cc_start: 0.8814 (ptpt) cc_final: 0.8383 (ptmm) REVERT: B 1001 LEU cc_start: 0.8894 (mt) cc_final: 0.8531 (mt) REVERT: C 141 LEU cc_start: 0.8051 (tp) cc_final: 0.7775 (tp) REVERT: C 458 LYS cc_start: 0.4025 (mttt) cc_final: 0.3539 (mmtm) REVERT: C 462 LYS cc_start: 0.8023 (mttt) cc_final: 0.7526 (mmtm) REVERT: C 719 THR cc_start: 0.8090 (t) cc_final: 0.7761 (p) REVERT: C 754 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8267 (tp) REVERT: C 765 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7570 (mtm110) REVERT: C 983 ARG cc_start: 0.8109 (mtp-110) cc_final: 0.7800 (ttm110) REVERT: C 1139 ASP cc_start: 0.6952 (t0) cc_final: 0.6356 (m-30) REVERT: D 177 MET cc_start: -0.1162 (mmp) cc_final: -0.1658 (mtt) REVERT: D 720 ILE cc_start: 0.7750 (mt) cc_final: 0.7522 (pt) REVERT: D 1076 THR cc_start: 0.6892 (OUTLIER) cc_final: 0.6572 (m) REVERT: D 1090 PRO cc_start: 0.7333 (Cg_endo) cc_final: 0.7103 (Cg_exo) outliers start: 77 outliers final: 50 residues processed: 406 average time/residue: 0.1762 time to fit residues: 117.8466 Evaluate side-chains 373 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 321 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1106 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 358 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 368 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 246 optimal weight: 0.4980 chunk 354 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 206 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 606 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN C1108 ASN C1142 GLN D 690 GLN D1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.147905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.120766 restraints weight = 116834.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120829 restraints weight = 85822.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.121192 restraints weight = 55716.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.121627 restraints weight = 50048.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.121791 restraints weight = 43817.573| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.5777 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= 0.121 Angle : 0.584 11.623 41297 Z= 0.292 Chirality : 0.044 0.281 4603 Planarity : 0.004 0.053 5332 Dihedral : 4.217 50.128 4025 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.58 % Allowed : 19.12 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.62 (0.13), residues: 3700 helix: -0.31 (0.18), residues: 836 sheet: -0.36 (0.21), residues: 565 loop : -1.62 (0.12), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.033 0.001 TYR C 365 PHE 0.018 0.001 PHE C1103 TRP 0.008 0.001 TRP A 473 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00277 (30314) covalent geometry : angle 0.57933 (41213) SS BOND : bond 0.00394 ( 42) SS BOND : angle 1.69917 ( 84) hydrogen bonds : bond 0.03417 ( 834) hydrogen bonds : angle 5.48304 ( 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 409 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 324 time to evaluate : 0.851 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 62 MET cc_start: -0.2800 (tpt) cc_final: -0.4735 (ptm) REVERT: A 63 ASN cc_start: 0.3856 (m-40) cc_final: 0.3508 (t0) REVERT: A 67 ASP cc_start: 0.7090 (m-30) cc_final: 0.6836 (m-30) REVERT: A 82 MET cc_start: 0.3706 (ptp) cc_final: 0.2968 (ptp) REVERT: A 249 MET cc_start: 0.0021 (mmt) cc_final: -0.1825 (mtm) REVERT: A 480 MET cc_start: 0.2231 (mtt) cc_final: 0.1660 (mtp) REVERT: A 566 TRP cc_start: -0.0459 (p-90) cc_final: -0.0824 (p-90) REVERT: A 579 MET cc_start: 0.0255 (mmp) cc_final: -0.0169 (mmt) REVERT: B 92 PHE cc_start: 0.5117 (m-80) cc_final: 0.4750 (m-10) REVERT: B 298 GLU cc_start: 0.8058 (tp30) cc_final: 0.7798 (mt-10) REVERT: B 303 LEU cc_start: 0.8409 (mp) cc_final: 0.7971 (tt) REVERT: C 141 LEU cc_start: 0.8044 (tp) cc_final: 0.7754 (tp) REVERT: C 306 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: C 458 LYS cc_start: 0.4193 (mttt) cc_final: 0.3707 (mmtm) REVERT: C 754 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8284 (tp) REVERT: C 765 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7577 (mtm110) REVERT: C 983 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7819 (ttm110) REVERT: C 1139 ASP cc_start: 0.6949 (t0) cc_final: 