Starting phenix.real_space_refine on Wed Jun 25 21:14:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvp_32856/06_2025/7wvp_32856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvp_32856/06_2025/7wvp_32856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wvp_32856/06_2025/7wvp_32856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvp_32856/06_2025/7wvp_32856.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvp_32856/06_2025/7wvp_32856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvp_32856/06_2025/7wvp_32856.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 18942 2.51 5 N 4926 2.21 5 O 5590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.96s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'TRANS': 1002} Chain breaks: 7 Chain: "D" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Time building chain proxies: 18.35, per 1000 atoms: 0.62 Number of scatterers: 29601 At special positions: 0 Unit cell: (149.741, 134.439, 234.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5590 8.00 N 4926 7.00 C 18942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.29 Conformation dependent library (CDL) restraints added in 3.8 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: 4.32 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: 14.32 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9366 1.34 - 1.47: 7598 1.47 - 1.59: 13156 1.59 - 1.72: 0 1.72 - 1.85: 194 Bond restraints: 30314 Sorted by residual: bond pdb=" CA ILE C 584 " pdb=" C ILE C 584 " ideal model delta sigma weight residual 1.526 1.474 0.051 1.01e-02 9.80e+03 2.59e+01 bond pdb=" N GLU C 583 " pdb=" CA GLU C 583 " ideal model delta sigma weight residual 1.456 1.397 0.059 1.21e-02 6.83e+03 2.40e+01 bond pdb=" CA ASN B 331 " pdb=" C ASN B 331 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.35e-02 5.49e+03 1.97e+01 bond pdb=" CA PHE B 490 " pdb=" C PHE B 490 " ideal model delta sigma weight residual 1.520 1.564 -0.044 1.02e-02 9.61e+03 1.84e+01 bond pdb=" CA ILE C 584 " pdb=" CB ILE C 584 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.11e-02 8.12e+03 1.25e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 40391 2.60 - 5.21: 708 5.21 - 7.81: 82 7.81 - 10.41: 26 10.41 - 13.02: 6 Bond angle restraints: 41213 Sorted by residual: angle pdb=" N GLY B 526 " pdb=" CA GLY B 526 " pdb=" C GLY B 526 " ideal model delta sigma weight residual 112.10 122.07 -9.97 1.23e+00 6.61e-01 6.57e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 112.90 105.56 7.34 9.60e-01 1.09e+00 5.85e+01 angle pdb=" N SER C 155 " pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 108.60 119.47 -10.87 1.46e+00 4.69e-01 5.54e+01 angle pdb=" C VAL C 159 " pdb=" CA VAL C 159 " pdb=" CB VAL C 159 " ideal model delta sigma weight residual 111.29 100.84 10.45 1.64e+00 3.72e-01 4.06e+01 angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 108.19 100.22 7.97 1.29e+00 6.01e-01 3.82e+01 ... (remaining 41208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16466 17.96 - 35.92: 1293 35.92 - 53.88: 229 53.88 - 71.85: 66 71.85 - 89.81: 23 Dihedral angle restraints: 18077 sinusoidal: 7135 harmonic: 10942 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 -177.19 -89.81 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.16 -87.16 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -170.65 84.65 1 1.00e+01 1.00e-02 8.70e+01 ... (remaining 18074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4098 0.091 - 0.182: 448 0.182 - 0.273: 51 0.273 - 0.364: 3 0.364 - 0.455: 3 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA SER C 155 " pdb=" N SER C 155 " pdb=" C SER C 155 " pdb=" CB SER C 155 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA VAL C 159 " pdb=" N VAL C 159 " pdb=" C VAL C 159 " pdb=" CB VAL C 159 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 4600 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.064 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO C 987 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.064 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO B 987 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " -0.064 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO D 987 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " -0.053 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 9941 2.85 - 3.36: 22207 3.36 - 3.87: 49860 3.87 - 4.39: 53417 4.39 - 4.90: 93562 Nonbonded interactions: 228987 Sorted by model distance: nonbonded pdb=" O SER C 758 " pdb=" OG SER C 758 " model vdw 2.335 3.040 nonbonded pdb=" O SER B 446 " pdb=" OG SER B 446 " model vdw 2.339 3.040 nonbonded pdb=" O ALA D 879 " pdb=" OG1 THR D 883 " model vdw 2.346 3.040 nonbonded pdb=" O LEU D 966 " pdb=" OG SER D 975 " model vdw 2.352 3.040 nonbonded pdb=" O GLN B1002 " pdb=" OG1 THR B1006 " model vdw 2.354 3.040 ... (remaining 228982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 72.820 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.160 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30356 Z= 0.255 Angle : 0.851 13.017 41297 Z= 0.496 Chirality : 0.055 0.455 4603 Planarity : 0.007 0.095 5332 Dihedral : 13.448 87.356 10901 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 0.40 % Allowed : 5.93 % Favored : 93.68 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.10), residues: 3700 helix: -5.13 (0.04), residues: 806 sheet: -1.55 (0.19), residues: 567 loop : -2.78 (0.10), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 302 HIS 0.005 0.001 HIS A 493 PHE 0.018 0.001 PHE B 347 TYR 0.022 0.001 TYR A 385 ARG 0.006 0.000 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.31755 ( 834) hydrogen bonds : angle 11.54427 ( 2412) SS BOND : bond 0.00513 ( 42) SS BOND : angle 1.47139 ( 84) covalent geometry : bond 0.00483 (30314) covalent geometry : angle 0.84893 (41213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 868 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.4306 (t80) cc_final: 0.3994 (t80) REVERT: A 48 TRP cc_start: 0.1316 (t60) cc_final: 0.0582 (t60) REVERT: A 82 MET cc_start: 0.4902 (mtm) cc_final: 0.4686 (ptp) REVERT: A 249 MET cc_start: 0.0110 (mmt) cc_final: -0.0171 (mpp) REVERT: A 360 MET cc_start: 0.1903 (mmm) cc_final: 0.0977 (tpt) REVERT: A 383 MET cc_start: 0.6268 (tpt) cc_final: 0.5951 (tpt) REVERT: A 480 MET cc_start: -0.4374 (mtt) cc_final: -0.5286 (tpp) REVERT: A 586 ASN cc_start: 0.6374 (p0) cc_final: 0.5970 (p0) REVERT: A 589 GLU cc_start: 0.7449 (pm20) cc_final: 0.7125 (pm20) REVERT: B 43 PHE cc_start: 0.7100 (t80) cc_final: 0.6818 (t80) REVERT: B 78 ARG cc_start: 0.8864 (mtt180) cc_final: 0.8638 (mpt180) REVERT: B 99 ASN cc_start: 0.6992 (m-40) cc_final: 0.6675 (t0) REVERT: B 157 PHE cc_start: 0.6347 (t80) cc_final: 0.5826 (p90) REVERT: B 192 PHE cc_start: 0.7748 (m-80) cc_final: 0.7517 (m-10) REVERT: B 237 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7555 (ptp-170) REVERT: B 307 THR cc_start: 0.8332 (m) cc_final: 0.7251 (p) REVERT: B 313 TYR cc_start: 0.6919 (m-80) cc_final: 0.6234 (m-80) REVERT: B 340 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6583 (mp0) REVERT: B 437 ASN cc_start: 0.8147 (t0) cc_final: 0.7703 (t0) REVERT: B 535 LYS cc_start: 0.8730 (mttt) cc_final: 0.8352 (mmtt) REVERT: B 695 TYR cc_start: 0.7983 (p90) cc_final: 0.7600 (p90) REVERT: B 698 SER cc_start: 0.8401 (t) cc_final: 0.7629 (p) REVERT: B 725 GLU cc_start: 0.6429 (mt-10) cc_final: 0.5748 (mt-10) REVERT: B 727 LEU cc_start: 0.7770 (mt) cc_final: 0.7523 (mp) REVERT: B 752 LEU cc_start: 0.8781 (mp) cc_final: 0.8501 (mp) REVERT: B 776 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7851 (ptpp) REVERT: B 780 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 819 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7125 (mt-10) REVERT: B 822 LEU cc_start: 0.8016 (mt) cc_final: 0.7794 (mt) REVERT: B 856 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8216 (mmmt) REVERT: B 868 GLU cc_start: 0.7663 (mp0) cc_final: 0.7433 (mm-30) REVERT: B 869 MET cc_start: 0.8279 (mtp) cc_final: 0.8017 (mtp) REVERT: B 873 TYR cc_start: 0.7784 (m-80) cc_final: 0.7466 (m-80) REVERT: B 933 LYS cc_start: 0.8540 (mttt) cc_final: 0.8172 (mttm) REVERT: B 954 HIS cc_start: 0.7471 (m170) cc_final: 0.7009 (m170) REVERT: B 980 ILE cc_start: 0.9181 (mm) cc_final: 0.8835 (tp) REVERT: B 981 PHE cc_start: 0.7994 (t80) cc_final: 0.7725 (t80) REVERT: B 997 ILE cc_start: 0.9410 (tt) cc_final: 0.9165 (mm) REVERT: B 1010 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7640 (mm110) REVERT: B 1017 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 1018 ILE cc_start: 0.8970 (tp) cc_final: 0.8749 (mm) REVERT: B 1040 VAL cc_start: 0.8785 (t) cc_final: 0.8243 (t) REVERT: B 1050 MET cc_start: 0.6237 (ptp) cc_final: 0.5686 (ptp) REVERT: B 1092 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7178 (mm-30) REVERT: C 37 TYR cc_start: 0.6813 (p90) cc_final: 0.6168 (p90) REVERT: C 43 PHE cc_start: 0.7307 (t80) cc_final: 0.7007 (t80) REVERT: C 128 ILE cc_start: 0.8845 (mt) cc_final: 0.8433 (mm) REVERT: C 133 PHE cc_start: 0.6974 (m-80) cc_final: 0.6276 (m-10) REVERT: C 135 PHE cc_start: 0.6753 (m-80) cc_final: 0.5766 (m-10) REVERT: C 186 PHE cc_start: 0.4878 (m-80) cc_final: 0.4670 (m-80) REVERT: C 221 SER cc_start: 0.7998 (t) cc_final: 0.7428 (p) REVERT: C 229 LEU cc_start: 0.8877 (mt) cc_final: 0.8586 (pt) REVERT: C 293 LEU cc_start: 0.7436 (tp) cc_final: 0.7151 (tp) REVERT: C 304 LYS cc_start: 0.8473 (tppp) cc_final: 0.8086 (mmmt) REVERT: C 339 ASP cc_start: 0.7808 (m-30) cc_final: 0.7394 (m-30) REVERT: C 358 ILE cc_start: 0.6452 (mt) cc_final: 0.6012 (tt) REVERT: C 368 LEU cc_start: 0.8875 (mm) cc_final: 0.8641 (mt) REVERT: C 396 TYR cc_start: 0.7172 (m-10) cc_final: 0.6832 (m-80) REVERT: C 421 TYR cc_start: 0.7744 (m-80) cc_final: 0.7336 (m-10) REVERT: C 453 TYR cc_start: 0.3218 (p90) cc_final: 0.2985 (p90) REVERT: C 495 TYR cc_start: 0.5417 (m-80) cc_final: 0.4150 (m-80) REVERT: C 505 HIS cc_start: 0.6375 (m-70) cc_final: 0.5081 (m-70) REVERT: C 532 ASN cc_start: 0.8447 (t0) cc_final: 0.7909 (t0) REVERT: C 546 LEU cc_start: 0.6049 (mt) cc_final: 0.5814 (mt) REVERT: C 658 ASN cc_start: 0.6124 (m-40) cc_final: 0.5696 (t0) REVERT: C 695 TYR cc_start: 0.7385 (p90) cc_final: 0.6907 (p90) REVERT: C 717 ASN cc_start: 0.5964 (m-40) cc_final: 0.5454 (t0) REVERT: C 762 GLN cc_start: 0.8638 (mt0) cc_final: 0.8186 (mp10) REVERT: C 773 GLU cc_start: 0.7711 (pt0) cc_final: 0.6915 (pt0) REVERT: C 775 ASP cc_start: 0.8263 (m-30) cc_final: 0.7968 (m-30) REVERT: C 776 LYS cc_start: 0.8489 (mtmm) cc_final: 0.7976 (mtmm) REVERT: C 869 MET cc_start: 0.8367 (mtp) cc_final: 0.7735 (mtp) REVERT: C 872 GLN cc_start: 0.8478 (mt0) cc_final: 0.8197 (mt0) REVERT: C 873 TYR cc_start: 0.7937 (m-80) cc_final: 0.7471 (m-80) REVERT: C 902 MET cc_start: 0.7522 (ttp) cc_final: 0.7194 (ttm) REVERT: C 950 ASP cc_start: 0.8036 (t0) cc_final: 0.7586 (p0) REVERT: C 954 HIS cc_start: 0.7790 (m-70) cc_final: 0.7349 (m90) REVERT: C 957 GLN cc_start: 0.8194 (mt0) cc_final: 0.7640 (tm-30) REVERT: C 964 LYS cc_start: 0.8548 (mttt) cc_final: 0.7987 (mtmm) REVERT: C 1014 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7665 (tpp80) REVERT: C 1028 LYS cc_start: 0.8869 (mttt) cc_final: 0.8573 (mttp) REVERT: C 1050 MET cc_start: 0.4899 (ptp) cc_final: 0.4682 (ptp) REVERT: C 1109 PHE cc_start: 0.5997 (p90) cc_final: 0.5275 (p90) REVERT: C 1115 ILE cc_start: 0.7563 (mt) cc_final: 0.7342 (mm) REVERT: D 49 HIS cc_start: 0.8014 (t70) cc_final: 0.7734 (t-90) REVERT: D 53 ASP cc_start: 0.7200 (t0) cc_final: 0.6660 (t0) REVERT: D 168 PHE cc_start: 0.7713 (t80) cc_final: 0.7290 (t80) REVERT: D 170 TYR cc_start: 0.8125 (t80) cc_final: 0.7145 (t80) REVERT: D 204 TYR cc_start: 0.6707 (m-80) cc_final: 0.5986 (m-80) REVERT: D 205 SER cc_start: 0.7839 (t) cc_final: 0.7616 (p) REVERT: D 206 LYS cc_start: 0.8630 (tptt) cc_final: 0.8405 (tptp) REVERT: D 287 ASP cc_start: 0.8234 (t0) cc_final: 0.7672 (t70) REVERT: D 300 LYS cc_start: 0.8182 (mttt) cc_final: 0.7767 (mtpt) REVERT: D 310 LYS cc_start: 0.8068 (tttt) cc_final: 0.7601 (ttmm) REVERT: D 314 GLN cc_start: 0.8208 (tt0) cc_final: 0.7884 (tm-30) REVERT: D 318 PHE cc_start: 0.6924 (t80) cc_final: 0.6676 (t80) REVERT: D 320 VAL cc_start: 0.7867 (t) cc_final: 0.7383 (t) REVERT: D 533 LEU cc_start: 0.8810 (tt) cc_final: 0.8527 (mm) REVERT: D 557 LYS cc_start: 0.8109 (mttt) cc_final: 0.7901 (mmtt) REVERT: D 654 GLU cc_start: 0.7000 (tt0) cc_final: 0.6679 (tp30) REVERT: D 719 THR cc_start: 0.6808 (t) cc_final: 0.6117 (t) REVERT: D 725 GLU cc_start: 0.6241 (mt-10) cc_final: 0.5957 (mt-10) REVERT: D 746 SER cc_start: 0.7230 (t) cc_final: 0.6837 (t) REVERT: D 759 PHE cc_start: 0.7060 (m-10) cc_final: 0.6679 (m-80) REVERT: D 762 GLN cc_start: 0.8579 (mt0) cc_final: 0.8340 (mt0) REVERT: D 765 ARG cc_start: 0.8257 (mtt180) cc_final: 0.8032 (ttm110) REVERT: D 773 GLU cc_start: 0.8213 (tp30) cc_final: 0.7903 (tp30) REVERT: D 776 LYS cc_start: 0.7734 (tptm) cc_final: 0.7336 (tptm) REVERT: D 780 GLU cc_start: 0.6489 (mt-10) cc_final: 0.5691 (mt-10) REVERT: D 864 LEU cc_start: 0.8221 (tp) cc_final: 0.8015 (tt) REVERT: D 872 GLN cc_start: 0.8469 (mt0) cc_final: 0.7893 (tm-30) REVERT: D 873 TYR cc_start: 0.7464 (m-10) cc_final: 0.7224 (m-80) REVERT: D 887 THR cc_start: 0.7280 (p) cc_final: 0.6922 (p) REVERT: D 888 PHE cc_start: 0.7527 (p90) cc_final: 0.6468 (p90) REVERT: D 907 ASN cc_start: 0.8490 (m-40) cc_final: 0.8274 (m-40) REVERT: D 933 LYS cc_start: 0.8728 (mttt) cc_final: 0.8410 (tppt) REVERT: D 945 LEU cc_start: 0.7818 (mt) cc_final: 0.7501 (mt) REVERT: D 969 LYS cc_start: 0.8532 (mttt) cc_final: 0.8229 (mmmt) REVERT: D 992 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8565 (mm-40) REVERT: D 1000 ARG cc_start: 0.7407 (mtt180) cc_final: 0.6511 (mtp85) REVERT: D 1001 LEU cc_start: 0.8890 (mt) cc_final: 0.8670 (mt) REVERT: D 1017 GLU cc_start: 0.7657 (pt0) cc_final: 0.7233 (tm-30) REVERT: D 1018 ILE cc_start: 0.8834 (tp) cc_final: 0.8433 (mt) REVERT: D 1019 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7511 (tpp-160) REVERT: D 1075 PHE cc_start: 0.7765 (m-80) cc_final: 0.7120 (m-80) REVERT: D 1104 VAL cc_start: 0.7055 (t) cc_final: 0.6670 (p) REVERT: D 1120 THR cc_start: 0.8369 (p) cc_final: 0.8151 (p) outliers start: 13 outliers final: 3 residues processed: 878 average time/residue: 0.4380 time to fit residues: 598.9890 Evaluate side-chains 653 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 650 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 583 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.0970 chunk 281 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 0.0770 chunk 150 optimal weight: 0.8980 chunk 291 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 63 ASN A 81 GLN A 98 GLN A 159 ASN A 210 ASN A 277 ASN A 338 ASN A 378 HIS ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 546 ASN A 578 ASN A 586 ASN A 598 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 606 ASN B 751 ASN B 762 GLN B 774 GLN B 957 GLN B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 437 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS D 99 ASN D 196 ASN D 334 ASN D 477 ASN D 658 ASN D 751 ASN D1088 HIS ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.184307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.146348 restraints weight = 86370.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.149929 restraints weight = 49519.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.152157 restraints weight = 32604.722| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30356 Z= 0.138 Angle : 0.635 16.369 41297 Z= 0.328 Chirality : 0.045 0.205 4603 Planarity : 0.005 0.067 5332 Dihedral : 4.681 67.604 4028 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 2.25 % Allowed : 12.86 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.11), residues: 3700 helix: -2.98 (0.12), residues: 825 sheet: -0.72 (0.20), residues: 544 loop : -2.24 (0.11), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 104 HIS 0.006 0.001 HIS B 207 PHE 0.024 0.002 PHE D1109 TYR 0.023 0.001 TYR D 660 ARG 0.008 0.001 ARG C 983 Details of bonding type rmsd hydrogen bonds : bond 0.05279 ( 834) hydrogen bonds : angle 6.66849 ( 2412) SS BOND : bond 0.00310 ( 42) SS BOND : angle 1.49588 ( 84) covalent geometry : bond 0.00292 (30314) covalent geometry : angle 0.63232 (41213) *********************** 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 786 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 712 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5621 (mtm) cc_final: 0.5393 (ptp) REVERT: A 190 MET cc_start: 0.4528 (ppp) cc_final: 0.3583 (pmm) REVERT: A 360 MET cc_start: 0.1095 (mmm) cc_final: 0.0484 (mmm) REVERT: A 368 ASP cc_start: 0.1935 (t0) cc_final: 0.1508 (t0) REVERT: A 417 HIS cc_start: 0.1051 (t70) cc_final: 0.0801 (t-170) REVERT: A 455 MET cc_start: 0.7203 (ttt) cc_final: 0.6591 (ttt) REVERT: A 480 MET cc_start: -0.4881 (mtt) cc_final: -0.5240 (mmt) REVERT: B 83 VAL cc_start: 0.7955 (t) cc_final: 0.7710 (p) REVERT: B 157 PHE cc_start: 0.6026 (t80) cc_final: 0.5480 (p90) REVERT: B 298 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 307 THR cc_start: 0.8364 (m) cc_final: 0.7922 (p) REVERT: B 313 TYR cc_start: 0.6999 (m-80) cc_final: 0.6779 (m-80) REVERT: B 347 PHE cc_start: 0.3917 (p90) cc_final: 0.3024 (p90) REVERT: B 365 TYR cc_start: 0.4653 (m-10) cc_final: 0.4016 (m-10) REVERT: B 369 TYR cc_start: 0.6392 (m-10) cc_final: 0.4846 (m-10) REVERT: B 595 VAL cc_start: 0.7065 (t) cc_final: 0.6676 (m) REVERT: B 698 SER cc_start: 0.8534 (t) cc_final: 0.7852 (p) REVERT: B 723 THR cc_start: 0.7640 (t) cc_final: 0.7196 (p) REVERT: B 752 LEU cc_start: 0.8735 (mp) cc_final: 0.8467 (mp) REVERT: B 776 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7929 (mtmm) REVERT: B 820 ASP cc_start: 0.7621 (m-30) cc_final: 0.7370 (m-30) REVERT: B 821 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8215 (mm) REVERT: B 822 LEU cc_start: 0.8235 (mt) cc_final: 0.7970 (mt) REVERT: B 856 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8227 (mmmm) REVERT: B 872 GLN cc_start: 0.7570 (mt0) cc_final: 0.7355 (tm-30) REVERT: B 873 TYR cc_start: 0.7751 (m-80) cc_final: 0.7531 (m-80) REVERT: B 933 LYS cc_start: 0.8896 (mttt) cc_final: 0.8444 (mmtm) REVERT: B 960 ASN cc_start: 0.8301 (p0) cc_final: 0.7817 (p0) REVERT: B 964 LYS cc_start: 0.8287 (ptpp) cc_final: 0.7784 (ptpp) REVERT: B 997 ILE cc_start: 0.9169 (tt) cc_final: 0.8873 (mm) REVERT: B 1002 GLN cc_start: 0.7886 (tp40) cc_final: 0.7281 (tp40) REVERT: B 1010 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7949 (mm-40) REVERT: B 1029 MET cc_start: 0.8185 (mmm) cc_final: 0.7791 (mmm) REVERT: B 1120 THR cc_start: 0.5489 (OUTLIER) cc_final: 0.5264 (m) REVERT: C 54 LEU cc_start: 0.8343 (mt) cc_final: 0.8012 (pt) REVERT: C 104 TRP cc_start: 0.6480 (m-90) cc_final: 0.6252 (m-90) REVERT: C 133 PHE cc_start: 0.6830 (m-80) cc_final: 0.6279 (m-80) REVERT: C 293 LEU cc_start: 0.8256 (tp) cc_final: 0.7930 (tp) REVERT: C 309 GLU cc_start: 0.7603 (tp30) cc_final: 0.7368 (tp30) REVERT: C 358 ILE cc_start: 0.6677 (mt) cc_final: 0.5986 (tt) REVERT: C 733 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7916 (mtpt) REVERT: C 739 THR cc_start: 0.7837 (p) cc_final: 0.7449 (p) REVERT: C 759 PHE cc_start: 0.6444 (t80) cc_final: 0.5229 (t80) REVERT: C 773 GLU cc_start: 0.7704 (pt0) cc_final: 0.7078 (pt0) REVERT: C 775 ASP cc_start: 0.7973 (m-30) cc_final: 0.7482 (m-30) REVERT: C 776 LYS cc_start: 0.8673 (mtmm) cc_final: 0.7905 (mtmm) REVERT: C 869 MET cc_start: 0.8228 (mtp) cc_final: 0.7855 (mtp) REVERT: C 921 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8122 (mmmt) REVERT: C 949 GLN cc_start: 0.7157 (tp-100) cc_final: 0.6669 (tp-100) REVERT: C 954 HIS cc_start: 0.7598 (m-70) cc_final: 0.7211 (m170) REVERT: C 964 LYS cc_start: 0.8579 (mttt) cc_final: 0.8265 (mtpp) REVERT: C 979 ASP cc_start: 0.7989 (t0) cc_final: 0.7732 (t0) REVERT: C 1005 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8554 (tp40) REVERT: C 1013 ILE cc_start: 0.8839 (pt) cc_final: 0.8575 (mt) REVERT: C 1014 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7970 (tpp80) REVERT: C 1028 LYS cc_start: 0.8744 (mttt) cc_final: 0.8456 (mttp) REVERT: D 55 PHE cc_start: 0.6588 (m-10) cc_final: 0.6294 (m-10) REVERT: D 196 ASN cc_start: 0.7550 (t0) cc_final: 0.6936 (t0) REVERT: D 300 LYS cc_start: 0.8573 (mttt) cc_final: 0.8256 (mtpp) REVERT: D 320 VAL cc_start: 0.8056 (t) cc_final: 0.7557 (t) REVERT: D 533 LEU cc_start: 0.8769 (tt) cc_final: 0.8216 (mm) REVERT: D 746 SER cc_start: 0.7862 (t) cc_final: 0.7648 (t) REVERT: D 762 GLN cc_start: 0.8356 (mt0) cc_final: 0.8048 (mt0) REVERT: D 773 GLU cc_start: 0.7942 (tp30) cc_final: 0.7056 (tp30) REVERT: D 775 ASP cc_start: 0.7187 (p0) cc_final: 0.6782 (p0) REVERT: D 888 PHE cc_start: 0.7549 (p90) cc_final: 0.6865 (p90) REVERT: D 933 LYS cc_start: 0.8746 (mttt) cc_final: 0.8459 (tppt) REVERT: D 1010 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7761 (tm-30) REVERT: D 1018 ILE cc_start: 0.8861 (tp) cc_final: 0.8296 (mt) REVERT: D 1110 TYR cc_start: 0.7847 (t80) cc_final: 0.7470 (t80) outliers start: 74 outliers final: 52 residues processed: 755 average time/residue: 0.4363 time to fit residues: 523.7266 Evaluate side-chains 682 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 628 time to evaluate : 4.