Starting phenix.real_space_refine on Wed Jun 25 21:11:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk5_32559/06_2025/7wk5_32559.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk5_32559/06_2025/7wk5_32559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk5_32559/06_2025/7wk5_32559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk5_32559/06_2025/7wk5_32559.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk5_32559/06_2025/7wk5_32559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk5_32559/06_2025/7wk5_32559.cif" } resolution = 3.66 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= 0.006 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 18942 2.51 5 N 4926 2.21 5 O 5590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.95s 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: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Chain: "D" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Time building chain proxies: 16.23, per 1000 atoms: 0.55 Number of scatterers: 29601 At special positions: 0 Unit cell: (149.741, 134.439, 234.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5590 8.00 N 4926 7.00 C 18942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 3.7 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: 3.54 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: 11.60 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9365 1.34 - 1.47: 7599 1.47 - 1.59: 13156 1.59 - 1.72: 0 1.72 - 1.85: 194 Bond restraints: 30314 Sorted by residual: bond pdb=" CA ILE C 584 " pdb=" C ILE C 584 " ideal model delta sigma weight residual 1.526 1.474 0.051 1.01e-02 9.80e+03 2.59e+01 bond pdb=" N GLU C 583 " pdb=" CA GLU C 583 " ideal model delta sigma weight residual 1.456 1.397 0.059 1.21e-02 6.83e+03 2.40e+01 bond pdb=" CA ILE C 584 " pdb=" CB ILE C 584 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" CA LEU D 585 " pdb=" C LEU D 585 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" CA GLU C 583 " pdb=" C GLU C 583 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.20e-02 6.94e+03 1.23e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 40412 2.60 - 5.21: 693 5.21 - 7.81: 82 7.81 - 10.41: 22 10.41 - 13.02: 4 Bond angle restraints: 41213 Sorted by residual: angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 112.90 105.56 7.34 9.60e-01 1.09e+00 5.85e+01 angle pdb=" C ALA A 413 " pdb=" N THR A 414 " pdb=" CA THR A 414 " ideal model delta sigma weight residual 120.94 132.27 -11.33 1.90e+00 2.77e-01 3.55e+01 angle pdb=" N ILE D 584 " pdb=" CA ILE D 584 " pdb=" C ILE D 584 " ideal model delta sigma weight residual 109.30 102.36 6.94 1.25e+00 6.40e-01 3.08e+01 angle pdb=" C CYS B 480 " pdb=" N ASN B 481 " pdb=" CA ASN B 481 " ideal model delta sigma weight residual 122.46 130.11 -7.65 1.41e+00 5.03e-01 2.94e+01 angle pdb=" N VAL A 293 " pdb=" CA VAL A 293 " pdb=" C VAL A 293 " ideal model delta sigma weight residual 113.43 107.59 5.84 1.09e+00 8.42e-01 2.87e+01 ... (remaining 41208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16470 17.96 - 35.92: 1294 35.92 - 53.88: 227 53.88 - 71.85: 63 71.85 - 89.81: 23 Dihedral angle restraints: 18077 sinusoidal: 7135 harmonic: 10942 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 -177.19 -89.81 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.16 -87.16 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -170.65 84.65 1 1.00e+01 1.00e-02 8.70e+01 ... (remaining 18074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4108 0.091 - 0.182: 445 0.182 - 0.273: 47 0.273 - 0.364: 2 0.364 - 0.455: 1 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA GLN B1142 " pdb=" N GLN B1142 " pdb=" C GLN B1142 " pdb=" CB GLN B1142 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN C 481 " pdb=" N ASN C 481 " pdb=" C ASN C 481 " pdb=" CB ASN C 481 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4600 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.064 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO C 987 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.064 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO B 987 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " -0.064 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO D 987 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " -0.053 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 2 2.30 - 2.95: 12301 2.95 - 3.60: 38552 3.60 - 4.25: 67877 4.25 - 4.90: 110158 Nonbonded interactions: 228890 Sorted by model distance: nonbonded pdb=" CD1 ILE B 472 " pdb=" CE2 PHE B 490 " model vdw 1.646 3.760 nonbonded pdb=" CD1 ILE B 472 " pdb=" CZ PHE B 490 " model vdw 2.225 3.760 nonbonded pdb=" O SER C 758 " pdb=" OG SER C 758 " model vdw 2.335 3.040 nonbonded pdb=" O SER B 446 " pdb=" OG SER B 446 " model vdw 2.339 3.040 nonbonded pdb=" O ALA D 879 " pdb=" OG1 THR D 883 " model vdw 2.346 3.040 ... (remaining 228885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 63.040 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30356 Z= 0.248 Angle : 0.839 13.017 41297 Z= 0.486 Chirality : 0.054 0.455 4603 Planarity : 0.007 0.095 5332 Dihedral : 13.401 87.356 10901 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 0.27 % Allowed : 5.81 % Favored : 93.