0.6357 (m-30) REVERT: D 720 ILE cc_start: 0.7863 (mt) cc_final: 0.7608 (pt) REVERT: D 868 GLU cc_start: 0.6247 (mm-30) cc_final: 0.5843 (mm-30) REVERT: D 1076 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6789 (m) REVERT: D 1090 PRO cc_start: 0.7381 (Cg_endo) cc_final: 0.7122 (Cg_exo) outliers start: 85 outliers final: 63 residues processed: 388 average time/residue: 0.1716 time to fit residues: 110.1913 Evaluate side-chains 377 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 311 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 181 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 336 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 217 optimal weight: 0.0170 chunk 225 optimal weight: 0.0470 chunk 128 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 343 optimal weight: 0.6980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN C 137 ASN C 505 HIS C 606 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C 955 ASN D 690 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.149271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.122277 restraints weight = 117466.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.122558 restraints weight = 86246.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.122767 restraints weight = 59666.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.123083 restraints weight = 53493.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.123433 restraints weight = 43934.334| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30356 Z= 0.098 Angle : 0.568 11.650 41297 Z= 0.281 Chirality : 0.044 0.270 4603 Planarity : 0.004 0.049 5332 Dihedral : 4.071 49.755 4025 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.07 % Allowed : 19.64 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.51 (0.13), residues: 3700 helix: -0.20 (0.18), residues: 842 sheet: -0.30 (0.21), residues: 558 loop : -1.55 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 765 TYR 0.020 0.001 TYR C 365 PHE 0.019 0.001 PHE D 888 TRP 0.011 0.001 TRP A 473 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00220 (30314) covalent geometry : angle 0.56396 (41213) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.55342 ( 84) hydrogen bonds : bond 0.03280 ( 834) hydrogen bonds : angle 5.34385 ( 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 412 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 344 time to evaluate : 1.026 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: A 62 MET cc_start: -0.2656 (tpt) cc_final: -0.4470 (ptm) REVERT: A 63 ASN cc_start: 0.3895 (m-40) cc_final: 0.3592 (t0) REVERT: A 67 ASP cc_start: 0.7021 (m-30) cc_final: 0.6765 (m-30) REVERT: A 249 MET cc_start: -0.0081 (mmt) cc_final: -0.1929 (mtm) REVERT: A 480 MET cc_start: 0.2191 (mtt) cc_final: 0.1590 (mtp) REVERT: A 566 TRP cc_start: -0.0264 (p-90) cc_final: -0.0629 (p-90) REVERT: A 579 MET cc_start: 0.0127 (mmp) cc_final: -0.0145 (mmt) REVERT: B 92 PHE cc_start: 0.5223 (m-80) cc_final: 0.4943 (m-10) REVERT: B 303 LEU cc_start: 0.8403 (mp) cc_final: 0.8021 (tt) REVERT: C 141 LEU cc_start: 0.8059 (tp) cc_final: 0.7754 (tp) REVERT: C 306 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: C 458 LYS cc_start: 0.4150 (mttt) cc_final: 0.3629 (mmtm) REVERT: C 719 THR cc_start: 0.8046 (t) cc_final: 0.7808 (p) REVERT: C 754 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (tp) REVERT: C 814 LYS cc_start: 0.7622 (mttt) cc_final: 0.6918 (mmmt) REVERT: C 884 SER cc_start: 0.5838 (OUTLIER) cc_final: 0.4990 (m) REVERT: C 983 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7730 (ttm110) REVERT: C 1139 ASP cc_start: 0.6959 (t0) cc_final: 0.6326 (m-30) REVERT: D 720 ILE cc_start: 0.7975 (mt) cc_final: 0.7705 (pt) REVERT: D 1076 THR cc_start: 0.7110 (OUTLIER) cc_final: 0.6782 (m) REVERT: D 1090 PRO cc_start: 0.7254 (Cg_endo) cc_final: 0.7022 (Cg_exo) outliers start: 68 outliers final: 49 residues processed: 392 average time/residue: 0.1649 time to fit residues: 106.5277 Evaluate side-chains 367 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 314 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1106 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 337 optimal weight: 0.7980 chunk 293 optimal weight: 6.9990 chunk 100 optimal weight: 0.0970 chunk 151 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 354 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C 606 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 978 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.148748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.122362 restraints weight = 116577.