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.0060 chunk 175 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 213 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 98 GLN A 210 ASN A 401 HIS A 522 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 448 ASN B 751 ASN B 762 GLN B 824 ASN B 895 GLN B 978 ASN B1088 HIS B1119 ASN C 271 GLN C 519 HIS C 709 ASN C 926 GLN C 965 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN D 658 ASN D 965 GLN D1074 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.182144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.143878 restraints weight = 86622.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.147216 restraints weight = 49880.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.149360 restraints weight = 32794.106| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30356 Z= 0.123 Angle : 0.606 12.964 41297 Z= 0.309 Chirality : 0.044 0.191 4603 Planarity : 0.004 0.090 5332 Dihedral : 4.405 58.482 4025 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.04 % Allowed : 15.87 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.12), residues: 3700 helix: -1.61 (0.16), residues: 831 sheet: -0.45 (0.21), residues: 540 loop : -1.94 (0.11), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 478 HIS 0.010 0.001 HIS C1088 PHE 0.022 0.002 PHE B 490 TYR 0.017 0.001 TYR D 660 ARG 0.008 0.001 ARG D 765 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 834) hydrogen bonds : angle 5.99438 ( 2412) SS BOND : bond 0.00380 ( 42) SS BOND : angle 1.32627 ( 84) covalent geometry : bond 0.00265 (30314) covalent geometry : angle 0.60390 (41213) *********************** 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 746 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 646 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5245 (ppp) cc_final: 0.4255 (pmm) REVERT: A 360 MET cc_start: 0.1475 (mmm) cc_final: 0.0984 (mmm) REVERT: A 368 ASP cc_start: 0.1977 (t0) cc_final: 0.1634 (t0) REVERT: A 417 HIS cc_start: 0.1082 (t70) cc_final: 0.0829 (t-170) REVERT: A 455 MET cc_start: 0.7204 (ttt) cc_final: 0.6603 (ttt) REVERT: A 578 ASN cc_start: 0.7394 (m110) cc_final: 0.7009 (t0) REVERT: A 579 MET cc_start: 0.5475 (mpp) cc_final: 0.4784 (mmp) REVERT: B 157 PHE cc_start: 0.6189 (t80) cc_final: 0.5876 (p90) REVERT: B 278 LYS cc_start: 0.8027 (tptt) cc_final: 0.7810 (tptt) REVERT: B 298 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 307 THR cc_start: 0.8392 (m) cc_final: 0.8010 (p) REVERT: B 313 TYR cc_start: 0.7042 (m-80) cc_final: 0.6770 (m-80) REVERT: B 347 PHE cc_start: 0.4045 (p90) cc_final: 0.3138 (p90) REVERT: B 569 ILE cc_start: 0.8037 (pt) cc_final: 0.7570 (mp) REVERT: B 595 VAL cc_start: 0.7150 (t) cc_final: 0.6773 (m) REVERT: B 698 SER cc_start: 0.8546 (t) cc_final: 0.7688 (p) REVERT: B 727 LEU cc_start: 0.7894 (mt) cc_final: 0.7474 (mp) REVERT: B 808 ASP cc_start: 0.7427 (t0) cc_final: 0.7227 (t70) REVERT: B 820 ASP cc_start: 0.7881 (m-30) cc_final: 0.7536 (m-30) REVERT: B 822 LEU cc_start: 0.8313 (mt) cc_final: 0.7970 (mt) REVERT: B 856 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8270 (mmmm) REVERT: B 933 LYS cc_start: 0.8872 (mttt) cc_final: 0.8442 (mmtm) REVERT: B 960 ASN cc_start: 0.8419 (p0) cc_final: 0.7986 (p0) REVERT: B 964 LYS cc_start: 0.8454 (ptpp) cc_final: 0.7904 (ptpp) REVERT: B 996 LEU cc_start: 0.9223 (tp) cc_final: 0.8892 (tt) REVERT: B 997 ILE cc_start: 0.9184 (tt) cc_final: 0.8897 (mm) REVERT: B 1002 GLN cc_start: 0.7969 (tp40) cc_final: 0.7374 (tp40) REVERT: B 1005 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: B 1010 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8031 (mm-40) REVERT: B 1019 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7795 (mtp180) REVERT: B 1029 MET cc_start: 0.8233 (mmm) cc_final: 0.7867 (mmm) REVERT: B 1091 ARG cc_start: 0.6052 (ttp80) cc_final: 0.5750 (ttp-110) REVERT: C 104 TRP cc_start: 0.6610 (m-90) cc_final: 0.6346 (m-90) REVERT: C 133 PHE cc_start: 0.7035 (m-80) cc_final: 0.6441 (m-80) REVERT: C 358 ILE cc_start: 0.6406 (mt) cc_final: 0.5771 (tt) REVERT: C 532 ASN cc_start: 0.7433 (t0) cc_final: 0.7231 (t0) REVERT: C 733 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7867 (mtpt) REVERT: C 773 GLU cc_start: 0.7803 (pt0) cc_final: 0.7217 (pt0) REVERT: C 775 ASP cc_start: 0.7880 (m-30) cc_final: 0.7446 (m-30) REVERT: C 776 LYS cc_start: 0.8636 (mtmm) cc_final: 0.7930 (mtmm) REVERT: C 821 LEU cc_start: 0.8655 (mt) cc_final: 0.8338 (mt) REVERT: C 873 TYR cc_start: 0.7718 (m-80) cc_final: 0.7298 (m-80) REVERT: C 921 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8227 (mmmt) REVERT: C 928 ASN cc_start: 0.8192 (m-40) cc_final: 0.7577 (p0) REVERT: C 949 GLN cc_start: 0.7374 (tp-100) cc_final: 0.6984 (tp-100) REVERT: C 953 ASN cc_start: 0.7889 (p0) cc_final: 0.7686 (p0) REVERT: C 954 HIS cc_start: 0.7651 (m-70) cc_final: 0.7004 (m-70) REVERT: C 957 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7101 (tm-30) REVERT: C 964 LYS cc_start: 0.8703 (mttt) cc_final: 0.8217 (mtpp) REVERT: C 979 ASP cc_start: 0.8136 (t0) cc_final: 0.7927 (t0) REVERT: C 983 ARG cc_start: 0.8411 (ptm-80) cc_final: 0.7885 (ptm-80) REVERT: C 984 LEU cc_start: 0.8815 (mt) cc_final: 0.8591 (tp) REVERT: C 1005 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8435 (tp40) REVERT: C 1013 ILE cc_start: 0.8856 (pt) cc_final: 0.8655 (mt) REVERT: C 1014 ARG cc_start: 0.8404 (mtt180) cc_final: 0.7998 (tpp80) REVERT: C 1028 LYS cc_start: 0.8707 (mttt) cc_final: 0.8481 (mttp) REVERT: C 1109 PHE cc_start: 0.5789 (p90) cc_final: 0.5581 (p90) REVERT: D 55 PHE cc_start: 0.6744 (m-80) cc_final: 0.6297 (m-10) REVERT: D 196 ASN cc_start: 0.7667 (t0) cc_final: 0.7260 (t0) REVERT: D 298 GLU cc_start: 0.8250 (tp30) cc_final: 0.8038 (tp30) REVERT: D 300 LYS cc_start: 0.8544 (mttt) cc_final: 0.8176 (mtpt) REVERT: D 320 VAL cc_start: 0.8102 (t) cc_final: 0.7544 (m) REVERT: D 533 LEU cc_start: 0.8736 (tt) cc_final: 0.8239 (mm) REVERT: D 764 LYS cc_start: 0.9045 (tppp) cc_final: 0.8689 (tppt) REVERT: D 776 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7796 (mtmm) REVERT: D 888 PHE cc_start: 0.7694 (p90) cc_final: 0.7042 (p90) REVERT: D 933 LYS cc_start: 0.8820 (mttt) cc_final: 0.8530 (tppt) REVERT: D 966 LEU cc_start: 0.8783 (mt) cc_final: 0.8489 (mt) REVERT: D 969 LYS cc_start: 0.8478 (mppt) cc_final: 0.8202 (mmmm) REVERT: D 1010 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 1018 ILE cc_start: 0.8695 (tp) cc_final: 0.8374 (mt) REVERT: D 1019 ARG cc_start: 0.8273 (ttt90) cc_final: 0.8003 (tpp-160) outliers start: 100 outliers final: 66 residues processed: 706 average time/residue: 0.4041 time to fit residues: 458.2693 Evaluate side-chains 670 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 603 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 254 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 278 optimal weight: 0.6980 chunk 327 optimal weight: 0.0370 chunk 33 optimal weight: 9.9990 chunk 255 optimal weight: 0.7980 chunk 48 optimal weight: 0.0000 chunk 265 optimal weight: 0.4980 chunk 127 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 955 ASN B 957 GLN C 606 ASN C 703 ASN C 762 GLN C 926 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 613 GLN D 751 ASN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.181555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.4253 r_free = 0.4253 target = 0.143375 restraints weight = 85869.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.146279 restraints weight = 48901.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.148633 restraints weight = 32227.666| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.4197 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= 0.112 Angle : 0.589 11.185 41297 Z= 0.298 Chirality : 0.044 0.171 4603 Planarity : 0.004 0.058 5332 Dihedral : 4.271 57.718 4025 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.47 % Allowed : 17.24 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3700 helix: -1.10 (0.17), residues: 852 sheet: -0.22 (0.21), residues: 546 loop : -1.75 (0.12), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 64 HIS 0.009 0.001 HIS A 401 PHE 0.024 0.001 PHE D 759 TYR 0.023 0.001 TYR B 655 ARG 0.009 0.000 ARG C 765 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 834) hydrogen bonds : angle 5.67559 ( 2412) SS BOND : bond 0.00283 ( 42) SS BOND : angle 1.13706 ( 84) covalent geometry : bond 0.00246 (30314) covalent geometry : angle 0.58753 (41213) *********************** 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 751 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 637 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5149 (ppp) cc_final: 0.4545 (pmm) REVERT: A 360 MET cc_start: 0.1383 (mmm) cc_final: 0.0794 (mmm) REVERT: A 368 ASP cc_start: 0.1928 (t0) cc_final: 0.1514 (t0) REVERT: A 408 MET cc_start: 0.5930 (pmm) cc_final: 0.5676 (pmm) REVERT: A 417 HIS cc_start: 0.1033 (t70) cc_final: 0.0818 (t-170) REVERT: A 455 MET cc_start: 0.5964 (ttt) cc_final: 0.5531 (ttt) REVERT: A 578 ASN cc_start: 0.7536 (m110) cc_final: 0.7243 (t0) REVERT: A 579 MET cc_start: 0.6246 (mpp) cc_final: 0.5712 (mmp) REVERT: B 157 PHE cc_start: 0.6364 (t80) cc_final: 0.5951 (p90) REVERT: B 298 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 307 THR cc_start: 0.8364 (m) cc_final: 0.7851 (p) REVERT: B 313 TYR cc_start: 0.7015 (m-80) cc_final: 0.6782 (m-80) REVERT: B 347 PHE cc_start: 0.4027 (p90) cc_final: 0.3066 (p90) REVERT: B 490 PHE cc_start: 0.1970 (OUTLIER) cc_final: -0.0263 (t80) REVERT: B 569 ILE cc_start: 0.8101 (pt) cc_final: 0.7645 (mp) REVERT: B 595 VAL cc_start: 0.7222 (t) cc_final: 0.6782 (m) REVERT: B 698 SER cc_start: 0.8463 (t) cc_final: 0.7596 (p) REVERT: B 820 ASP cc_start: 0.7865 (m-30) cc_final: 0.7519 (m-30) REVERT: B 822 LEU cc_start: 0.8311 (mt) cc_final: 0.7963 (mt) REVERT: B 856 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8322 (mmmm) REVERT: B 872 GLN cc_start: 0.7448 (tp40) cc_final: 0.6856 (tm-30) REVERT: B 873 TYR cc_start: 0.7855 (m-80) cc_final: 0.7426 (m-80) REVERT: B 933 LYS cc_start: 0.8869 (mttt) cc_final: 0.8431 (mmtm) REVERT: B 955 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7814 (p0) REVERT: B 960 ASN cc_start: 0.8275 (p0) cc_final: 0.7969 (p0) REVERT: B 964 LYS cc_start: 0.8481 (ptpp) cc_final: 0.7898 (ptpp) REVERT: B 996 LEU cc_start: 0.9227 (tp) cc_final: 0.9021 (tt) REVERT: B 997 ILE cc_start: 0.9135 (tt) cc_final: 0.8886 (mm) REVERT: B 1002 GLN cc_start: 0.7878 (tp40) cc_final: 0.7184 (tp40) REVERT: B 1010 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7994 (mm-40) REVERT: B 1029 MET cc_start: 0.8280 (mmm) cc_final: 0.7959 (mmm) REVERT: B 1031 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6217 (mm-30) REVERT: C 104 TRP cc_start: 0.6582 (m-90) cc_final: 0.6355 (m-90) REVERT: C 135 PHE cc_start: 0.6397 (m-80) cc_final: 0.5758 (m-80) REVERT: C 223 LEU cc_start: 0.8185 (mp) cc_final: 0.7972 (tp) REVERT: C 358 ILE cc_start: 0.6181 (mt) cc_final: 0.5572 (tt) REVERT: C 516 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5795 (tm-30) REVERT: C 532 ASN cc_start: 0.7461 (t0) cc_final: 0.7159 (t0) REVERT: C 699 LEU cc_start: 0.7983 (mp) cc_final: 0.7734 (mp) REVERT: C 733 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8032 (mtpt) REVERT: C 740 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6861 (tpp) REVERT: C 773 GLU cc_start: 0.7898 (pt0) cc_final: 0.7376 (pt0) REVERT: C 775 ASP cc_start: 0.7909 (m-30) cc_final: 0.7487 (m-30) REVERT: C 776 LYS cc_start: 0.8671 (mtmm) cc_final: 0.7967 (mtmm) REVERT: C 821 LEU cc_start: 0.8663 (mt) cc_final: 0.8330 (mt) REVERT: C 873 TYR cc_start: 0.7718 (m-80) cc_final: 0.7374 (m-80) REVERT: C 902 MET cc_start: 0.6651 (ttm) cc_final: 0.6294 (ttm) REVERT: C 907 ASN cc_start: 0.7920 (m-40) cc_final: 0.7713 (m110) REVERT: C 921 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8327 (mmmt) REVERT: C 949 GLN cc_start: 0.7445 (tp-100) cc_final: 0.6866 (tp-100) REVERT: C 953 ASN cc_start: 0.7851 (p0) cc_final: 0.7619 (p0) REVERT: C 954 HIS cc_start: 0.7674 (m-70) cc_final: 0.6950 (m-70) REVERT: C 957 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7271 (tm-30) REVERT: C 964 LYS cc_start: 0.8652 (mttt) cc_final: 0.8437 (mttt) REVERT: C 983 ARG cc_start: 0.8369 (ptm-80) cc_final: 0.7861 (ptm-80) REVERT: C 984 LEU cc_start: 0.8791 (mt) cc_final: 0.8564 (tp) REVERT: C 1005 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8469 (tp40) REVERT: C 1014 ARG cc_start: 0.8448 (mtt180) cc_final: 0.8058 (tpp80) REVERT: C 1019 ARG cc_start: 0.8173 (tpp-160) cc_final: 0.7810 (tpp-160) REVERT: C 1023 ASN cc_start: 0.8434 (m110) cc_final: 0.7804 (m-40) REVERT: C 1028 LYS cc_start: 0.8756 (mttt) cc_final: 0.8546 (mttp) REVERT: C 1109 PHE cc_start: 0.5727 (p90) cc_final: 0.5520 (p90) REVERT: D 48 LEU cc_start: 0.7983 (mp) cc_final: 0.7737 (mm) REVERT: D 55 PHE cc_start: 0.6649 (m-80) cc_final: 0.6367 (m-10) REVERT: D 83 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7497 (m) REVERT: D 131 CYS cc_start: 0.3656 (OUTLIER) cc_final: 0.1877 (m) REVERT: D 196 ASN cc_start: 0.7676 (t0) cc_final: 0.7252 (t0) REVERT: D 287 ASP cc_start: 0.8331 (t70) cc_final: 0.8038 (t70) REVERT: D 298 GLU cc_start: 0.8242 (tp30) cc_final: 0.7747 (tp30) REVERT: D 300 LYS cc_start: 0.8507 (mttt) cc_final: 0.8212 (mtpp) REVERT: D 320 VAL cc_start: 0.8325 (t) cc_final: 0.7644 (m) REVERT: D 533 LEU cc_start: 0.8648 (tt) cc_final: 0.8162 (mm) REVERT: D 762 GLN cc_start: 0.8288 (mt0) cc_final: 0.8028 (mt0) REVERT: D 765 ARG cc_start: 0.8539 (ttp-110) cc_final: 0.8203 (ttm110) REVERT: D 772 VAL cc_start: 0.8804 (t) cc_final: 0.8507 (p) REVERT: D 773 GLU cc_start: 0.8238 (tp30) cc_final: 0.7608 (tp30) REVERT: D 775 ASP cc_start: 0.7717 (p0) cc_final: 0.7162 (p0) REVERT: D 776 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7328 (mtmm) REVERT: D 888 PHE cc_start: 0.7740 (p90) cc_final: 0.7059 (p90) REVERT: D 933 LYS cc_start: 0.8830 (mttt) cc_final: 0.8466 (tppt) REVERT: D 966 LEU cc_start: 0.8808 (mt) cc_final: 0.8522 (mt) REVERT: D 1010 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7790 (tm-30) REVERT: D 1018 ILE cc_start: 0.8654 (tp) cc_final: 0.8362 (mt) REVERT: D 1019 ARG cc_start: 0.8377 (ttt90) cc_final: 0.8072 (tpp-160) outliers start: 114 outliers final: 70 residues processed: 705 average time/residue: 0.4103 time to fit residues: 463.2284 Evaluate side-chains 680 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 604 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 116 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 321 optimal weight: 0.8980 chunk 92 optimal weight: 0.0070 chunk 222 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 343 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 474 GLN C 703 ASN C 895 GLN C 926 GLN C 965 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 606 ASN D 613 GLN D 965 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.177652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.138364 restraints weight = 83226.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.141247 restraints weight = 47666.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.143522 restraints weight = 31583.113| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30356 Z= 0.168 Angle : 0.644 11.895 41297 Z= 0.330 Chirality : 0.046 0.239 4603 Planarity : 0.004 0.055 5332 Dihedral : 4.403 56.890 4024 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.92 % Allowed : 18.97 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3700 helix: -0.75 (0.18), residues: 857 sheet: -0.35 (0.20), residues: 578 loop : -1.62 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 104 HIS 0.006 0.001 HIS A 401 PHE 0.027 0.002 PHE B 490 TYR 0.023 0.002 TYR C 674 ARG 0.011 0.001 ARG C 765 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 834) hydrogen bonds : angle 5.67279 ( 2412) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.49304 ( 84) covalent geometry : bond 0.00362 (30314) covalent geometry : angle 0.64132 (41213) *********************** 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 767 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 638 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5799 (ppp) cc_final: 0.4974 (pmm) REVERT: A 360 MET cc_start: 0.1957 (mmm) cc_final: 0.1177 (mmm) REVERT: A 455 MET cc_start: 0.6679 (ttt) cc_final: 0.6370 (ttt) REVERT: A 578 ASN cc_start: 0.7601 (m110) cc_final: 0.7197 (t0) REVERT: B 294 ASP cc_start: 0.7816 (t70) cc_final: 0.7599 (t0) REVERT: B 298 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8373 (tm-30) REVERT: B 307 THR cc_start: 0.8348 (m) cc_final: 0.7941 (p) REVERT: B 347 PHE cc_start: 0.4032 (p90) cc_final: 0.3143 (p90) REVERT: B 569 ILE cc_start: 0.8301 (pt) cc_final: 0.7886 (mp) REVERT: B 595 VAL cc_start: 0.7481 (t) cc_final: 0.7041 (m) REVERT: B 698 SER cc_start: 0.8515 (t) cc_final: 0.7599 (p) REVERT: B 727 LEU cc_start: 0.7736 (mt) cc_final: 0.7417 (mp) REVERT: B 776 LYS cc_start: 0.8275 (mtpp) cc_final: 0.7975 (ptpp) REVERT: B 820 ASP cc_start: 0.8245 (m-30) cc_final: 0.7853 (m-30) REVERT: B 822 LEU cc_start: 0.8400 (mt) cc_final: 0.8095 (mt) REVERT: B 872 GLN cc_start: 0.7718 (tp40) cc_final: 0.7052 (tm-30) REVERT: B 933 LYS cc_start: 0.8999 (mttt) cc_final: 0.8540 (mmtm) REVERT: B 960 ASN cc_start: 0.8423 (p0) cc_final: 0.8137 (p0) REVERT: B 964 LYS cc_start: 0.8624 (ptpp) cc_final: 0.8103 (ptpp) REVERT: B 981 PHE cc_start: 0.7746 (t80) cc_final: 0.7498 (t80) REVERT: B 1002 GLN cc_start: 0.7918 (tp40) cc_final: 0.7349 (tp40) REVERT: B 1010 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8014 (mm-40) REVERT: B 1031 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6476 (mm-30) REVERT: C 59 PHE cc_start: 0.8106 (m-10) cc_final: 0.7777 (m-80) REVERT: C 108 THR cc_start: 0.8017 (m) cc_final: 0.7764 (p) REVERT: C 135 PHE cc_start: 0.6779 (m-80) cc_final: 0.6144 (m-10) REVERT: C 358 ILE cc_start: 0.6281 (mt) cc_final: 0.5683 (tt) REVERT: C 532 ASN cc_start: 0.7688 (t0) cc_final: 0.7395 (t0) REVERT: C 697 MET cc_start: 0.7597 (tmm) cc_final: 0.7293 (ppp) REVERT: C 733 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8067 (mtpt) REVERT: C 740 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6589 (tpp) REVERT: C 773 GLU cc_start: 0.7970 (pt0) cc_final: 0.7517 (pt0) REVERT: C 775 ASP cc_start: 0.7997 (m-30) cc_final: 0.7542 (m-30) REVERT: C 776 LYS cc_start: 0.8748 (mtmm) cc_final: 0.8081 (mtmm) REVERT: C 821 LEU cc_start: 0.8719 (mt) cc_final: 0.8430 (mt) REVERT: C 921 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8447 (mmmt) REVERT: C 949 GLN cc_start: 0.7769 (tp-100) cc_final: 0.7127 (tp-100) REVERT: C 953 ASN cc_start: 0.8034 (p0) cc_final: 0.7770 (p0) REVERT: C 954 HIS cc_start: 0.7779 (m-70) cc_final: 0.7084 (m-70) REVERT: C 957 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7421 (tm-30) REVERT: C 964 LYS cc_start: 0.8932 (mttt) cc_final: 0.8449 (mtpp) REVERT: C 983 ARG cc_start: 0.8340 (ptm-80) cc_final: 0.7962 (ptm-80) REVERT: C 1014 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8068 (tpp80) REVERT: D 48 LEU cc_start: 0.8038 (mp) cc_final: 0.7790 (mm) REVERT: D 55 PHE cc_start: 0.6716 (m-80) cc_final: 0.6393 (m-10) REVERT: D 131 CYS cc_start: 0.4234 (OUTLIER) cc_final: 0.2453 (m) REVERT: D 196 