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : -2.77 (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 0.00487 ( 42) SS BOND : angle 1.49335 ( 84) covalent geometry : bond 0.00477 (30314) covalent geometry : angle 0.83669 (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 750 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 741 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: -0.2111 (tpt) cc_final: -0.3053 (ptp) REVERT: A 171 GLU cc_start: 0.5789 (tt0) cc_final: 0.5419 (mm-30) REVERT: A 190 MET cc_start: -0.0018 (ppp) cc_final: -0.1075 (ptt) REVERT: A 223 ILE cc_start: 0.3571 (mm) cc_final: 0.2477 (mm) REVERT: A 249 MET cc_start: 0.1231 (mmt) cc_final: 0.0043 (mtt) REVERT: A 431 ASP cc_start: 0.5078 (p0) cc_final: 0.4233 (p0) REVERT: A 566 TRP cc_start: -0.1016 (p-90) cc_final: -0.1593 (p-90) REVERT: B 41 LYS cc_start: 0.6654 (mttt) cc_final: 0.6016 (mmmt) REVERT: B 54 LEU cc_start: 0.7411 (tp) cc_final: 0.6347 (pp) REVERT: B 118 LEU cc_start: 0.8213 (mt) cc_final: 0.7953 (mt) REVERT: B 296 LEU cc_start: 0.7432 (tp) cc_final: 0.7076 (tp) REVERT: B 309 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8511 (tp30) REVERT: B 731 MET cc_start: 0.8178 (mtp) cc_final: 0.7728 (mtt) REVERT: B 751 ASN cc_start: 0.9134 (m-40) cc_final: 0.8932 (m-40) REVERT: B 755 GLN cc_start: 0.8254 (mt0) cc_final: 0.7835 (mp10) REVERT: B 770 ILE cc_start: 0.9044 (pt) cc_final: 0.8694 (pt) REVERT: B 772 VAL cc_start: 0.8624 (m) cc_final: 0.8403 (p) REVERT: B 776 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8221 (tptp) REVERT: B 868 GLU cc_start: 0.8351 (mp0) cc_final: 0.7945 (mm-30) REVERT: B 869 MET cc_start: 0.8371 (mtp) cc_final: 0.7956 (mtp) REVERT: B 896 ILE cc_start: 0.7059 (mm) cc_final: 0.6746 (tp) REVERT: B 921 LYS cc_start: 0.8199 (mttt) cc_final: 0.7716 (tptt) REVERT: B 925 ASN cc_start: 0.7714 (m-40) cc_final: 0.7453 (m-40) REVERT: B 931 ILE cc_start: 0.7997 (mm) cc_final: 0.7626 (mm) REVERT: B 964 LYS cc_start: 0.8709 (ptpp) cc_final: 0.8478 (mtmm) REVERT: B 1001 LEU cc_start: 0.9342 (mt) cc_final: 0.9073 (tt) REVERT: B 1009 THR cc_start: 0.9129 (p) cc_final: 0.8863 (t) REVERT: B 1013 ILE cc_start: 0.8813 (pt) cc_final: 0.8587 (mt) REVERT: B 1038 LYS cc_start: 0.8283 (mttt) cc_final: 0.7974 (mtpp) REVERT: B 1050 MET cc_start: 0.6496 (ptp) cc_final: 0.6229 (ptp) REVERT: B 1103 PHE cc_start: 0.6579 (m-80) cc_final: 0.6164 (m-80) REVERT: C 293 LEU cc_start: 0.8333 (tp) cc_final: 0.7333 (tp) REVERT: C 298 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: C 314 GLN cc_start: 0.8187 (tt0) cc_final: 0.7886 (mm-40) REVERT: C 458 LYS cc_start: 0.4085 (mttt) cc_final: 0.3766 (mmtm) REVERT: C 462 LYS cc_start: 0.8156 (mttt) cc_final: 0.7896 (mmtm) REVERT: C 695 TYR cc_start: 0.7120 (p90) cc_final: 0.6520 (p90) REVERT: C 712 ILE cc_start: 0.6556 (tt) cc_final: 0.6325 (tt) REVERT: C 732 THR cc_start: 0.8622 (m) cc_final: 0.8331 (p) REVERT: C 814 LYS cc_start: 0.7793 (mttt) cc_final: 0.7092 (mmmt) REVERT: C 864 LEU cc_start: 0.7846 (tp) cc_final: 0.7589 (tt) REVERT: C 902 MET cc_start: 0.7461 (ttp) cc_final: 0.6937 (ttm) REVERT: C 933 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8457 (tptp) REVERT: C 962 LEU cc_start: 0.8973 (tp) cc_final: 0.8695 (tp) REVERT: C 1014 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8162 (mmm160) REVERT: C 1043 CYS cc_start: 0.1639 (m) cc_final: 0.1127 (m) REVERT: C 1071 GLN cc_start: 0.7327 (mt0) cc_final: 0.6974 (mp10) REVERT: C 1139 ASP cc_start: 0.6697 (t0) cc_final: 0.6138 (m-30) REVERT: D 40 ASP cc_start: 0.6422 (p0) cc_final: 0.6175 (t70) REVERT: D 287 ASP cc_start: 0.8149 (t0) cc_final: 0.7676 (t0) REVERT: D 310 LYS cc_start: 0.7937 (tttt) cc_final: 0.7391 (tppt) REVERT: D 503 VAL cc_start: 0.2409 (OUTLIER) cc_final: 0.2000 (p) REVERT: D 660 TYR cc_start: 0.7114 (m-80) cc_final: 0.6768 (m-10) REVERT: D 725 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6195 (tm-30) REVERT: D 790 LYS cc_start: 0.8349 (mttt) cc_final: 0.7854 (mmmt) REVERT: D 887 THR cc_start: 0.7089 (p) cc_final: 0.6852 (p) REVERT: D 888 PHE cc_start: 0.6255 (p90) cc_final: 0.6012 (p90) REVERT: D 978 ASN cc_start: 0.8628 (m-40) cc_final: 0.8348 (m110) outliers start: 9 outliers final: 2 residues processed: 749 average time/residue: 0.4336 time to fit residues: 504.4280 Evaluate side-chains 421 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 417 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 217 optimal weight: 0.9990 chunk 337 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 61 ASN A 63 ASN A 81 GLN A 98 GLN A 159 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 378 HIS A 522 GLN A 546 ASN A 572 ASN A 578 ASN A 586 ASN A 598 GLN B 234 ASN B 536 ASN B 564 GLN B 606 ASN B 613 GLN B 955 ASN B 965 GLN B 992 GLN B1023 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 519 HIS C 606 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 955 ASN C1023 ASN C1101 HIS D 87 ASN D 121 ASN D 334 ASN D 477 ASN D 751 ASN D 787 GLN D 895 GLN D 949 GLN D 953 ASN D 954 HIS D1088 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.154151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.127742 restraints weight = 116258.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.128751 restraints weight = 77716.