Starting phenix.real_space_refine on Fri Feb 6 05:38:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wfq_65935/02_2026/9wfq_65935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wfq_65935/02_2026/9wfq_65935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wfq_65935/02_2026/9wfq_65935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wfq_65935/02_2026/9wfq_65935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wfq_65935/02_2026/9wfq_65935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wfq_65935/02_2026/9wfq_65935.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.070 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 108 5.16 5 C 14526 2.51 5 N 3798 2.21 5 O 4042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22474 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 11237 Classifications: {'peptide': 1422} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1363} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 14.36, per 1000 atoms: 0.64 Number of scatterers: 22474 At special positions: 0 Unit cell: (190.3, 115.5, 157.3, 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 108 16.00 O 4042 8.00 N 3798 7.00 C 14526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 32 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 32 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 955.2 milliseconds 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5296 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 10 sheets defined 67.7% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.541A pdb=" N CYS A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.996A pdb=" N ASP A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 36 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 57 removed outlier: 3.612A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 95 removed outlier: 4.019A pdb=" N ASN A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.768A pdb=" N LEU A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 132 removed outlier: 3.544A pdb=" N GLY A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 removed outlier: 4.268A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.770A pdb=" N TYR A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.599A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.513A pdb=" N LYS A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.727A pdb=" N ASP A 258 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 259 " --> pdb=" O GLU A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 267 through 280 removed outlier: 3.556A pdb=" N LEU A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 removed outlier: 3.880A pdb=" N LEU A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.981A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 removed outlier: 4.086A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.579A pdb=" N SER A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 removed outlier: 3.620A pdb=" N TYR A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 364 through 385 removed outlier: 3.503A pdb=" N ARG A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 405 removed outlier: 4.030A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N THR A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.553A pdb=" N GLN A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 Proline residue: A 424 - end of helix removed outlier: 3.512A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 451 removed outlier: 3.708A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 487 removed outlier: 3.675A pdb=" N THR A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.830A pdb=" N LYS A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 530 removed outlier: 3.683A pdb=" N PHE A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 4.085A pdb=" N THR A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 595 removed outlier: 4.016A pdb=" N ALA A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Proline residue: A 569 - end of helix removed outlier: 3.934A pdb=" N MET A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.919A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 582 " --> pdb=" O THR A 578 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 664 removed outlier: 3.574A pdb=" N LEU A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 705 through 716 removed outlier: 3.542A pdb=" N ALA A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 727 through 731 removed outlier: 3.712A pdb=" N LEU A 730 " --> pdb=" O GLY A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 757 removed outlier: 3.557A pdb=" N ALA A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 781 removed outlier: 3.615A pdb=" N GLN A 777 " --> pdb=" O HIS A 773 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 778 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 805 removed outlier: 3.935A pdb=" N SER A 803 " --> pdb=" O HIS A 800 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 804 " --> pdb=" O PHE A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 829 through 839 Processing helix chain 'A' and resid 904 through 916 removed outlier: 4.130A pdb=" N LEU A 908 " --> pdb=" O SER A 904 