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.121608 restraints weight = 79483.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.122130 restraints weight = 55552.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.122551 restraints weight = 46543.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.122669 restraints weight = 41806.824| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30356 Z= 0.103 Angle : 0.586 11.719 41297 Z= 0.288 Chirality : 0.044 0.258 4603 Planarity : 0.004 0.052 5332 Dihedral : 4.027 48.456 4025 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.07 % Allowed : 20.22 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.44 (0.13), residues: 3700 helix: -0.17 (0.18), residues: 854 sheet: -0.23 (0.21), residues: 554 loop : -1.51 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 765 TYR 0.028 0.001 TYR B 91 PHE 0.023 0.001 PHE C 906 TRP 0.008 0.001 TRP A 473 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00235 (30314) covalent geometry : angle 0.58270 (41213) SS BOND : bond 0.00349 ( 42) SS BOND : angle 1.49370 ( 84) hydrogen bonds : bond 0.03257 ( 834) hydrogen bonds : angle 5.29804 ( 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 393 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 325 time to evaluate : 0.796 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: A 62 MET cc_start: -0.2508 (tpt) cc_final: -0.4242 (ptm) REVERT: A 63 ASN cc_start: 0.3961 (m-40) cc_final: 0.3709 (t0) REVERT: A 67 ASP cc_start: 0.7031 (m-30) cc_final: 0.6776 (m-30) REVERT: A 82 MET cc_start: 0.3425 (ptp) cc_final: 0.3135 (ptt) REVERT: A 249 MET cc_start: -0.0062 (mmt) cc_final: -0.1898 (mtm) REVERT: A 259 ILE cc_start: 0.7856 (mm) cc_final: 0.7537 (tp) REVERT: A 363 LYS cc_start: -0.1053 (mptt) cc_final: -0.2682 (mtpt) REVERT: A 480 MET cc_start: 0.2161 (mtt) cc_final: 0.1608 (mtp) REVERT: A 586 ASN cc_start: 0.7109 (p0) cc_final: 0.6598 (p0) REVERT: A 589 GLU cc_start: 0.7416 (pm20) cc_final: 0.7099 (mm-30) REVERT: B 92 PHE cc_start: 0.5117 (m-80) cc_final: 0.4895 (m-10) REVERT: B 303 LEU cc_start: 0.8396 (mp) cc_final: 0.8014 (tt) REVERT: B 818 ILE cc_start: 0.8890 (mp) cc_final: 0.8689 (mt) REVERT: C 141 LEU cc_start: 0.8071 (tp) cc_final: 0.7776 (tp) REVERT: C 306 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: C 458 LYS cc_start: 0.4186 (mttt) cc_final: 0.3672 (mmtm) REVERT: C 719 THR cc_start: 0.8139 (t) cc_final: 0.7892 (p) REVERT: C 754 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8232 (tp) REVERT: C 983 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.7900 (ttm110) REVERT: C 1018 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8044 (mt) REVERT: C 1139 ASP cc_start: 0.7018 (t0) cc_final: 0.6342 (m-30) REVERT: D 720 ILE cc_start: 0.7989 (mt) cc_final: 0.7700 (pt) REVERT: D 868 GLU cc_start: 0.6346 (mm-30) cc_final: 0.6094 (tp30) REVERT: D 1076 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6811 (m) REVERT: D 1090 PRO cc_start: 0.7274 (Cg_endo) cc_final: 0.7031 (Cg_exo) outliers start: 68 outliers final: 51 residues processed: 371 average time/residue: 0.1729 time to fit residues: 105.6239 Evaluate side-chains 370 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 51 optimal weight: 8.9990 chunk 257 optimal weight: 0.1980 chunk 303 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 235 optimal weight: 0.0020 chunk 210 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS A 535 HIS A 599 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 978 ASN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 953 ASN D1002 GLN D1058 HIS ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.144797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.117364 restraints weight = 116877.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.117027 restraints weight = 96107.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.117544 restraints weight = 63273.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.117919 restraints weight = 51495.