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.128763 restraints weight = 50294.323| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.3019 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= 0.152 Angle : 0.645 12.752 41297 Z= 0.334 Chirality : 0.045 0.241 4603 Planarity : 0.006 0.082 5332 Dihedral : 4.568 59.187 4029 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.95 % Rotamer: Outliers : 2.52 % Allowed : 11.95 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -3.21 (0.11), residues: 3700 helix: -2.92 (0.12), residues: 789 sheet: -1.00 (0.20), residues: 597 loop : -2.24 (0.11), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 566 HIS 0.008 0.001 HIS D1048 PHE 0.026 0.002 PHE D 970 TYR 0.018 0.001 TYR C 707 ARG 0.008 0.001 ARG C 983 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 834) hydrogen bonds : angle 6.64222 ( 2412) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.38692 ( 84) covalent geometry : bond 0.00330 (30314) covalent geometry : angle 0.64234 (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 519 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 436 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: -0.2462 (tpt) cc_final: -0.4075 (ptp) REVERT: A 67 ASP cc_start: 0.6522 (m-30) cc_final: 0.6256 (m-30) REVERT: A 171 GLU cc_start: 0.5117 (tt0) cc_final: 0.4776 (mm-30) REVERT: A 190 MET cc_start: -0.0091 (ppp) cc_final: -0.0429 (ptt) REVERT: A 249 MET cc_start: 0.1450 (mmt) cc_final: -0.0370 (ttm) REVERT: A 408 MET cc_start: 0.1009 (mtm) cc_final: 0.0636 (mpp) REVERT: A 431 ASP cc_start: 0.4008 (p0) cc_final: 0.3467 (p0) REVERT: A 455 MET cc_start: -0.0981 (ppp) cc_final: -0.1520 (ppp) REVERT: A 480 MET cc_start: 0.2471 (mtt) cc_final: 0.1736 (mtp) REVERT: A 554 LEU cc_start: -0.1146 (mt) cc_final: -0.1679 (pp) REVERT: A 566 TRP cc_start: -0.0652 (p-90) cc_final: -0.1178 (p-90) REVERT: A 572 ASN cc_start: 0.5762 (p0) cc_final: 0.5534 (m-40) REVERT: A 579 MET cc_start: 0.1146 (OUTLIER) cc_final: 0.0494 (mmt) REVERT: A 586 ASN cc_start: 0.4820 (p0) cc_final: 0.3757 (m-40) REVERT: A 589 GLU cc_start: 0.7013 (pm20) cc_final: 0.6720 (mm-30) REVERT: B 54 LEU cc_start: 0.7797 (tp) cc_final: 0.6821 (pp) REVERT: B 759 PHE cc_start: 0.7023 (m-80) cc_final: 0.6759 (m-80) REVERT: C 458 LYS cc_start: 0.3739 (mttt) cc_final: 0.3451 (mmtm) REVERT: C 462 LYS cc_start: 0.8010 (mttt) cc_final: 0.7744 (mmtt) REVERT: C 754 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8063 (tp) REVERT: C 814 LYS cc_start: 0.7253 (mttt) cc_final: 0.6906 (mmmt) REVERT: C 955 ASN cc_start: 0.7862 (m110) cc_final: 0.7589 (m110) REVERT: C 1139 ASP cc_start: 0.6925 (t0) cc_final: 0.6182 (m-30) REVERT: D 177 MET cc_start: -0.1212 (mmp) cc_final: -0.2924 (mtt) REVERT: D 814 LYS cc_start: 0.6978 (mmpt) cc_final: 0.6570 (mmmt) REVERT: D 949 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7527 (tp40) REVERT: D 965 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7665 (tp40) REVERT: D 1024 LEU cc_start: 0.8072 (tp) cc_final: 0.7822 (tt) outliers start: 83 outliers final: 47 residues processed: 490 average time/residue: 0.4308 time to fit residues: 340.3001 Evaluate side-chains 391 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 984 LEU 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: 0.9980 chunk 175 optimal weight: 0.2980 chunk 333 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 127 optimal weight: 0.0040 chunk 141 optimal weight: 0.8980 chunk 96 optimal weight: 0.1980 chunk 319 optimal weight: 7.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 606 ASN B1101 HIS B1135 ASN C 394 ASN C 606 ASN C 717 ASN C 907 ASN C 955 ASN C1023 ASN D 658 ASN D 913 GLN D 953 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.154489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.127572 restraints weight = 117210.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.128810 restraints weight = 75510.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.129286 restraints weight = 46260.331| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30356 Z= 0.107 Angle : 0.580 11.700 41297 Z= 0.292 Chirality : 0.044 0.242 4603 Planarity : 0.004 0.061 5332 Dihedral : 4.174 59.930 4025 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.13 % Allowed : 14.38 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.38 (0.12), residues: 3700 helix: -1.41 (0.17), residues: 810 sheet: -0.58 (0.20), residues: 575 loop : -2.00 (0.11), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1102 HIS 0.006 0.001 HIS D1048 PHE 0.022 0.001 PHE D 970 TYR 0.016 0.001 TYR D 655 ARG 0.006 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 834) hydrogen bonds : angle 5.96474 ( 2412) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.11124 ( 84) covalent geometry : bond 0.00232 (30314) covalent geometry : angle 0.57840 (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 460 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 390 time to evaluate : 5.406 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: A 67 ASP cc_start: 0.6883 (m-30) cc_final: 0.6657 (m-30) REVERT: A 171 GLU cc_start: 0.5142 (tt0) cc_final: 0.4778 (mm-30) REVERT: A 190 MET cc_start: -0.0697 (ppp) cc_final: -0.0914 (ptt) REVERT: A 249 MET cc_start: 0.1430 (mmt) cc_final: -0.0334 (ttm) REVERT: A 408 MET cc_start: 0.0947 (mtm) cc_final: 0.0572 (mpp) REVERT: A 480 MET cc_start: 0.2163 (mtt) cc_final: 0.1446 (mtp) REVERT: A 554 LEU cc_start: -0.1112 (mt) cc_final: -0.1671 (pp) REVERT: A 566 TRP cc_start: -0.0750 (p-90) cc_final: -0.1368 (p-90) REVERT: A 579 MET cc_start: 0.0955 (mmt) cc_final: 0.0449 (mmt) REVERT: A 589 GLU cc_start: 0.7129 (pm20) cc_final: 0.6877 (mm-30) REVERT: B 54 LEU cc_start: 0.7798 (tp) cc_final: 0.6750 (pp) REVERT: B 421 TYR cc_start: 0.3952 (m-80) cc_final: 0.3729 (m-80) REVERT: B 755 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: B 1050 MET cc_start: 0.6067 (ptp) cc_final: 0.5712 (ptp) REVERT: C 340 GLU cc_start: 0.7201 (pp20) cc_final: 