ASN cc_start: 0.7697 (t0) cc_final: 0.7204 (t0) REVERT: D 287 ASP cc_start: 0.8453 (t70) cc_final: 0.8233 (t70) REVERT: D 298 GLU cc_start: 0.8227 (tp30) cc_final: 0.7472 (tp30) REVERT: D 300 LYS cc_start: 0.8554 (mttt) cc_final: 0.8206 (mtpt) REVERT: D 533 LEU cc_start: 0.8716 (tt) cc_final: 0.8219 (mm) REVERT: D 557 LYS cc_start: 0.6221 (mmtm) cc_final: 0.6017 (mmtt) REVERT: D 606 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7737 (t0) REVERT: D 731 MET cc_start: 0.7496 (ptm) cc_final: 0.7013 (ptm) REVERT: D 762 GLN cc_start: 0.8350 (mt0) cc_final: 0.8069 (mt0) REVERT: D 765 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8259 (ttm110) REVERT: D 772 VAL cc_start: 0.8875 (t) cc_final: 0.8554 (p) REVERT: D 775 ASP cc_start: 0.7811 (p0) cc_final: 0.7459 (p0) REVERT: D 776 LYS cc_start: 0.8317 (mtmm) cc_final: 0.8073 (mtmm) REVERT: D 888 PHE cc_start: 0.7853 (p90) cc_final: 0.7169 (p90) REVERT: D 933 LYS cc_start: 0.8927 (mttt) cc_final: 0.8579 (tppt) REVERT: D 966 LEU cc_start: 0.9003 (mt) cc_final: 0.8733 (mt) REVERT: D 969 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8318 (mmmm) REVERT: D 1010 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 1018 ILE cc_start: 0.8699 (tp) cc_final: 0.8415 (mt) REVERT: D 1019 ARG cc_start: 0.8453 (ttt90) cc_final: 0.8140 (tpp-160) outliers start: 129 outliers final: 89 residues processed: 705 average time/residue: 0.4143 time to fit residues: 469.5391 Evaluate side-chains 699 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 607 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1031 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 291 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 49 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 207 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN D 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.176066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.136947 restraints weight = 83180.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.140092 restraints weight = 47023.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.142363 restraints weight = 30785.815| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30356 Z= 0.156 Angle : 0.646 13.472 41297 Z= 0.328 Chirality : 0.046 0.192 4603 Planarity : 0.004 0.075 5332 Dihedral : 4.473 58.036 4024 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.20 % Allowed : 20.52 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3700 helix: -0.57 (0.18), residues: 854 sheet: -0.32 (0.20), residues: 573 loop : -1.54 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 104 HIS 0.009 0.001 HIS A 417 PHE 0.033 0.002 PHE D 392 TYR 0.022 0.002 TYR C 674 ARG 0.012 0.001 ARG D1091 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 834) hydrogen bonds : angle 5.59692 ( 2412) SS BOND : bond 0.00357 ( 42) SS BOND : angle 1.54195 ( 84) covalent geometry : bond 0.00340 (30314) covalent geometry : angle 0.64326 (41213) *********************** 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 768 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 630 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5782 (ppp) cc_final: 0.5054 (pmm) REVERT: A 360 MET cc_start: 0.1790 (mmm) cc_final: 0.0998 (mmm) REVERT: A 455 MET cc_start: 0.6503 (ttt) cc_final: 0.6241 (ttt) REVERT: A 578 ASN cc_start: 0.7719 (m110) cc_final: 0.7357 (t0) REVERT: B 294 ASP cc_start: 0.7948 (t70) cc_final: 0.7733 (t70) REVERT: B 298 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 307 THR cc_start: 0.8419 (m) cc_final: 0.7958 (p) REVERT: B 347 PHE cc_start: 0.4134 (p90) cc_final: 0.3139 (p90) REVERT: B 438 SER cc_start: 0.5704 (OUTLIER) cc_final: 0.4785 (p) REVERT: B 559 PHE cc_start: 0.4985 (OUTLIER) cc_final: 0.3874 (m-80) REVERT: B 569 ILE cc_start: 0.8453 (pt) cc_final: 0.8093 (mp) REVERT: B 595 VAL cc_start: 0.7439 (t) cc_final: 0.6997 (m) REVERT: B 698 SER cc_start: 0.8495 (t) cc_final: 0.7593 (p) REVERT: B 748 GLU cc_start: 0.8332 (pm20) cc_final: 0.8109 (pm20) REVERT: B 752 LEU cc_start: 0.8962 (mp) cc_final: 0.8762 (mp) REVERT: B 759 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: B 820 ASP cc_start: 0.8399 (m-30) cc_final: 0.7881 (m-30) REVERT: B 822 LEU cc_start: 0.8470 (mt) cc_final: 0.8153 (mt) REVERT: B 856 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8386 (mmmm) REVERT: B 872 GLN cc_start: 0.7790 (tp40) cc_final: 0.7075 (tm-30) REVERT: B 933 LYS cc_start: 0.9057 (mttt) cc_final: 0.8591 (mmtm) REVERT: B 960 ASN cc_start: 0.8533 (p0) cc_final: 0.8321 (p0) REVERT: B 964 LYS cc_start: 0.8752 (ptpp) cc_final: 0.8194 (ptpp) REVERT: B 1002 GLN cc_start: 0.8099 (tp40) cc_final: 0.7392 (tp40) REVERT: B 1010 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8126 (mm-40) REVERT: B 1029 MET cc_start: 0.8355 (mmm) cc_final: 0.7993 (mmm) REVERT: B 1031 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6405 (mm-30) REVERT: B 1101 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6028 (m170) REVERT: C 108 THR cc_start: 0.8020 (m) cc_final: 0.7786 (p) REVERT: C 135 PHE cc_start: 0.6987 (m-80) cc_final: 0.6417 (m-10) REVERT: C 223 LEU cc_start: 0.8402 (mp) cc_final: 0.8144 (tp) REVERT: C 309 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7412 (mm-30) REVERT: C 358 ILE cc_start: 0.6270 (mt) cc_final: 0.5851 (tt) REVERT: C 532 ASN cc_start: 0.7895 (t0) cc_final: 0.7523 (t0) REVERT: C 733 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8173 (mtpt) REVERT: C 740 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6726 (tpp) REVERT: C 765 ARG cc_start: 0.8760 (ttm110) cc_final: 0.8379 (ptp90) REVERT: C 773 GLU cc_start: 0.8094 (pt0) cc_final: 0.7674 (pt0) REVERT: C 775 ASP cc_start: 0.8056 (m-30) cc_final: 0.7564 (m-30) REVERT: C 776 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8104 (mtmm) REVERT: C 868 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 873 TYR cc_start: 0.8021 (m-80) cc_final: 0.7688 (m-80) REVERT: C 921 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8450 (mmmt) REVERT: C 949 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7148 (tp-100) REVERT: C 953 ASN cc_start: 0.8084 (p0) cc_final: 0.7806 (p0) REVERT: C 954 HIS cc_start: 0.7888 (m-70) cc_final: 0.7172 (m-70) REVERT: C 957 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 983 ARG cc_start: 0.8306 (ptm-80) cc_final: 0.8033 (ptm-80) REVERT: C 1005 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8367 (tp40) REVERT: C 1014 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8177 (tpp80) REVERT: C 1019 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.7639 (tpt170) REVERT: C 1109 PHE cc_start: 0.5846 (p90) cc_final: 0.5572 (p90) REVERT: C 1110 TYR cc_start: 0.7454 (t80) cc_final: 0.7246 (t80) REVERT: D 55 PHE cc_start: 0.6804 (m-80) cc_final: 0.6584 (m-10) REVERT: D 131 CYS cc_start: 0.4227 (OUTLIER) cc_final: 0.2514 (m) REVERT: D 196 ASN cc_start: 0.7735 (t0) cc_final: 0.7365 (t0) REVERT: D 234 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7209 (p0) REVERT: D 277 LEU cc_start: 0.7454 (mt) cc_final: 0.7224 (mt) REVERT: D 287 ASP cc_start: 0.8547 (t70) cc_final: 0.8323 (t70) REVERT: D 298 GLU cc_start: 0.8158 (tp30) cc_final: 0.7617 (tp30) REVERT: D 300 LYS cc_start: 0.8443 (mttt) cc_final: 0.8075 (mtpt) REVERT: D 326 ILE cc_start: 0.4399 (OUTLIER) cc_final: 0.4099 (tp) REVERT: D 533 LEU cc_start: 0.8738 (tt) cc_final: 0.8204 (mm) REVERT: D 660 TYR cc_start: 0.5656 (m-10) cc_final: 0.5406 (m-10) REVERT: D 731 MET cc_start: 0.7667 (ptm) cc_final: 0.7092 (ptm) REVERT: D 762 GLN cc_start: 0.8464 (mt0) cc_final: 0.8120 (mt0) REVERT: D 765 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8323 (ttm110) REVERT: D 772 VAL cc_start: 0.8845 (t) cc_final: 0.8601 (p) REVERT: D 775 ASP cc_start: 0.7914 (p0) cc_final: 0.7555 (p0) REVERT: D 776 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8072 (mtmm) REVERT: D 819 GLU cc_start: 0.8204 (tp30) cc_final: 0.7971 (tp30) REVERT: D 888 PHE cc_start: 0.7950 (p90) cc_final: 0.7324 (p90) REVERT: D 933 LYS cc_start: 0.8976 (mttt) cc_final: 0.8615 (tppt) REVERT: D 962 LEU cc_start: 0.9046 (mt) cc_final: 0.8655 (mt) REVERT: D 966 LEU cc_start: 0.9132 (mt) cc_final: 0.8850 (mt) REVERT: D 969 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8334 (mmmm) REVERT: D 1010 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 1018 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8493 (mt) REVERT: D 1019 ARG cc_start: 0.8542 (ttt90) cc_final: 0.8174 (tpp-160) outliers start: 138 outliers final: 94 residues processed: 704 average time/residue: 0.4095 time to fit residues: 462.9313 Evaluate side-chains 705 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 602 time to evaluate : 4.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1031 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 191 optimal weight: 0.4980 chunk 240 optimal weight: 0.0050 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 193 optimal weight: 0.2980 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 914 ASN C1064 HIS D 606 ASN D 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.175526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.137061 restraints weight = 83491.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.139984 restraints weight = 47061.