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 909 " --> pdb=" O TRP A 905 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 947 removed outlier: 3.650A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET A 923 " --> pdb=" O TRP A 919 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 927 " --> pdb=" O MET A 923 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER A 938 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 947 " --> pdb=" O SER A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 1002 removed outlier: 3.936A pdb=" N TYR A 959 " --> pdb=" O GLY A 955 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 962 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 967 " --> pdb=" O TYR A 963 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 973 " --> pdb=" O GLY A 969 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 981 " --> pdb=" O ASN A 977 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE A 982 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 983 " --> pdb=" O TYR A 979 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A1002 " --> pdb=" O HIS A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'A' and resid 1015 through 1030 removed outlier: 4.157A pdb=" N ASP A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A1025 " --> pdb=" O ALA A1021 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE A1027 " --> pdb=" O ASP A1023 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A1028 " --> pdb=" O LEU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1056 removed outlier: 3.534A pdb=" N VAL A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A1043 " --> pdb=" O MET A1039 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A1048 " --> pdb=" O GLN A1044 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 removed outlier: 3.559A pdb=" N LEU A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A1061 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1056 through 1062' Processing helix chain 'A' and resid 1063 through 1090 removed outlier: 3.836A pdb=" N VAL A1068 " --> pdb=" O MET A1064 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A1074 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A1076 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR A1077 " --> pdb=" O ALA A1073 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N THR A1080 " --> pdb=" O TYR A1076 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU A1083 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A1089 " --> pdb=" O LYS A1085 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1097 Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 3.922A pdb=" N GLU A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A1104 " --> pdb=" O GLY A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1111 Processing helix chain 'A' and resid 1112 through 1114 No H-bonds generated for 'chain 'A' and resid 1112 through 1114' Processing helix chain 'A' and resid 1117 through 1128 removed outlier: 3.825A pdb=" N ILE A1121 " --> pdb=" O ARG A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1135 removed outlier: 3.731A pdb=" N VAL A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1143 removed outlier: 3.573A pdb=" N ASN A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1157 removed outlier: 4.025A pdb=" N ILE A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1166 removed outlier: 3.633A pdb=" N ALA A1162 " --> pdb=" O THR A1158 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A1166 " --> pdb=" O ALA A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1177 through 1187 removed outlier: 3.546A pdb=" N LEU A1181 " --> pdb=" O SER A1177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1184 " --> pdb=" O GLY A1180 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A1185 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1202 removed outlier: 3.543A pdb=" N LEU A1193 " --> pdb=" O ILE A1189 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A1199 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A1201 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1218 removed outlier: 4.004A pdb=" N TYR A1216 " --> pdb=" O ARG A1212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A1218 " --> pdb=" O GLY A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1290 removed outlier: 3.689A pdb=" N ASN A1287 " --> pdb=" O SER A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1317 Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1344 through 1355 Processing helix chain 'A' and resid 1357 through 1363 removed outlier: 3.603A pdb=" N ILE A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1370 removed outlier: 3.668A pdb=" N ASP A1369 " --> pdb=" O LEU A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1396 removed outlier: 3.786A pdb=" N ARG A1384 " --> pdb=" O SER A1380 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1425 removed outlier: 4.181A pdb=" N LEU A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A1425 " --> pdb=" O ILE A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1466 removed outlier: 3.606A pdb=" N ASN A1466 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1477 Processing helix chain 'A' and resid 1479 through 1498 removed outlier: 3.507A