0.6638 (tp30) REVERT: C 458 LYS cc_start: 0.3783 (mttt) cc_final: 0.3499 (mmtm) REVERT: C 462 LYS cc_start: 0.8022 (mttt) cc_final: 0.7715 (mmtt) REVERT: C 754 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8013 (tp) REVERT: C 759 PHE cc_start: 0.6670 (t80) cc_final: 0.6317 (t80) REVERT: C 983 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.7310 (ptm160) REVERT: C 1139 ASP cc_start: 0.6862 (t0) cc_final: 0.6113 (m-30) REVERT: D 84 LEU cc_start: 0.7802 (mp) cc_final: 0.7218 (mm) REVERT: D 177 MET cc_start: -0.1397 (mmp) cc_final: -0.3031 (mtt) outliers start: 70 outliers final: 50 residues processed: 428 average time/residue: 0.4486 time to fit residues: 318.8319 Evaluate side-chains 379 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 254 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 255 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 265 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 285 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 221 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 606 ASN B 751 ASN B 949 GLN B 953 ASN C 953 ASN C 955 ASN C 960 ASN C1023 ASN D 913 GLN D 949 GLN D 953 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.153342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.128769 restraints weight = 116079.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.127901 restraints weight = 76524.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.128080 restraints weight = 57070.815| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30356 Z= 0.110 Angle : 0.567 11.682 41297 Z= 0.282 Chirality : 0.043 0.188 4603 Planarity : 0.004 0.150 5332 Dihedral : 4.061 56.724 4025 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.65 % Allowed : 15.11 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.92 (0.13), residues: 3700 helix: -0.82 (0.18), residues: 835 sheet: -0.33 (0.21), residues: 576 loop : -1.78 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS D1048 PHE 0.019 0.001 PHE D 888 TYR 0.021 0.001 TYR B 91 ARG 0.012 0.000 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 834) hydrogen bonds : angle 5.61309 ( 2412) SS BOND : bond 0.00269 ( 42) SS BOND : angle 1.10739 ( 84) covalent geometry : bond 0.00242 (30314) covalent geometry : angle 0.56549 (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 442 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 355 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.6867 (m-30) cc_final: 0.6567 (m-30) REVERT: A 190 MET cc_start: -0.1016 (ppp) cc_final: -0.1382 (ptt) REVERT: A 249 MET cc_start: 0.1447 (mmt) cc_final: -0.0453 (ttm) REVERT: A 408 MET cc_start: 0.1055 (mtm) cc_final: 0.0690 (mpp) REVERT: A 480 MET cc_start: 0.2313 (mtt) cc_final: 0.1609 (mtp) REVERT: A 554 LEU cc_start: -0.1081 (mt) cc_final: -0.1668 (pp) REVERT: A 566 TRP cc_start: -0.0645 (p-90) cc_final: -0.1368 (p-90) REVERT: A 579 MET cc_start: 0.0787 (mmt) cc_final: 0.0183 (mmt) REVERT: A 586 ASN cc_start: 0.4272 (p0) cc_final: 0.2744 (t0) REVERT: B 755 GLN cc_start: 0.8203 (mp10) cc_final: 0.7856 (mp10) REVERT: B 1050 MET cc_start: 0.6295 (ptp) cc_final: 0.5980 (ptp) REVERT: C 141 LEU cc_start: 0.7601 (tp) cc_final: 0.7333 (tp) REVERT: C 340 GLU cc_start: 0.7017 (pp20) cc_final: 0.6542 (tp30) REVERT: C 458 LYS cc_start: 0.3817 (mttt) cc_final: 0.3468 (mmtm) REVERT: C 462 LYS cc_start: 0.7937 (mttt) cc_final: 0.7644 (mmtm) REVERT: C 754 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8031 (tp) REVERT: C 759 PHE cc_start: 0.6835 (t80) cc_final: 0.6625 (t80) REVERT: C 814 LYS cc_start: 0.6903 (mmmt) cc_final: 0.6696 (mmmt) REVERT: C 983 ARG cc_start: 0.7604 (mtp-110) cc_final: 0.7370 (ttm110) REVERT: C 1139 ASP cc_start: 0.6982 (t0) cc_final: 0.6185 (m-30) REVERT: D 177 MET cc_start: -0.1309 (mmp) cc_final: -0.2941 (mtt) REVERT: D 334 ASN cc_start: 0.7967 (t0) cc_final: 0.7058 (m110) REVERT: D 764 LYS cc_start: 0.8530 (mttp) cc_final: 0.8327 (mttp) REVERT: D 949 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6976 (tp40) outliers start: 87 outliers final: 66 residues processed: 403 average time/residue: 0.3906 time to fit residues: 254.9032 Evaluate side-chains 383 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 315 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 116 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 92 optimal weight: 0.1980 chunk 222 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- 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 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 245 HIS ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 606 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 121 ASN C 137 ASN C 437 ASN C 606 ASN C 787 GLN C 953 ASN C 955 ASN C1023 ASN C1108 ASN C1142 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN D 606 ASN D 690 GLN D1058 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.146338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.119474 restraints weight = 116093.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.118592 restraints weight = 83120.