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.142231 restraints weight = 30817.286| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30356 Z= 0.132 Angle : 0.637 13.112 41297 Z= 0.320 Chirality : 0.045 0.259 4603 Planarity : 0.004 0.051 5332 Dihedral : 4.418 59.753 4024 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.95 % Allowed : 21.77 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 3700 helix: -0.50 (0.18), residues: 862 sheet: -0.23 (0.21), residues: 578 loop : -1.47 (0.12), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 104 HIS 0.028 0.001 HIS C 207 PHE 0.042 0.002 PHE D 392 TYR 0.032 0.001 TYR B 369 ARG 0.009 0.000 ARG C 765 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 834) hydrogen bonds : angle 5.54708 ( 2412) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.58602 ( 84) covalent geometry : bond 0.00291 (30314) covalent geometry : angle 0.63350 (41213) *********************** 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 761 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 631 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5720 (ppp) cc_final: 0.5211 (pmm) REVERT: A 360 MET cc_start: 0.1801 (mmm) cc_final: 0.1088 (mmm) REVERT: A 455 MET cc_start: 0.6491 (ttt) cc_final: 0.6255 (ttt) REVERT: A 578 ASN cc_start: 0.7873 (m110) cc_final: 0.7576 (t0) REVERT: B 279 TYR cc_start: 0.8411 (m-80) cc_final: 0.8033 (m-10) REVERT: B 298 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8306 (tm-30) REVERT: B 307 THR cc_start: 0.8465 (m) cc_final: 0.8101 (p) REVERT: B 309 GLU cc_start: 0.8369 (mp0) cc_final: 0.8016 (mp0) REVERT: B 313 TYR cc_start: 0.7054 (m-80) cc_final: 0.6763 (m-80) REVERT: B 347 PHE cc_start: 0.4101 (p90) cc_final: 0.3098 (p90) REVERT: B 365 TYR cc_start: 0.5162 (m-10) cc_final: 0.4256 (m-10) REVERT: B 369 TYR cc_start: 0.6050 (m-10) cc_final: 0.5677 (m-10) REVERT: B 438 SER cc_start: 0.5723 (OUTLIER) cc_final: 0.4825 (p) REVERT: B 559 PHE cc_start: 0.5096 (OUTLIER) cc_final: 0.3987 (m-80) REVERT: B 565 PHE cc_start: 0.7185 (p90) cc_final: 0.6690 (p90) REVERT: B 569 ILE cc_start: 0.8493 (pt) cc_final: 0.8157 (mp) REVERT: B 595 VAL cc_start: 0.7447 (t) cc_final: 0.6969 (m) REVERT: B 698 SER cc_start: 0.8455 (t) cc_final: 0.7558 (p) REVERT: B 748 GLU cc_start: 0.8140 (pm20) cc_final: 0.7927 (pm20) REVERT: B 752 LEU cc_start: 0.8867 (mp) cc_final: 0.8665 (mp) REVERT: B 759 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: B 776 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7895 (ptpp) REVERT: B 808 ASP cc_start: 0.7753 (t0) cc_final: 0.7426 (t70) REVERT: B 820 ASP cc_start: 0.8453 (m-30) cc_final: 0.7965 (m-30) REVERT: B 822 LEU cc_start: 0.8460 (mt) cc_final: 0.8157 (mt) REVERT: B 856 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8345 (mmmm) REVERT: B 933 LYS cc_start: 0.9055 (mttt) cc_final: 0.8597 (mmtm) REVERT: B 964 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8209 (ptpp) REVERT: B 1002 GLN cc_start: 0.8018 (tp40) cc_final: 0.7362 (tp40) REVERT: B 1010 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8118 (mm-40) REVERT: B 1017 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8196 (tm-30) REVERT: B 1031 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6441 (mm-30) REVERT: C 108 THR cc_start: 0.8029 (m) cc_final: 0.7820 (p) REVERT: C 135 PHE cc_start: 0.6940 (m-80) cc_final: 0.6391 (m-10) REVERT: C 207 HIS cc_start: 0.6957 (t-170) cc_final: 0.6503 (m170) REVERT: C 223 LEU cc_start: 0.8433 (mp) cc_final: 0.8144 (tp) REVERT: C 309 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7383 (mm-30) REVERT: C 358 ILE cc_start: 0.6373 (mt) cc_final: 0.5718 (tt) REVERT: C 407 VAL cc_start: 0.6849 (p) cc_final: 0.6482 (t) REVERT: C 532 ASN cc_start: 0.7722 (t0) cc_final: 0.7367 (t0) REVERT: C 726 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7855 (mt) REVERT: C 733 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8228 (mtpt) REVERT: C 765 ARG cc_start: 0.8717 (ttm110) cc_final: 0.8366 (ptp90) REVERT: C 773 GLU cc_start: 0.8060 (pt0) cc_final: 0.7654 (pt0) REVERT: C 775 ASP cc_start: 0.7961 (m-30) cc_final: 0.7464 (m-30) REVERT: C 776 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8086 (mtmm) REVERT: C 868 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7845 (mm-30) REVERT: C 921 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8440 (mmmt) REVERT: C 926 GLN cc_start: 0.8216 (tt0) cc_final: 0.8004 (tt0) REVERT: C 949 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7107 (tp-100) REVERT: C 953 ASN cc_start: 0.8021 (p0) cc_final: 0.7732 (p0) REVERT: C 954 HIS cc_start: 0.7809 (m-70) cc_final: 0.7137 (m-70) REVERT: C 957 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 1005 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8247 (tp-100) REVERT: C 1014 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8064 (tpp80) REVERT: C 1019 ARG cc_start: 0.8274 (tpp-160) cc_final: 0.7671 (tpt170) REVERT: C 1086 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7543 (mmmt) REVERT: C 1109 PHE cc_start: 0.5696 (p90) cc_final: 0.5466 (p90) REVERT: C 1110 TYR cc_start: 0.7530 (t80) cc_final: 0.7325 (t80) REVERT: D 55 PHE cc_start: 0.6756 (m-80) cc_final: 0.6507 (m-10) REVERT: D 131 CYS cc_start: 0.4286 (OUTLIER) cc_final: 0.3077 (m) REVERT: D 196 ASN cc_start: 0.7805 (t0) cc_final: 0.7448 (t0) REVERT: D 277 LEU cc_start: 0.7480 (mt) cc_final: 0.7219 (mt) REVERT: D 287 ASP cc_start: 0.8508 (t70) cc_final: 0.8254 (t70) REVERT: D 300 LYS cc_start: 0.8382 (mttt) cc_final: 0.8028 (mtpt) REVERT: D 543 PHE cc_start: 0.8124 (m-10) cc_final: 0.7850 (m-80) REVERT: D 660 TYR cc_start: 0.5696 (m-10) cc_final: 0.5440 (m-10) REVERT: D 731 MET cc_start: 0.7652 (ptm) cc_final: 0.7064 (ptm) REVERT: D 752 LEU cc_start: 0.8667 (mp) cc_final: 0.8426 (mp) REVERT: D 762 GLN cc_start: 0.8447 (mt0) cc_final: 0.8095 (mt0) REVERT: D 765 ARG cc_start: 0.8698 (ttp-110) cc_final: 0.8317 (ttm110) REVERT: D 772 VAL cc_start: 0.8783 (t) cc_final: 0.8480 (p) REVERT: D 888 PHE cc_start: 0.7911 (p90) cc_final: 0.7422 (p90) REVERT: D 933 LYS cc_start: 0.8972 (mttt) cc_final: 0.8609 (tppt) REVERT: D 962 LEU cc_start: 0.9026 (mt) cc_final: 0.8614 (mt) REVERT: D 966 LEU cc_start: 0.9137 (mt) cc_final: 0.8860 (mt) REVERT: D 969 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8274 (mmmm) REVERT: D 1010 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7771 (tm-30) REVERT: D 1019 ARG cc_start: 0.8490 (ttt90) cc_final: 0.7751 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8708 (m110) cc_final: 0.7984 (m110) outliers start: 130 outliers final: 97 residues processed: 705 average time/residue: 0.4038 time to fit residues: 458.7595 Evaluate side-chains 706 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 604 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1060 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 63 optimal weight: 1.9990 chunk 369 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 352 optimal weight: 0.0770 chunk 54 optimal weight: 0.6980 chunk 314 optimal weight: 2.9990 chunk 345 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1088 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 907 ASN D 965 GLN ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.175070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136110 restraints weight = 83947.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.138829 restraints weight = 47495.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.141136 restraints weight = 31225.235| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5961 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= 0.137 Angle : 0.655 13.209 41297 Z= 0.329 Chirality : 0.045 0.244 4603 Planarity : 0.004 0.051 5332 Dihedral : 4.461 57.121 4024 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.74 % Allowed : 22.07 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 3700 helix: -0.44 (0.18), residues: 863 sheet: -0.26 (0.20), residues: 616 loop : -1.43 (0.12), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 104 HIS 0.007 0.001 HIS A 417 PHE 0.035 0.002 PHE D 392 TYR 0.024 0.002 TYR D 873 ARG 0.007 0.001 ARG C 634 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 834) hydrogen bonds : angle 5.53081 ( 2412) SS BOND : bond 0.00497 ( 42) SS BOND : angle 1.58319 ( 84) covalent geometry : bond 0.00303 (30314) covalent geometry : angle 0.65130 (41213) *********************** 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 748 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 625 time to evaluate : 3.230 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 190 MET cc_start: 0.5849 (ppp) cc_final: 0.5210 (pmm) REVERT: A 199 TYR cc_start: 0.4482 (t80) cc_final: 0.4274 (t80) REVERT: A 360 MET cc_start: 0.1872 (mmm) cc_final: 0.1083 (mmm) REVERT: A 578 ASN cc_start: 0.7926 (m110) cc_final: 0.7592 (t0) REVERT: A 589 GLU cc_start: 0.7624 (pp20) cc_final: 0.7366 (pm20) REVERT: B 78 ARG cc_start: 0.7188 (mpt180) cc_final: 0.6612 (mmt-90) REVERT: B 279 TYR cc_start: 0.8333 (m-80) cc_final: 0.7973 (m-10) REVERT: B 298 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 307 THR cc_start: 0.8534 (m) cc_final: 0.8139 (p) REVERT: B 309 GLU cc_start: 0.8368 (mp0) cc_final: 0.8000 (mp0) REVERT: B 313 TYR cc_start: 0.7046 (m-80) cc_final: 0.6741 (m-80) REVERT: B 347 PHE cc_start: 0.4104 (p90) cc_final: 0.3190 (p90) REVERT: B 365 TYR cc_start: 0.5466 (m-10) cc_final: 0.4690 (m-10) REVERT: B 369 TYR cc_start: 0.6144 (m-10) cc_final: 0.5832 (m-10) REVERT: B 438 SER cc_start: 0.5686 (OUTLIER) cc_final: 0.4785 (p) REVERT: B 559 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.4119 (m-80) REVERT: B 565 PHE cc_start: 0.7277 (p90) cc_final: 0.6758 (p90) REVERT: B 569 ILE cc_start: 0.8522 (pt) cc_final: 0.8203 (mp) REVERT: B 595 VAL cc_start: 0.7506 (t) cc_final: 0.7038 (m) REVERT: B 698 SER cc_start: 0.8351 (t) cc_final: 0.7545 (p) REVERT: B 748 GLU cc_start: 0.8190 (pm20) cc_final: 0.7741 (mp0) REVERT: B 759 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: B 776 LYS cc_start: 0.8343 (mtpp) cc_final: 0.7921 (ptpp) REVERT: B 808 ASP cc_start: 0.7822 (t0) cc_final: 0.7544 (t0) REVERT: B 820 ASP cc_start: 0.8490 (m-30) cc_final: 0.8037 (m-30) REVERT: B 822 LEU cc_start: 0.8479 (mt) cc_final: 0.8167 (mt) REVERT: B 856 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8522 (mmmm) REVERT: B 872 GLN cc_start: 0.7873 (tp40) cc_final: 0.7044 (tm-30) REVERT: B 933 LYS cc_start: 0.9061 (mttt) cc_final: 0.8594 (mmtm) REVERT: B 964 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8132 (ptpp) REVERT: B 981 PHE cc_start: 0.7920 (t80) cc_final: 0.7255 (t80) REVERT: B 995 ARG cc_start: 0.8355 (mtm110) cc_final: 0.8110 (ttp80) REVERT: B 1002 GLN cc_start: 0.8015 (tp40) cc_final: 0.7348 (tp40) REVERT: B 1010 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8107 (mm-40) REVERT: B 1017 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 1029 MET cc_start: 0.8367 (mmm) cc_final: 0.7931 (mmm) REVERT: B 1031 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6470 (mm-30) REVERT: B 1101 