pdb=" N GLU A1484 " --> pdb=" O ALA A1480 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG A1487 " --> pdb=" O ALA A1483 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 removed outlier: 3.540A pdb=" N CYS B 10 " --> pdb=" O ILE B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.996A pdb=" N ASP B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 36 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 57 removed outlier: 3.611A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 95 removed outlier: 4.019A pdb=" N ASN B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.768A pdb=" N LEU B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 132 removed outlier: 3.544A pdb=" N GLY B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 removed outlier: 4.267A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 146 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 169 through 192 removed outlier: 3.770A pdb=" N TYR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 178 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 187 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.599A pdb=" N PHE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 removed outlier: 3.513A pdb=" N LYS B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.728A pdb=" N ASP B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 259 " --> pdb=" O GLU B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 259' Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 267 through 280 removed outlier: 3.555A pdb=" N LEU B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 removed outlier: 3.879A pdb=" N LEU B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.980A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 removed outlier: 4.085A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.580A pdb=" N SER B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 359 removed outlier: 3.619A pdb=" N TYR B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 351 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 364 through 385 removed outlier: 3.502A pdb=" N ARG B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 405 removed outlier: 4.030A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 399 " --> pdb=" O GLN B 395 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N THR B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 removed outlier: 3.553A pdb=" N GLN B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 436 Proline residue: B 424 - end of helix removed outlier: 3.512A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 451 removed outlier: 3.708A pdb=" N GLY B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.675A pdb=" N THR B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.829A pdb=" N LYS B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 530 removed outlier: 3.685A pdb=" N PHE B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 505 " --> pdb=" O GLN B 501 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 547 removed outlier: 4.085A pdb=" N THR B 537 " --> pdb=" O PRO B 533 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 595 removed outlier: 4.016A pdb=" N ALA B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 568 " --> pdb=" O ALA B 564 " (cutoff:3.500A) Proline residue: B 569 - end of helix removed outlier: 3.935A pdb=" N MET B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Proline residue: B 574 - end of helix removed outlier: 3.918A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 582 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 589 " --> pdb=" O VAL B 585 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 590 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 664 removed outlier: 3.573A pdb=" N LEU B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 Processing helix chain 'B' and resid 705 through 716 removed outlier: 3.542A pdb=" N ALA B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 724 Processing helix chain 'B' and resid 727 through 731 removed outlier: 3.711A pdb=" N LEU B 730 " --> pdb=" O GLY B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 757 removed outlier: 3.557A pdb=" N ALA B 753 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 781 removed outlier: 3.616A pdb=" N GLN B 777 " --> pdb=" O HIS B 773 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 778 " --> pdb=" O VAL B 774 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 779 " --> pdb=" O GLY B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 805 removed outlier: 3.935A pdb=" N SER B 803 " --> pdb=" O HIS B 800 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 804 " --> pdb=" O PHE B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 829 through 839 Processing helix chain 'B' and resid 904 through 916 removed outlier: 4.130A pdb=" N LEU B 908 " --> pdb=" O SER B 904 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 909 " --> pdb=" O TRP B 905 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 910 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 947 removed outlier: 3.649A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET B 923 " --> pdb=" O TRP B 919 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 927 " --> pdb=" O MET B 923 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 932 " --> pdb=" O TYR B 928 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 935 " --> pdb=" O THR B 931 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B 938 " --> pdb=" O PHE B 934 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 942 " --> pdb=" O SER B 938 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 947 " --> pdb=" O SER B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 1002 removed outlier: 3.937A pdb=" N TYR B 959 " --> pdb=" O GLY B 955 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 961 " --> pdb=" O LEU B 957 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 962 " --> pdb=" O PHE B 958 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 967 " --> pdb=" O TYR B 963 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 972 " --> pdb=" O PHE B 968 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 973 " --> pdb=" O GLY B 969 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 974 " --> pdb=" O GLN B 970 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 975 " --> pdb=" O VAL B 971 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 981 " --> pdb=" O ASN B 977 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 982 " --> pdb=" O SER B 978 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 986 " --> pdb=" O ILE B 982 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 990 " --> pdb=" O LEU B 986 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS B 991 " --> pdb=" O TYR B 987 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER B 999 " --> pdb=" O ASN B 995 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B1002 " --> pdb=" O HIS B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1011 Processing helix chain 'B' and resid 1015 through 1030 removed outlier: 4.157A pdb=" N ASP B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU B1024 " --> pdb=" O PHE B1020 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B1025 " --> pdb=" O ALA B1021 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B1027 " --> pdb=" O ASP B1023 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B1028 " --> pdb=" O LEU B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1056 removed outlier: 3.535A pdb=" N VAL B1035 " --> pdb=" O VAL B1031 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B1043 " --> pdb=" O MET B1039 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN B1044 " --> pdb=" O GLY B1040 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B1048 " --> pdb=" O GLN B1044 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B1049 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1062 removed outlier: 3.559A pdb=" N LEU B1060 " --> pdb=" O SER B1056 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP B1061 " --> pdb=" O THR B1057 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1056 through 1062' Processing helix chain 'B' and resid 1063 through 1090 removed outlier: 3.836A pdb=" N VAL B1068 " --> pdb=" O MET B1064 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B1070 " --> pdb=" O LEU B1066 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B1074 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B1075 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR B1076 " --> pdb=" O GLY B1072 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B1077 " --> pdb=" O ALA B1073 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N THR B1080 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU B1083 " --> pdb=" O ASN B1079 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B1089 " --> pdb=" O LYS B1085 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE B1090 " --> pdb=" O ARG B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1097 Processing helix chain 'B' and resid 1097 through 1105 removed outlier: 3.922A pdb=" N GLU B1101 " --> pdb=" O ALA B1097 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B1104 " --> pdb=" O GLY B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1111 Processing helix chain 'B' and resid 1112 through 1114 No H-bonds generated for 'chain 'B' and resid 1112 through 1114' Processing helix chain 'B' and resid 1117 through 1128 removed outlier: 3.824A pdb=" N ILE B1121 " --> pdb=" O ARG B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1135 removed outlier: 3.731A pdb=" N VAL B1135 " --> pdb=" O ARG B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1143 removed outlier: 3.573A pdb=" N ASN B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG B1141 " --> pdb=" O MET B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1157 removed outlier: 4.025A pdb=" N ILE B1155 " --> pdb=" O GLY B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1166 removed outlier: 3.633A pdb=" N ALA B1162 " --> pdb=" O THR B1158 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN B1166 " --> pdb=" O ALA B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1171 through 1175 Processing helix chain 'B' and resid 1177 through 1187 removed outlier: 3.546A pdb=" N LEU B1181 " --> pdb=" O SER B1177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B1184 " --> pdb=" O GLY B1180 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR B1185 " --> pdb=" O LEU B1181 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B1187 " --> pdb=" O LEU B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1202 removed outlier: 3.542A pdb=" N LEU B1193 " --> pdb=" O ILE B1189 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B1199 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B1201 " --> pdb=" O LEU B1197 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B1202 " --> pdb=" O ARG B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1218 removed outlier: 4.004A pdb=" N TYR B1216 " --> pdb=" O ARG B1212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B1217 " --> pdb=" O VAL B1213 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B1218 " --> pdb=" O GLY B1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1290 removed outlier: 3.689A pdb=" N ASN B1287 " --> pdb=" O SER B1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 1311 through 1317 Processing helix chain 'B' and resid 1332 through 1338 Processing helix chain 'B' and resid 1344 through 1355 Processing helix chain 'B' and resid 1357 through 1363 removed outlier: 3.603A pdb=" N ILE B1361 " --> pdb=" O LEU B1357 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1370 removed outlier: 3.668A pdb=" N ASP B1369 " --> pdb=" O LEU B1366 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1396 removed outlier: 3.786A pdb=" N ARG B1384 " --> pdb=" O SER B1380 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B1385 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B1395 " --> pdb=" O ARG B1391 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1425 removed outlier: 4.181A pdb=" N LEU B1416 " --> pdb=" O ARG B1412 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B1422 " --> pdb=" O GLN B1418 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE B1425 " --> pdb=" O ILE B1421 " (cutoff:3.500A) Processing helix chain 'B' and resid 1459 through 1466 removed outlier: 3.606A pdb=" N ASN B1466 " --> pdb=" O ASN B1462 " (cutoff:3.500A) Processing helix chain 'B' and resid 1469 through 1477 Processing helix chain 'B' and resid 1479 through 1498 removed outlier: 3.507A pdb=" N GLU B1484 " --> pdb=" O ALA B1480 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B1487 " --> pdb=" O ALA B1483 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 637 through 639 removed outlier: 3.612A pdb=" N ILE A 614 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 680 through 683 removed outlier: 6.331A pdb=" N TYR A 761 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 795 " --> pdb=" O TYR A 761 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE A 763 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 644 " --> pdb=" O ARG A 807 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 809 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 646 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL A 811 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 648 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A 818 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N HIS A 812 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1265 through 1266 removed outlier: 5.552A pdb=" N ASP A1246 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG A1299 " --> pdb=" O ASP A1246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1399 through 1403 removed outlier: 6.277A pdb=" N LEU A1400 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A1433 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A1402 " --> pdb=" O ILE A1433 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1449 " --> pdb=" O VAL A1275 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A1458 " --> pdb=" O ILE A1446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA7, first strand: chain 'B' and resid 637 through 639 removed outlier: 3.614A pdb=" N ILE B 614 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 680 through 683 removed outlier: 6.331A pdb=" N TYR B 761 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL B 795 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE B 763 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 644 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 809 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 646 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 811 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 648 " --> pdb=" O VAL B 811 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU B 818 " --> pdb=" O LEU B 810 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N HIS B 812 " --> pdb=" O VAL B 816 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL B 816 " --> pdb=" O HIS B 812 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1265 through 1266 removed outlier: 5.552A pdb=" N ASP B1246 " --> pdb=" O ARG B1299 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG B1299 " --> pdb=" O ASP B1246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1399 through 1403 removed outlier: 6.277A pdb=" N LEU B1400 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B1433 " --> pdb=" O LEU B1400 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B1402 " --> pdb=" O ILE B1433 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B1449 " --> pdb=" O VAL