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.119076 restraints weight = 63892.069| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30356 Z= 0.247 Angle : 0.743 12.218 41297 Z= 0.383 Chirality : 0.048 0.179 4603 Planarity : 0.005 0.073 5332 Dihedral : 5.014 46.462 4025 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.53 % Allowed : 16.54 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.09 (0.13), residues: 3700 helix: -0.89 (0.17), residues: 855 sheet: -0.90 (0.20), residues: 599 loop : -1.78 (0.12), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 633 HIS 0.013 0.002 HIS D1048 PHE 0.030 0.003 PHE B 927 TYR 0.026 0.003 TYR D 741 ARG 0.009 0.001 ARG B 905 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 834) hydrogen bonds : angle 6.22238 ( 2412) SS BOND : bond 0.00540 ( 42) SS BOND : angle 1.98402 ( 84) covalent geometry : bond 0.00543 (30314) covalent geometry : angle 0.73847 (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 479 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 363 time to evaluate : 3.932 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: A 63 ASN cc_start: 0.3418 (m-40) cc_final: 0.3055 (t0) REVERT: A 67 ASP cc_start: 0.7046 (m-30) cc_final: 0.6783 (m-30) REVERT: A 249 MET cc_start: 0.0334 (mmt) cc_final: -0.1607 (mtm) REVERT: A 408 MET cc_start: 0.1095 (mtm) cc_final: 0.0770 (mpp) REVERT: A 480 MET cc_start: 0.2615 (mtt) cc_final: 0.2205 (mtp) REVERT: A 554 LEU cc_start: -0.0869 (mt) cc_final: -0.1614 (pp) REVERT: A 566 TRP cc_start: -0.0134 (p-90) cc_final: -0.0609 (p-90) REVERT: A 579 MET cc_start: 0.0330 (mmp) cc_final: -0.0196 (mmt) REVERT: A 586 ASN cc_start: 0.5079 (p0) cc_final: 0.4830 (p0) REVERT: B 298 GLU cc_start: 0.8149 (tp30) cc_final: 0.7931 (mt-10) REVERT: B 755 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: B 1050 MET cc_start: 0.6808 (ptp) cc_final: 0.6320 (ptp) REVERT: C 141 LEU cc_start: 0.7944 (tp) cc_final: 0.7665 (tp) REVERT: C 340 GLU cc_start: 0.7246 (pp20) cc_final: 0.6617 (tp30) REVERT: C 462 LYS cc_start: 0.7839 (mttt) cc_final: 0.7438 (mmtm) REVERT: C 726 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7366 (mp) REVERT: C 774 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7902 (mp10) REVERT: C 983 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.8022 (ttm110) REVERT: C 1139 ASP cc_start: 0.6970 (t0) cc_final: 0.6407 (m-30) REVERT: D 40 ASP cc_start: 0.6345 (t0) cc_final: 0.6101 (m-30) REVERT: D 707 TYR cc_start: 0.6045 (t80) cc_final: 0.5795 (t80) REVERT: D 720 ILE cc_start: 0.7698 (mt) cc_final: 0.7488 (pt) REVERT: D 949 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7669 (mm-40) REVERT: D 1090 PRO cc_start: 0.7233 (Cg_endo) cc_final: 0.6951 (Cg_exo) outliers start: 116 outliers final: 73 residues processed: 438 average time/residue: 0.4713 time to fit residues: 342.4947 Evaluate side-chains 379 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 303 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 777 ASN Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 221 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1023 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN D 30 ASN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN D 422 ASN ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN D 953 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.145407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.118258 restraints weight = 117146.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.118373 restraints weight = 85544.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.118333 restraints weight = 59795.370| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30356 Z= 0.207 Angle : 0.688 11.457 41297 Z= 0.351 Chirality : 0.047 0.203 4603 Planarity : 0.005 0.062 5332 Dihedral : 4.923 36.491 4024 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.10 % Allowed : 18.64 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.03 (0.13), residues: 3700 helix: -0.68 (0.17), residues: 860 sheet: -0.89 (0.21), residues: 567 loop : -1.80 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 633 HIS 0.007 0.001 HIS C 49 PHE 0.024 0.002 PHE B 888 TYR 0.015 0.002 TYR C 365 ARG 0.012 0.001 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 834) hydrogen bonds : angle 6.17955 ( 2412) SS BOND : bond 0.00738 ( 42) SS BOND : angle 1.98608 ( 84) covalent geometry : bond 0.00470 (30314) covalent geometry : angle 0.68304 (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 426 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 324 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.3050 (m-40) cc_final: 0.2546 (t0) REVERT: A 67 ASP cc_start: 0.6829 (m-30) cc_final: 0.6571 (m-30) REVERT: A 123 MET cc_start: -0.5140 (tpp) cc_final: -0.5451 (ttm) REVERT: A 249 MET cc_start: 0.0150 (mmt) cc_final: -0.1803 (mtt) REVERT: A 408 MET cc_start: 0.0333 (mtm) cc_final: 0.0058 (mpp) REVERT: A 431 ASP cc_start: 0.6670 (m-30) cc_final: 0.6419 (t0) REVERT: A 480 MET cc_start: 0.2939 (mtt) cc_final: 0.2403 (mtp) REVERT: A 566 TRP cc_start: 0.0182 (p-90) cc_final: -0.0078 (p-90) REVERT: B 755 GLN cc_start: 0.8388 (mp10) cc_final: 0.8135 (mt0) REVERT: B 1050 MET cc_start: 0.6808 (ptp) cc_final: 0.6335 (ptp) REVERT: C 141 LEU cc_start: 0.7914 (tp) cc_final: 0.7611 (tp) REVERT: C 462 LYS cc_start: 0.7887 (mttt) cc_final: 0.7561 (mmtt) REVERT: C 754 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8325 (tp) REVERT: C 759 PHE cc_start: 0.7184 (t80) cc_final: 0.6893 (t80) REVERT: C 983 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8156 (ttm110) REVERT: C 1029 MET cc_start: 0.7808 (mmm) cc_final: 0.7534 (tpt) REVERT: C 1139 ASP cc_start: 0.6904 (t0) cc_final: 0.6391 (m-30) REVERT: D 40 ASP cc_start: 0.6708 (t0) cc_final: 0.6119 (m-30) REVERT: D 1090 PRO cc_start: 0.7378 (Cg_endo) cc_final: 0.7086 (Cg_exo) outliers start: 102 outliers final: 80 residues processed: 394 average time/residue: 0.3992 time to fit residues: 256.8614 Evaluate side-chains 384 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 303 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 191 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 241 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 290 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 221 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 137 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN D 422 ASN D 949 GLN D 953 ASN D 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.146284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.119487 restraints weight = 116220.