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.5821 (m90) REVERT: C 135 PHE cc_start: 0.7015 (m-80) cc_final: 0.6519 (m-10) REVERT: C 223 LEU cc_start: 0.8431 (mp) cc_final: 0.8174 (tp) REVERT: C 294 ASP cc_start: 0.7668 (t0) cc_final: 0.7197 (t0) REVERT: C 358 ILE cc_start: 0.6348 (mt) cc_final: 0.5684 (tt) REVERT: C 407 VAL cc_start: 0.7147 (p) cc_final: 0.6841 (t) REVERT: C 532 ASN cc_start: 0.7650 (t0) cc_final: 0.7300 (t0) REVERT: C 726 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7996 (mt) REVERT: C 733 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8408 (mtpt) REVERT: C 773 GLU cc_start: 0.8064 (pt0) cc_final: 0.7683 (pt0) REVERT: C 775 ASP cc_start: 0.7990 (m-30) cc_final: 0.7515 (m-30) REVERT: C 776 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8093 (mtmm) REVERT: C 868 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7890 (mm-30) REVERT: C 873 TYR cc_start: 0.7976 (m-80) cc_final: 0.7637 (m-80) REVERT: C 921 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8447 (mmmt) REVERT: C 949 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7112 (tp-100) REVERT: C 953 ASN cc_start: 0.8031 (p0) cc_final: 0.7759 (p0) REVERT: C 954 HIS cc_start: 0.7859 (m-70) cc_final: 0.7185 (m-70) REVERT: C 957 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7561 (tm-30) REVERT: C 1005 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8181 (tp-100) REVERT: C 1014 ARG cc_start: 0.8417 (mtt180) cc_final: 0.8043 (tpp80) REVERT: C 1019 ARG cc_start: 0.8284 (tpp-160) cc_final: 0.7680 (tpt170) REVERT: C 1086 LYS cc_start: 0.7818 (mmmt) cc_final: 0.7542 (mmmt) REVERT: C 1109 PHE cc_start: 0.5701 (p90) cc_final: 0.5388 (p90) REVERT: D 131 CYS cc_start: 0.4589 (OUTLIER) cc_final: 0.1088 (m) REVERT: D 133 PHE cc_start: 0.5106 (OUTLIER) cc_final: 0.3153 (m-80) REVERT: D 169 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7427 (mm-30) REVERT: D 196 ASN cc_start: 0.7955 (t0) cc_final: 0.7609 (t0) REVERT: D 277 LEU cc_start: 0.7506 (mt) cc_final: 0.7194 (mt) REVERT: D 287 ASP cc_start: 0.8467 (t70) cc_final: 0.8198 (t70) REVERT: D 300 LYS cc_start: 0.8313 (mttt) cc_final: 0.7970 (mtpt) REVERT: D 533 LEU cc_start: 0.8674 (tt) cc_final: 0.8220 (mm) REVERT: D 655 TYR cc_start: 0.7554 (t80) cc_final: 0.7173 (t80) REVERT: D 660 TYR cc_start: 0.5624 (m-10) cc_final: 0.5395 (m-10) REVERT: D 731 MET cc_start: 0.7614 (ptm) cc_final: 0.7170 (ptm) REVERT: D 752 LEU cc_start: 0.8684 (mp) cc_final: 0.8425 (mp) REVERT: D 765 ARG cc_start: 0.8707 (ttp-110) cc_final: 0.8325 (ttm110) REVERT: D 772 VAL cc_start: 0.8919 (t) cc_final: 0.8305 (p) REVERT: D 775 ASP cc_start: 0.7955 (p0) cc_final: 0.7605 (p0) REVERT: D 776 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8006 (mtmm) REVERT: D 872 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 888 PHE cc_start: 0.7896 (p90) cc_final: 0.7503 (p90) REVERT: D 933 LYS cc_start: 0.8989 (mttt) cc_final: 0.8615 (tppt) REVERT: D 962 LEU cc_start: 0.8994 (mt) cc_final: 0.8571 (mt) REVERT: D 966 LEU cc_start: 0.9153 (mt) cc_final: 0.8848 (mt) REVERT: D 969 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8307 (mmmm) REVERT: D 1010 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 1019 ARG cc_start: 0.8552 (ttt90) cc_final: 0.7951 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8697 (m110) cc_final: 0.8025 (m110) outliers start: 123 outliers final: 93 residues processed: 697 average time/residue: 0.4120 time to fit residues: 460.4724 Evaluate side-chains 711 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 611 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1031 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 295 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 323 optimal weight: 4.9990 chunk 331 optimal weight: 0.6980 chunk 301 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.174398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.135085 restraints weight = 84298.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.138005 restraints weight = 47697.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.140225 restraints weight = 31326.003| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30356 Z= 0.138 Angle : 0.665 13.082 41297 Z= 0.333 Chirality : 0.046 0.262 4603 Planarity : 0.004 0.053 5332 Dihedral : 4.457 54.001 4024 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.34 % Allowed : 22.83 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3700 helix: -0.39 (0.18), residues: 867 sheet: -0.26 (0.20), residues: 605 loop : -1.44 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 104 HIS 0.006 0.001 HIS A 417 PHE 0.043 0.002 PHE D 55 TYR 0.036 0.002 TYR D 873 ARG 0.015 0.001 ARG C 765 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 834) hydrogen bonds : angle 5.50070 ( 2412) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.47495 ( 84) covalent geometry : bond 0.00311 (30314) covalent geometry : angle 0.66216 (41213) *********************** 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 745 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 635 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5924 (ppp) cc_final: 0.5332 (pmm) REVERT: A 360 MET cc_start: 0.1747 (mmm) cc_final: 0.1094 (mmm) REVERT: A 368 ASP cc_start: 0.2223 (t0) cc_final: 0.1845 (t0) REVERT: A 455 MET cc_start: 0.6010 (ttt) cc_final: 0.5785 (ttt) REVERT: A 578 ASN cc_start: 0.8009 (m110) cc_final: 0.7700 (t0) REVERT: A 589 GLU cc_start: 0.7658 (pp20) cc_final: 0.7427 (pm20) REVERT: B 78 ARG cc_start: 0.7245 (mpt180) cc_final: 0.6633 (mmt-90) REVERT: B 164 ASN cc_start: 0.7206 (m-40) cc_final: 0.6349 (p0) REVERT: B 279 TYR cc_start: 0.8313 (m-80) cc_final: 0.7944 (m-10) REVERT: B 298 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8407 (tm-30) REVERT: B 307 THR cc_start: 0.8540 (m) cc_final: 0.8110 (p) REVERT: B 313 TYR cc_start: 0.7030 (m-80) cc_final: 0.6745 (m-80) REVERT: B 347 PHE cc_start: 0.4322 (p90) cc_final: 0.3305 (p90) REVERT: B 365 TYR cc_start: 0.5670 (m-10) cc_final: 0.4821 (m-10) REVERT: B 369 TYR cc_start: 0.6309 (m-10) cc_final: 0.5942 (m-10) REVERT: B 438 SER cc_start: 0.5692 (OUTLIER) cc_final: 0.4863 (p) REVERT: B 559 PHE cc_start: 0.5110 (OUTLIER) cc_final: 0.4018 (m-80) REVERT: B 565 PHE cc_start: 0.7299 (p90) cc_final: 0.6786 (p90) REVERT: B 569 ILE cc_start: 0.8546 (pt) cc_final: 0.8243 (mp) REVERT: B 595 VAL cc_start: 0.7539 (t) cc_final: 0.7075 (m) REVERT: B 698 SER cc_start: 0.8266 (t) cc_final: 0.7511 (p) REVERT: B 759 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: B 776 LYS cc_start: 0.8343 (mtpp) cc_final: 0.7904 (ptpp) REVERT: B 808 ASP cc_start: 0.7863 (t0) cc_final: 0.7572 (t0) REVERT: B 820 ASP cc_start: 0.8537 (m-30) cc_final: 0.8084 (m-30) REVERT: B 822 LEU cc_start: 0.8486 (mt) cc_final: 0.8176 (mt) REVERT: B 856 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8343 (mmmm) REVERT: B 872 GLN cc_start: 0.7850 (tp40) cc_final: 0.7059 (tm-30) REVERT: B 933 LYS cc_start: 0.9059 (mttt) cc_final: 0.8577 (mmtm) REVERT: B 964 LYS cc_start: 0.8722 (ptpp) cc_final: 0.8100 (ptpp) REVERT: B 981 PHE cc_start: 0.7865 (t80) cc_final: 0.7546 (t80) REVERT: B 995 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8156 (ttp80) REVERT: B 1002 GLN cc_start: 0.7976 (tp40) cc_final: 0.7315 (tp40) REVERT: B 1010 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8091 (mm-40) REVERT: B 1017 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 1029 MET cc_start: 0.8353 (mmm) cc_final: 0.7891 (mmm) REVERT: B 1031 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6472 (mm-30) REVERT: B 1101 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.5743 (m90) REVERT: C 135 PHE cc_start: 0.6999 (m-80) cc_final: 0.6490 (m-10) REVERT: C 223 LEU cc_start: 0.8503 (mp) cc_final: 0.8257 (tp) REVERT: C 294 ASP cc_start: 0.7515 (t0) cc_final: 0.7145 (t0) REVERT: C 358 ILE cc_start: 0.6421 (mt) cc_final: 0.5743 (tt) REVERT: C 532 ASN cc_start: 0.7691 (t0) cc_final: 0.7376 (t0) REVERT: C 726 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7765 (mt) REVERT: C 733 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8433 (mtpt) REVERT: C 773 GLU cc_start: 0.8027 (pt0) cc_final: 0.7664 (pt0) REVERT: C 775 ASP cc_start: 0.7953 (m-30) cc_final: 0.7409 (m-30) REVERT: C 776 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8100 (mtmm) REVERT: C 921 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8422 (mmmt) REVERT: C 949 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7133 (tp-100) REVERT: C 953 ASN cc_start: 0.7979 (p0) cc_final: 0.7711 (p0) REVERT: C 954 HIS cc_start: 0.7800 (m-70) cc_final: 0.7129 (m-70) REVERT: C 957 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 995 ARG cc_start: 0.8135 (ptp-170) cc_final: 0.7447 (ptt-90) REVERT: C 1005 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8169 (tp-100) REVERT: C 1014 ARG cc_start: 0.8388 (mtt180) cc_final: 0.8044 (tpp80) REVERT: C 1019 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7766 (tpt170) REVERT: C 1086 LYS cc_start: 0.7810 (mmmt) cc_final: 0.7530 (mmmt) REVERT: D 131 CYS cc_start: 0.4617 (OUTLIER) cc_final: 0.1316 (m) REVERT: D 133 PHE cc_start: 0.5030 (OUTLIER) cc_final: 0.2958 (m-80) REVERT: D 169 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7406 (mp0) REVERT: D 196 ASN cc_start: 0.7905 (t0) cc_final: 0.7455 (m-40) REVERT: D 287 ASP cc_start: 0.8475 (t70) cc_final: 0.8183 (t70) REVERT: D 300 LYS cc_start: 0.8298 (mttt) cc_final: 0.8019 (mtpt) REVERT: D 655 TYR cc_start: 0.7588 (t80) cc_final: 0.7110 (t80) REVERT: D 660 TYR cc_start: 0.5617 (m-10) cc_final: 0.5374 (m-10) REVERT: D 731 MET cc_start: 0.7604 (ptm) cc_final: 0.7148 (ptm) REVERT: D 752 LEU cc_start: 0.8681 (mp) cc_final: 0.8435 (mp) REVERT: D 765 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8311 (ttm110) REVERT: D 772 VAL cc_start: 0.8910 (t) cc_final: 0.8290 (p) REVERT: D 775 ASP cc_start: 0.7889 (p0) cc_final: 0.7588 (p0) REVERT: D 776 LYS cc_start: 0.8548 (mtmm) cc_final: 0.7965 (mtmm) REVERT: D 864 LEU cc_start: 0.8544 (tt) cc_final: 0.8342 (tt) REVERT: D 872 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7906 (tm-30) REVERT: D 888 PHE cc_start: 0.7860 (p90) cc_final: 0.7487 (p90) REVERT: D 921 LYS cc_start: 0.7863 (mppt) cc_final: 0.7484 (mppt) REVERT: D 933 LYS cc_start: 0.9056 (mttt) cc_final: 0.8603 (mmmm) REVERT: D 966 LEU cc_start: 0.9140 (mt) cc_final: 0.8823 (mt) REVERT: D 969 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8379 (mmmm) REVERT: D 1010 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 1017 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7674 (tm-30) REVERT: D 1019 ARG cc_start: 0.8537 (ttt90) cc_final: 0.7917 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8731 (m110) cc_final: 0.8009 (m110) outliers start: 110 outliers final: 84 residues processed: 700 average time/residue: 0.5844 time to fit residues: 669.5382 Evaluate side-chains 719 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 628 time to evaluate : 10.