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.118194 restraints weight = 42110.550| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30356 Z= 0.206 Angle : 0.704 11.788 41297 Z= 0.355 Chirality : 0.048 0.258 4603 Planarity : 0.004 0.046 5332 Dihedral : 4.761 44.917 4025 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.16 % Allowed : 20.31 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.77 (0.13), residues: 3700 helix: -0.37 (0.18), residues: 856 sheet: -0.65 (0.21), residues: 568 loop : -1.70 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 765 TYR 0.024 0.002 TYR B 91 PHE 0.022 0.002 PHE B 32 TRP 0.023 0.002 TRP B 104 HIS 0.008 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00472 (30314) covalent geometry : angle 0.69894 (41213) SS BOND : bond 0.00526 ( 42) SS BOND : angle 1.95204 ( 84) hydrogen bonds : bond 0.03964 ( 834) hydrogen bonds : angle 5.92128 ( 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 390 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 319 time to evaluate : 1.046 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: A 62 MET cc_start: -0.2454 (tpt) cc_final: -0.4625 (ptm) REVERT: A 63 ASN cc_start: 0.4035 (m-40) cc_final: 0.3615 (t0) REVERT: A 67 ASP cc_start: 0.6838 (m-30) cc_final: 0.6552 (m-30) REVERT: A 82 MET cc_start: 0.3227 (ptp) cc_final: 0.2533 (ptp) REVERT: A 249 MET cc_start: -0.0114 (mmt) cc_final: -0.1850 (mtt) REVERT: A 363 LYS cc_start: -0.0980 (mptt) cc_final: -0.2710 (mtpt) REVERT: A 462 MET cc_start: 0.2387 (mpp) cc_final: 0.2032 (mmp) REVERT: A 480 MET cc_start: 0.2864 (mtt) cc_final: 0.2335 (mtp) REVERT: A 566 TRP cc_start: -0.0028 (p-90) cc_final: -0.0295 (p-90) REVERT: B 303 LEU cc_start: 0.8425 (mp) cc_final: 0.7981 (tt) REVERT: B 418 ILE cc_start: 0.1113 (OUTLIER) cc_final: 0.0509 (pt) REVERT: C 141 LEU cc_start: 0.7826 (tp) cc_final: 0.7584 (tp) REVERT: C 458 LYS cc_start: 0.4208 (mttt) cc_final: 0.3805 (mmtm) REVERT: C 983 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.8044 (ttm110) REVERT: C 1139 ASP cc_start: 0.7012 (t0) cc_final: 0.6453 (m-30) REVERT: C 1147 SER cc_start: 0.6643 (t) cc_final: 0.6389 (p) REVERT: D 720 ILE cc_start: 0.8275 (mt) cc_final: 0.7967 (pt) REVERT: D 1040 VAL cc_start: 0.9040 (t) cc_final: 0.8799 (p) REVERT: D 1090 PRO cc_start: 0.7443 (Cg_endo) cc_final: 0.7177 (Cg_exo) outliers start: 71 outliers final: 59 residues processed: 366 average time/residue: 0.1731 time to fit residues: 104.9004 Evaluate side-chains 356 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1106 GLN 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: 8.9990 chunk 21 optimal weight: 10.0000 chunk 366 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 346 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 193 optimal weight: 0.3980 chunk 139 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 606 ASN C 901 GLN C 955 ASN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN D 953 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.145226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.118050 restraints weight = 117116.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.117393 restraints weight = 88884.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.118015 restraints weight = 62177.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.118311 restraints weight = 53015.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.118539 restraints weight = 44204.582| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30356 Z= 0.162 Angle : 0.668 24.433 41297 Z= 0.332 Chirality : 0.046 0.244 4603 Planarity : 0.004 0.052 5332 Dihedral : 4.704 47.010 4025 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.13 % Allowed : 21.04 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.79 (0.13), residues: 3700 helix: -0.36 (0.18), residues: 861 sheet: -0.79 (0.20), residues: 598 loop : -1.69 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 983 TYR 0.023 0.002 TYR C 365 PHE 0.020 0.002 PHE D 888 TRP 0.016 0.001 TRP B 104 HIS 0.006 0.001 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00370 (30314) covalent geometry : angle 0.66361 (41213) SS BOND : bond 0.00402 ( 42) SS BOND : angle 1.73102 ( 84) hydrogen bonds : bond 0.03676 ( 834) hydrogen bonds : angle 5.83045 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5542.20 seconds wall clock time: 96 minutes 30.45 seconds (5790.45 seconds total)