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.118574 restraints weight = 79292.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.119394 restraints weight = 62372.225| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30356 Z= 0.144 Angle : 0.626 11.621 41297 Z= 0.315 Chirality : 0.045 0.230 4603 Planarity : 0.004 0.052 5332 Dihedral : 4.657 36.822 4024 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.89 % Allowed : 19.40 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.89 (0.13), residues: 3700 helix: -0.46 (0.18), residues: 859 sheet: -0.90 (0.21), residues: 567 loop : -1.72 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 302 HIS 0.004 0.001 HIS C1048 PHE 0.023 0.002 PHE D 888 TYR 0.020 0.002 TYR C1110 ARG 0.006 0.001 ARG B1091 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 834) hydrogen bonds : angle 5.86532 ( 2412) SS BOND : bond 0.00419 ( 42) SS BOND : angle 2.01484 ( 84) covalent geometry : bond 0.00328 (30314) covalent geometry : angle 0.62001 (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 424 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 329 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.3201 (m-40) cc_final: 0.2686 (t0) REVERT: A 67 ASP cc_start: 0.6771 (m-30) cc_final: 0.6513 (m-30) REVERT: A 82 MET cc_start: 0.3414 (ptp) cc_final: 0.2645 (ptp) REVERT: A 249 MET cc_start: 0.0040 (mmt) cc_final: -0.1820 (mtm) REVERT: A 259 ILE cc_start: 0.7582 (mm) cc_final: 0.7247 (tp) REVERT: A 408 MET cc_start: 0.0040 (mtm) cc_final: -0.0272 (mpp) REVERT: A 480 MET cc_start: 0.2890 (mtt) cc_final: 0.2469 (mtp) REVERT: A 566 TRP cc_start: 0.0173 (p-90) cc_final: -0.0204 (p-90) REVERT: B 755 GLN cc_start: 0.8400 (mp10) cc_final: 0.8129 (mt0) REVERT: B 1050 MET cc_start: 0.6733 (ptp) cc_final: 0.6303 (ptp) REVERT: C 141 LEU cc_start: 0.8018 (tp) cc_final: 0.7726 (tp) REVERT: C 462 LYS cc_start: 0.7907 (mttt) cc_final: 0.7517 (mmtt) REVERT: C 754 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8297 (tp) REVERT: C 983 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.8052 (ttm110) REVERT: C 1139 ASP cc_start: 0.7028 (t0) cc_final: 0.6498 (m-30) REVERT: C 1147 SER cc_start: 0.6737 (t) cc_final: 0.6454 (p) REVERT: D 40 ASP cc_start: 0.6678 (t0) cc_final: 0.6121 (m-30) REVERT: D 1090 PRO cc_start: 0.7276 (Cg_endo) cc_final: 0.7034 (Cg_exo) outliers start: 95 outliers final: 66 residues processed: 394 average time/residue: 0.4060 time to fit residues: 266.2368 Evaluate side-chains 378 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 724 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 811 LYS Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 63 optimal weight: 6.9990 chunk 369 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 352 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 314 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 99 optimal weight: 6.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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 221 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 907 ASN C 953 ASN C 955 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN D 23 GLN D 953 ASN D 965 GLN D1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.146428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.120236 restraints weight = 116132.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.119158 restraints weight = 78490.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.119485 restraints weight = 61949.057| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.6360 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= 0.129 Angle : 0.628 11.365 41297 Z= 0.315 Chirality : 0.045 0.259 4603 Planarity : 0.004 0.047 5332 Dihedral : 4.541 37.306 4024 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.55 % Allowed : 20.01 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.78 (0.13), residues: 3700 helix: -0.36 (0.18), residues: 859 sheet: -0.80 (0.21), residues: 558 loop : -1.67 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.004 0.001 HIS C1064 PHE 0.024 0.001 PHE B 759 TYR 0.027 0.001 TYR C 612 ARG 0.008 0.000 ARG C 765 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 834) hydrogen bonds : angle 5.76246 ( 2412) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.88981 ( 84) covalent geometry : bond 0.00297 (30314) covalent geometry : angle 0.62304 (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 413 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 329 time to evaluate : 3.450 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: A 62 MET cc_start: -0.2442 (tpt) cc_final: -0.4656 (ptp) REVERT: A 67 ASP cc_start: 0.6777 (m-30) cc_final: 0.6511 (m-30) REVERT: A 82 MET cc_start: 0.3429 (ptp) cc_final: 0.2601 (ptp) REVERT: A 249 MET cc_start: -0.0090 (mmt) cc_final: -0.1849 (mtt) REVERT: A 259 ILE cc_start: 