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1031 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 320 optimal weight: 5.9990 chunk 259 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 294 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 188 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN ** D1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.171537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.132650 restraints weight = 82206.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135408 restraints weight = 46637.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.137609 restraints weight = 30702.413| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30356 Z= 0.191 Angle : 0.737 14.084 41297 Z= 0.374 Chirality : 0.047 0.220 4603 Planarity : 0.004 0.049 5332 Dihedral : 4.803 49.763 4024 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.98 % Allowed : 23.72 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3700 helix: -0.49 (0.18), residues: 881 sheet: -0.54 (0.19), residues: 669 loop : -1.48 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 104 HIS 0.006 0.001 HIS C 207 PHE 0.038 0.002 PHE B 490 TYR 0.031 0.002 TYR D 873 ARG 0.007 0.001 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 834) hydrogen bonds : angle 5.73236 ( 2412) SS BOND : bond 0.00374 ( 42) SS BOND : angle 1.71756 ( 84) covalent geometry : bond 0.00420 (30314) covalent geometry : angle 0.73393 (41213) ********************** 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 723 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 625 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.6527 (mm) cc_final: 0.6214 (mm) REVERT: A 360 MET cc_start: 0.1848 (mmm) cc_final: 0.1248 (mmm) REVERT: A 368 ASP cc_start: 0.2353 (t0) cc_final: 0.1905 (t0) REVERT: A 578 ASN cc_start: 0.7962 (m110) cc_final: 0.7576 (t0) REVERT: A 589 GLU cc_start: 0.7826 (pp20) cc_final: 0.7563 (pm20) REVERT: B 44 ARG cc_start: 0.8541 (mtt90) cc_final: 0.8271 (mpt-90) REVERT: B 78 ARG cc_start: 0.7279 (mpt180) cc_final: 0.6662 (mmt-90) REVERT: B 237 ARG cc_start: 0.7247 (ptp-170) cc_final: 0.7041 (ptp-170) REVERT: B 276 LEU cc_start: 0.8468 (mt) cc_final: 0.8247 (tt) REVERT: B 298 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8452 (tm-30) REVERT: B 307 THR cc_start: 0.8494 (m) cc_final: 0.7973 (p) REVERT: B 313 TYR cc_start: 0.7072 (m-80) cc_final: 0.6725 (m-80) REVERT: B 438 SER cc_start: 0.5873 (OUTLIER) cc_final: 0.5073 (p) REVERT: B 559 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.4446 (m-80) REVERT: B 565 PHE cc_start: 0.7397 (p90) cc_final: 0.6927 (p90) REVERT: B 569 ILE cc_start: 0.8628 (pt) cc_final: 0.8341 (mp) REVERT: B 580 GLN cc_start: 0.6888 (mt0) cc_final: 0.6647 (mp10) REVERT: B 595 VAL cc_start: 0.7535 (t) cc_final: 0.7035 (m) REVERT: B 698 SER cc_start: 0.8391 (t) cc_final: 0.7641 (p) REVERT: B 748 GLU cc_start: 0.8245 (mp0) cc_final: 0.7998 (mp0) REVERT: B 759 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: B 776 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7909 (ptpp) REVERT: B 796 TYR cc_start: 0.7062 (p90) cc_final: 0.6808 (p90) REVERT: B 808 ASP cc_start: 0.7951 (t0) cc_final: 0.7659 (t0) REVERT: B 820 ASP cc_start: 0.8666 (m-30) cc_final: 0.8212 (m-30) REVERT: B 822 LEU cc_start: 0.8595 (mt) cc_final: 0.8347 (mt) REVERT: B 856 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8442 (mmmm) REVERT: B 872 GLN cc_start: 0.7980 (tp40) cc_final: 0.7137 (tm-30) REVERT: B 933 LYS cc_start: 0.9162 (mttt) cc_final: 0.8674 (mmtm) REVERT: B 964 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8235 (ptpp) REVERT: B 981 PHE cc_start: 0.7994 (t80) cc_final: 0.7588 (t80) REVERT: B 995 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8281 (ttp80) REVERT: B 1002 GLN cc_start: 0.8154 (tp40) cc_final: 0.7461 (tp40) REVERT: B 1010 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8181 (mm-40) REVERT: B 1017 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 1023 ASN cc_start: 0.8582 (m-40) cc_final: 0.8062 (m110) REVERT: B 1029 MET cc_start: 0.8450 (mmm) cc_final: 0.8024 (mmm) REVERT: B 1031 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6526 (mm-30) REVERT: B 1101 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.5634 (m90) REVERT: C 135 PHE cc_start: 0.7099 (m-80) cc_final: 0.6561 (m-10) REVERT: C 193 VAL cc_start: 0.7242 (t) cc_final: 0.6890 (m) REVERT: C 358 ILE cc_start: 0.6548 (mt) cc_final: 0.5858 (tt) REVERT: C 532 ASN cc_start: 0.7608 (t0) cc_final: 0.7269 (t0) REVERT: C 698 SER cc_start: 0.7931 (t) cc_final: 0.7159 (m) REVERT: C 726 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8103 (mt) REVERT: C 733 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8328 (mtpt) REVERT: C 765 ARG cc_start: 0.8768 (ptp-110) cc_final: 0.8423 (ptp90) REVERT: C 773 GLU cc_start: 0.8099 (pt0) cc_final: 0.7838 (pt0) REVERT: C 775 ASP cc_start: 0.8032 (m-30) cc_final: 0.7357 (m-30) REVERT: C 776 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8173 (mtmm) REVERT: C 921 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8500 (mmmt) REVERT: C 949 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7236 (tp-100) REVERT: C 953 ASN cc_start: 0.8055 (p0) cc_final: 0.7761 (p0) REVERT: C 954 HIS cc_start: 0.7918 (m-70) cc_final: 0.7246 (m-70) REVERT: C 957 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 1005 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8224 (tp-100) REVERT: C 1014 ARG cc_start: 0.8496 (mtt180) cc_final: 0.8125 (tpp80) REVERT: C 1019 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.7761 (tpt170) REVERT: C 1086 LYS cc_start: 0.7778 (mmmt) cc_final: 0.7499 (mmmt) REVERT: D 133 PHE cc_start: 0.5217 (OUTLIER) cc_final: 0.3171 (m-80) REVERT: D 169 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7418 (mm-30) REVERT: D 196 ASN cc_start: 0.7937 (t0) cc_final: 0.7699 (m-40) REVERT: D 273 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: D 287 ASP cc_start: 0.8626 (t70) cc_final: 0.8371 (t70) REVERT: D 289 VAL cc_start: 0.9015 (t) cc_final: 0.8704 (p) REVERT: D 300 LYS cc_start: 0.8313 (mttt) cc_final: 0.7905 (mtpp) REVERT: D 312 ILE cc_start: 0.8502 (tp) cc_final: 0.8266 (tt) REVERT: D 660 TYR cc_start: 0.5782 (m-10) cc_final: 0.5509 (m-10) REVERT: D 731 MET cc_start: 0.7728 (ptm) cc_final: 0.7248 (ptm) REVERT: D 752 LEU cc_start: 0.8780 (mp) cc_final: 0.8513 (mp) REVERT: D 765 ARG cc_start: 0.8759 (ttp-110) cc_final: 0.8375 (ttm110) REVERT: D 775 ASP cc_start: 0.8026 (p0) cc_final: 0.7732 (p0) REVERT: D 776 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8450 (mtmm) REVERT: D 787 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7766 (mm-40) REVERT: D 804 GLN cc_start: 0.7968 (pm20) cc_final: 0.7054 (mm110) REVERT: D 859 THR cc_start: 0.8260 (m) cc_final: 0.7858 (p) REVERT: D 872 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7926 (tm-30) REVERT: D 888 PHE cc_start: 0.7889 (p90) cc_final: 0.7544 (p90) REVERT: D 921 LYS cc_start: 0.7988 (mppt) cc_final: 0.7580 (mppt) REVERT: D 933 LYS cc_start: 0.9067 (mttt) cc_final: 0.8630 (mmmm) REVERT: D 965 GLN cc_start: 0.8367 (mm110) cc_final: 0.7677 (mm-40) REVERT: D 966 LEU cc_start: 0.9241 (mt) cc_final: 0.8998 (mt) REVERT: D 969 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8438 (mmmm) REVERT: D 1017 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7820 (tm-30) REVERT: D 1019 ARG cc_start: 0.8616 (ttt90) cc_final: 0.7968 (tpp-160) REVERT: D 1023 ASN cc_start: 0.8813 (m110) cc_final: 0.8104 (m110) outliers start: 98 outliers final: 83 residues processed: 687 average time/residue: 0.4656 time to fit residues: 512.8355 Evaluate side-chains 695 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 606 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 377 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 755 GLN Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 954 HIS Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1031 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 337 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.172382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.133968 restraints weight = 83158.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.136354 restraints weight = 46594.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.138512 restraints weight = 30394.835| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.6802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30356 Z= 0.146 Angle : 0.712 13.087 41297 Z= 0.356 Chirality : 0.047 0.217 4603 Planarity : 0.004 0.051 5332 Dihedral : 4.667 45.498 4024 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.83 % Allowed : 24.45 % Favored : 72.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3700 helix: -0.39 (0.18), residues: 865 sheet: -0.53 (0.20), residues: 654 loop : -1.46 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 104 HIS 0.006 0.001 HIS C 207 PHE 0.034 0.002 PHE D 392 TYR 0.045 0.002 TYR B 489 ARG 0.008 0.001 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 834) hydrogen bonds : angle 5.57892 ( 2412) SS BOND : bond 0.00335 ( 42) SS BOND : angle 1.65155 ( 84) covalent geometry : bond 0.00328 (30314) covalent geometry : angle 0.70852 (41213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17335.06 seconds wall clock time: 304 minutes 8.66 seconds (18248.66 seconds total)