0.7492 (mm) cc_final: 0.7155 (tp) REVERT: A 408 MET cc_start: 0.0154 (mtm) cc_final: -0.0160 (mpp) REVERT: A 480 MET cc_start: 0.3259 (mtt) cc_final: 0.2895 (mtp) REVERT: A 566 TRP cc_start: -0.0091 (p-90) cc_final: -0.0405 (p-90) REVERT: B 303 LEU cc_start: 0.8477 (mp) cc_final: 0.8124 (tp) REVERT: B 755 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: B 759 PHE cc_start: 0.7360 (m-80) cc_final: 0.7132 (m-80) REVERT: B 1012 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9061 (tt) REVERT: B 1050 MET cc_start: 0.6717 (ptp) cc_final: 0.6318 (ptp) REVERT: C 141 LEU cc_start: 0.8042 (tp) cc_final: 0.7750 (tp) REVERT: C 458 LYS cc_start: 0.2952 (mmtm) cc_final: 0.1418 (tppt) REVERT: C 462 LYS cc_start: 0.7940 (mttt) cc_final: 0.7546 (mmtt) REVERT: C 517 LEU cc_start: 0.6807 (tp) cc_final: 0.6581 (tt) REVERT: C 754 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8347 (tp) REVERT: C 983 ARG cc_start: 0.8437 (mtp-110) cc_final: 0.8119 (ttm110) REVERT: C 1139 ASP cc_start: 0.7141 (t0) cc_final: 0.6567 (m-30) REVERT: D 40 ASP cc_start: 0.6680 (t0) cc_final: 0.6079 (m-30) REVERT: D 129 LYS cc_start: 0.8990 (mttt) cc_final: 0.8714 (tppt) REVERT: D 177 MET cc_start: -0.1175 (mmt) cc_final: -0.1419 (mmt) REVERT: D 900 MET cc_start: 0.6877 (mmm) cc_final: 0.6490 (mmt) REVERT: D 1076 THR cc_start: 0.7275 (OUTLIER) cc_final: 0.6914 (m) REVERT: D 1090 PRO cc_start: 0.7263 (Cg_endo) cc_final: 0.7021 (Cg_exo) outliers start: 84 outliers final: 65 residues processed: 386 average time/residue: 0.3963 time to fit residues: 251.2722 Evaluate side-chains 376 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 307 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 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 811 LYS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 295 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 40 optimal weight: 0.0020 chunk 36 optimal weight: 9.9990 chunk 323 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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 221 GLN ** A 287 GLN ** 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 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 955 ASN C1023 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.145638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.118439 restraints weight = 115590.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.117947 restraints weight = 92189.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.118700 restraints weight = 62913.794| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30356 Z= 0.146 Angle : 0.646 11.598 41297 Z= 0.326 Chirality : 0.045 0.276 4603 Planarity : 0.004 0.044 5332 Dihedral : 4.602 37.904 4024 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.55 % Allowed : 20.10 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.81 (0.13), residues: 3700 helix: -0.37 (0.18), residues: 854 sheet: -0.97 (0.20), residues: 621 loop : -1.65 (0.12), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.005 0.001 HIS C1048 PHE 0.024 0.002 PHE C 318 TYR 0.015 0.001 TYR C 917 ARG 0.006 0.001 ARG C 765 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 834) hydrogen bonds : angle 5.79643 ( 2412) SS BOND : bond 0.00449 ( 42) SS BOND : angle 2.02504 ( 84) covalent geometry : bond 0.00335 (30314) covalent geometry : angle 0.64048 (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 404 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 320 time to evaluate : 3.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: -0.2079 (tpt) cc_final: -0.4454 (ptp) REVERT: A 67 ASP cc_start: 0.6823 (m-30) cc_final: 0.6575 (m-30) REVERT: A 249 MET cc_start: -0.0021 (mmt) cc_final: -0.1736 (mtt) REVERT: A 408 MET cc_start: -0.0289 (mtm) cc_final: -0.0564 (mpp) REVERT: A 462 MET cc_start: 0.2543 (mpp) cc_final: 0.2257 (mmp) REVERT: A 480 MET cc_start: 0.3205 (mtt) cc_final: 0.2871 (mtp) REVERT: A 566 TRP cc_start: 0.0034 (p-90) cc_final: -0.0252 (p-90) REVERT: B 303 LEU cc_start: 0.8538 (mp) cc_final: 0.8195 (tp) REVERT: B 755 GLN cc_start: 0.8441 (mp10) cc_final: 0.8126 (mp10) REVERT: B 1012 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9144 (tt) REVERT: B 1050 MET cc_start: 0.6716 (ptp) cc_final: 0.6277 (ptp) REVERT: C 141 LEU cc_start: 0.7924 (tp) cc_final: 0.7616 (tp) REVERT: C 458 LYS cc_start: 0.2829 (mmtm) cc_final: 0.1389 (tppt) REVERT: C 462 LYS cc_start: 0.8066 (mttt) cc_final: 0.7644 (mmtt) REVERT: C 517 LEU cc_start: 0.6843 (tp) cc_final: 0.6632 (tt) REVERT: C 754 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8257 (tp) REVERT: C 1050 MET cc_start: 0.7398 (ptp) cc_final: 0.7146 (ptp) REVERT: C 1139 ASP cc_start: 0.6921 (t0) cc_final: 0.6407 (m-30) REVERT: C 1147 SER cc_start: 0.6685 (t) cc_final: 0.6432 (p) REVERT: D 40 ASP cc_start: 0.6733 (t0) cc_final: 0.6136 (m-30) REVERT: D 129 LYS cc_start: 0.9001 (mttt) cc_final: 0.8734 (tppt) REVERT: D 868 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6126 (mm-30) REVERT: D 900 MET cc_start: 0.6867 (mmm) cc_final: 0.6475 (mmt) REVERT: D 965 GLN cc_start: 0.8425 (tp40) cc_final: 0.8032 (tp-100) REVERT: D 1076 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.6982 (m) REVERT: D 1090 PRO cc_start: 0.7535 (Cg_endo) cc_final: 0.7263 (Cg_exo) outliers start: 84 outliers final: 71 residues processed: 378 average time/residue: 0.3924 time to fit residues: 242.2561 Evaluate side-chains 377 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 303 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 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 811 LYS Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 320 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 294 optimal weight: 0.0040 chunk 314 optimal weight: 0.9990 chunk 167 optimal weight: 0.0870 chunk 152 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.3368 ------------------------------------------------------------------------------- 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 221 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 955 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 690 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.147318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.121719 restraints weight = 116897.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120131 restraints weight = 86600.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.121177 restraints weight = 64176.356| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.6533 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= 0.113 Angle : 0.628 11.956 41297 Z= 0.312 Chirality : 0.045 0.306 4603 Planarity : 0.004 0.048 5332 Dihedral : 4.346 38.660 4024 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.58 % Allowed : 21.31 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.68 (0.13), residues: 3700 helix: -0.30 (0.18), residues: 848 sheet: -0.76 (0.20), residues: 620 loop : -1.59 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.024 0.001 PHE C 318 TYR 0.018 0.001 TYR C 612 ARG 0.010 0.000 ARG C 765 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 834) hydrogen bonds : angle 5.56429 ( 2412) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.75479 ( 84) covalent geometry : bond 0.00257 (30314) covalent geometry : angle 0.62329 (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 378 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 326 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: -0.2129 (tpt) cc_final: -0.4359 (ptp) REVERT: A 67 ASP cc_start: 0.6839 (m-30) cc_final: 0.6551 (m-30) REVERT: A 82 MET cc_start: 0.2960 (ptp) cc_final: 0.2584 (ptt) REVERT: A 249 MET cc_start: -0.0061 (mmt) cc_final: -0.1737 (mtt) REVERT: A 408 MET cc_start: 0.0358 (mtm) cc_final: 0.0059 (mpp) REVERT: A 462 MET cc_start: 0.2434 (mpp) cc_final: 0.2185 (mmp) REVERT: A 480 MET cc_start: 0.3269 (mtt) cc_final: 0.3009 (mtp) REVERT: B 303 LEU cc_start: 0.8450 (mp) cc_final: 0.8153 (tp) REVERT: B 755 GLN cc_start: 0.8407 (mp10) cc_final: 0.8071 (mp10) REVERT: B 1050 MET cc_start: 0.6557 (ptp) cc_final: 0.6233 (ptp) REVERT: C 141 LEU cc_start: 0.7966 (tp) cc_final: 0.7616 (tp) REVERT: C 458 LYS cc_start: 0.2891 (mmtm) cc_final: 0.1513 (tppt) REVERT: C 585 LEU cc_start: 0.6703 (tp) cc_final: 0.6408 (tp) REVERT: C 748 GLU cc_start: 0.7629 (mp0) cc_final: 0.7385 (mp0) REVERT: C 754 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 983 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.7937 (ttm110) REVERT: C 1139 ASP cc_start: 0.6948 (t0) cc_final: 0.6355 (m-30) REVERT: D 40 ASP cc_start: 0.6587 (t0) cc_final: 0.5968 (m-30) REVERT: D 129 LYS cc_start: 0.9011 (mttt) cc_final: 0.8688 (tppt) REVERT: D 900 MET cc_start: 0.6799 (mmm) cc_final: 0.6576 (mmt) REVERT: D 953 ASN cc_start: 0.8323 (m-40) cc_final: 0.8060 (m110) REVERT: D 965 GLN cc_start: 0.8366 (tp40) cc_final: 0.7997 (tp-100) REVERT: D 1076 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7034 (m) REVERT: D 1090 PRO cc_start: 0.7452 (Cg_endo) cc_final: 0.7222 (Cg_exo) outliers start: 52 outliers final: 40 residues processed: 362 average time/residue: 0.4061 time to fit residues: 242.9775 Evaluate side-chains 342 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 300 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 337 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 218 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 162 optimal weight: 0.0670 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- 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 221 GLN A 378 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 953 ASN C1005 GLN ** C1064 HIS ** 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 = 0.4569 r_free = 0.4569 target = 0.146124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.119466 restraints weight = 117437.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.119087 restraints weight = 97170.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.119609 restraints weight = 63035.002| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.6727 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= 0.130 Angle : 0.638 11.562 41297 Z= 0.318 Chirality : 0.045 0.298 4603 Planarity : 0.004 0.048 5332 Dihedral : 4.403 38.804 4024 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.76 % Allowed : 21.44 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.61 (0.13), residues: 3700 helix: -0.24 (0.18), residues: 852 sheet: -0.77 (0.19), residues: 633 loop : -1.53 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 566 HIS 0.007 0.001 HIS B1088 PHE 0.051 0.002 PHE B 817 TYR 0.016 0.001 TYR D 707 ARG 0.010 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 834) hydrogen bonds : angle 5.61521 ( 2412) SS BOND : bond 0.00380 ( 42) SS BOND : angle 1.75349 ( 84) covalent geometry : bond 0.00298 (30314) covalent geometry : angle 0.63374 (41213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10787.59 seconds wall clock time: 189 minutes 12.85 seconds (11352.85 seconds total)