B1275 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B1458 " --> pdb=" O ILE B1446 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2874 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7198 1.34 - 1.46: 5370 1.46 - 1.58: 10214 1.58 - 1.70: 0 1.70 - 1.82: 188 Bond restraints: 22970 Sorted by residual: bond pdb=" CG LEU B 972 " pdb=" CD2 LEU B 972 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.52e+00 bond pdb=" CG LEU A 972 " pdb=" CD2 LEU A 972 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" CZ ARG A 370 " pdb=" NH2 ARG A 370 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.13e+00 bond pdb=" CZ ARG B 370 " pdb=" NH2 ARG B 370 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 2.02e+00 bond pdb=" C ALA A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.25e-02 6.40e+03 1.84e+00 ... (remaining 22965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 30502 2.20 - 4.40: 597 4.40 - 6.60: 67 6.60 - 8.80: 12 8.80 - 11.00: 4 Bond angle restraints: 31182 Sorted by residual: angle pdb=" C ALA B 23 " pdb=" N ASN B 24 " pdb=" CA ASN B 24 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C ALA A 23 " pdb=" N ASN A 24 " pdb=" CA ASN A 24 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C THR A 946 " pdb=" N ASP A 947 " pdb=" CA ASP A 947 " ideal model delta sigma weight residual 122.46 128.16 -5.70 1.41e+00 5.03e-01 1.63e+01 angle pdb=" C THR B 946 " pdb=" N ASP B 947 " pdb=" CA ASP B 947 " ideal model delta sigma weight residual 122.46 128.16 -5.70 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N THR B1133 " pdb=" CA THR B1133 " pdb=" C THR B1133 " ideal model delta sigma weight residual 113.18 108.37 4.81 1.33e+00 5.65e-01 1.31e+01 ... (remaining 31177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 13238 15.76 - 31.52: 348 31.52 - 47.28: 86 47.28 - 63.04: 0 63.04 - 78.80: 4 Dihedral angle restraints: 13676 sinusoidal: 5452 harmonic: 8224 Sorted by residual: dihedral pdb=" CA ASP B1403 " pdb=" C ASP B1403 " pdb=" N GLU B1404 " pdb=" CA GLU B1404 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ASP A1403 " pdb=" C ASP A1403 " pdb=" N GLU A1404 " pdb=" CA GLU A1404 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLU A 166 " pdb=" C GLU A 166 " pdb=" N TYR A 167 " pdb=" CA TYR A 167 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 13673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2817 0.058 - 0.116: 681 0.116 - 0.173: 68 0.173 - 0.231: 6 0.231 - 0.289: 2 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CB VAL A 22 " pdb=" CA VAL A 22 " pdb=" CG1 VAL A 22 " pdb=" CG2 VAL A 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB VAL B 22 " pdb=" CA VAL B 22 " pdb=" CG1 VAL B 22 " pdb=" CG2 VAL B 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU B1013 " pdb=" CB LEU B1013 " pdb=" CD1 LEU B1013 " pdb=" CD2 LEU B1013 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 3571 not shown) Planarity restraints: 3936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 552 " -0.045 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO B 553 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 552 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO A 553 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1064 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A1065 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A1065 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1065 " 0.037 5.00e-02 4.00e+02 ... (remaining 3933 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6851 2.82 - 3.34: 20368 3.34 - 3.86: 35143 3.86 - 4.38: 40581 4.38 - 4.90: 66546 Nonbonded interactions: 169489 Sorted by model distance: nonbonded pdb=" O PRO B 703 " pdb=" OH TYR B 755 " model vdw 2.303 3.040 nonbonded pdb=" O PRO A 703 " pdb=" OH TYR A 755 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR A1077 " pdb=" OD1 ASN A1140 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR B1077 " pdb=" OD1 ASN B1140 " model vdw 2.307 3.040 nonbonded pdb=" OD2 ASP A 765 " pdb=" OG SER A 768 " model vdw 2.309 3.040 ... (remaining 169484 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.040 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.770 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 22972 Z= 0.220 Angle : 0.756 11.004 31186 Z= 0.415 Chirality : 0.047 0.289 3574 Planarity : 0.006 0.069 3936 Dihedral : 8.417 78.800 8374 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.11), residues: 2832 helix: -3.72 (0.07), residues: 1604 sheet: -0.88 (0.42), residues: 138 loop : -2.12 (0.16), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 567 TYR 0.013 0.002 TYR A 369 PHE 0.022 0.002 PHE B 700 TRP 0.039 0.002 TRP A 945 HIS 0.006 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00486 (22970) covalent geometry : angle 0.75601 (31182) SS BOND : bond 0.00401 ( 2) SS BOND : angle 1.59857 ( 4) hydrogen bonds : bond 0.31901 ( 984) hydrogen bonds : angle 9.40273 ( 2874) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.9216 (mt) cc_final: 0.8969 (pp) REVERT: A 155 MET cc_start: 0.8982 (mmt) cc_final: 0.8662 (mmm) REVERT: A 406 ASP cc_start: 0.7300 (m-30) cc_final: 0.7030 (m-30) REVERT: A 476 LYS cc_start: 0.9259 (tttt) cc_final: 0.9006 (ttpt) REVERT: A 481 MET cc_start: 0.8695 (tpp) cc_final: 0.8252 (tpp) REVERT: A 485 LEU cc_start: 0.9669 (mt) cc_final: 0.9249 (mt) REVERT: A 509 ASP cc_start: 0.9147 (m-30) cc_final: 0.8548 (p0) REVERT: A 532 ILE cc_start: 0.9121 (mt) cc_final: 0.8754 (mt) REVERT: A 570 LEU cc_start: 0.8845 (mt) cc_final: 0.8497 (tt) REVERT: A 746 GLN cc_start: 0.8884 (tp40) cc_final: 0.8543 (tp-100) REVERT: A 979 TYR cc_start: 0.7579 (t80) cc_final: 0.7188 (t80) REVERT: A 1022 LYS cc_start: 0.9166 (tttt) cc_final: 0.8952 (tppt) REVERT: A 1146 ARG cc_start: 0.8433 (mtt90) cc_final: 0.7858 (mtp180) REVERT: A 1425 PHE cc_start: 0.2708 (m-80) cc_final: 0.2174 (m-80) REVERT: B 114 LEU cc_start: 0.9216 (mt) cc_final: 0.8966 (pp) REVERT: B 155 MET cc_start: 0.8937 (mmt) cc_final: 0.8610 (mmm) REVERT: B 406 ASP cc_start: 0.7340 (m-30) cc_final: 0.7012 (m-30) REVERT: B 476 LYS cc_start: 0.9262 (tttt) cc_final: 0.9011 (ttpt) REVERT: B 481 MET cc_start: 0.8674 (tpp) cc_final: 0.8238 (tpp) REVERT: B 485 LEU cc_start: 0.9677 (mt) cc_final: 0.9258 (mt) REVERT: B 509 ASP cc_start: 0.9142 (m-30) cc_final: 0.8547 (p0) REVERT: B 532 ILE cc_start: 0.9095 (mt) cc_final: 0.8739 (mt) REVERT: B 570 LEU cc_start: 0.8843 (mt) cc_final: 0.8500 (tt) REVERT: B 593 VAL cc_start: 0.9483 (t) cc_final: 0.9283 (t) REVERT: B 746 GLN cc_start: 0.8905 (tp40) cc_final: 0.8561 (tp-100) REVERT: B 1022 LYS cc_start: 0.9146 (tttt) cc_final: 0.8920 (tppt) REVERT: B 1146 ARG cc_start: 0.8406 (mtt90) cc_final: 0.8136 (mtp-110) REVERT: B 1425 PHE cc_start: 0.2695 (m-80) cc_final: 0.2161 (m-80) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.1720 time to fit residues: 139.6611 Evaluate side-chains 265 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 74 ASN A 363 ASN A 415 GLN A 437 GLN A 697 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN A1128 ASN A1129 ASN B 43 GLN B 74 ASN B 363 ASN B 415 GLN B 437 GLN B 697 ASN B 746 GLN ** B 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B1128 ASN B1129 ASN B1493 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.113912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.083034 restraints weight = 83038.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080532 restraints weight = 56753.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.081251 restraints weight = 50085.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081377 restraints weight = 39275.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.081547 restraints weight = 36643.770| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22972 Z= 0.148 Angle : 0.632 10.154 31186 Z= 0.331 Chirality : 0.042 0.152 3574 Planarity : 0.005 0.052 3936 Dihedral : 5.179 19.776 3088 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.13), residues: 2832 helix: -1.82 (0.10), residues: 1722 sheet: -0.87 (0.39), residues: 148 loop : -1.84 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1250 TYR 0.030 0.002 TYR B 369 PHE 0.034 0.002 PHE A 191 TRP 0.015 0.002 TRP A 241 HIS 0.002 0.000 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00299 (22970) covalent geometry : angle 0.63208 (31182) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.42207 ( 4) hydrogen bonds : bond 0.06662 ( 984) hydrogen bonds : angle 5.53792 ( 2874) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.9510 (mt) cc_final: 0.9219 (pp) REVERT: A 125 MET cc_start: 0.8715 (ttt) cc_final: 0.8498 (ttt) REVERT: A 476 LYS cc_start: 0.9230 (tttt) cc_final: 0.8974 (ttpt) REVERT: A 481 MET cc_start: 0.8988 (tpp) cc_final: 0.8572 (tpp) REVERT: A 485 LEU cc_start: 0.9480 (mt) cc_final: 0.8970 (mt) REVERT: A 570 LEU cc_start: 0.8939 (mt) cc_final: 0.8467 (tt) REVERT: A 593 VAL cc_start: 0.9510 (t) cc_final: 0.9204 (t) REVERT: A 666 LEU cc_start: 0.8176 (tp) cc_final: 0.7769 (tp) REVERT: A 746 GLN cc_start: 0.9139 (tp40) cc_final: 0.8828 (tp-100) REVERT: A 750 MET cc_start: 0.9139 (mmm) cc_final: 0.8783 (mmm) REVERT: A 912 GLN cc_start: 0.8967 (tt0) cc_final: 0.8746 (mt0) REVERT: A 979 TYR cc_start: 0.8047 (t80) cc_final: 0.7684 (t80) REVERT: A 1022 LYS cc_start: 0.9183 (tttt) cc_final: 0.8701 (tppt) REVERT: A 1118 MET cc_start: 0.8573 (tpp) cc_final: 0.8315 (tpp) REVERT: A 1146 ARG cc_start: 0.8444 (mtt90) cc_final: 0.7683 (ttt180) REVERT: B 114 LEU cc_start: 0.9511 (mt) cc_final: 0.9224 (pp) REVERT: B 125 MET cc_start: 0.8711 (ttt) cc_final: 0.8502 (ttt) REVERT: B 476 LYS cc_start: 0.9238 (tttt) cc_final: 0.8973 (ttpt) REVERT: B 481 MET cc_start: 0.9014 (tpp) cc_final: 0.8580 (tpp) REVERT: B 485 LEU cc_start: 0.9483 (mt) cc_final: 0.8978 (mt) REVERT: B 570 LEU cc_start: 0.8936 (mt) cc_final: 0.8483 (tt) REVERT: B 593 VAL cc_start: 0.9507 (t) cc_final: 0.9197 (t) REVERT: B 666 LEU cc_start: 0.8158 (tp) cc_final: 0.7747 (tp) REVERT: B 746 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8834 (tp-100) REVERT: B 750 MET cc_start: 0.9145 (mmm) cc_final: 0.8786 (mmm) REVERT: B 912 GLN cc_start: 0.8971 (tt0) cc_final: 0.8750 (mt0) REVERT: B 1022 LYS cc_start: 0.9165 (tttt) cc_final: 0.8806 (tppt) REVERT: B 1118 MET cc_start: 0.8575 (tpp) cc_final: 0.8326 (tpp) REVERT: B 1146 ARG cc_start: 0.8438 (mtt90) cc_final: 0.7689 (ttt180) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.1584 time to fit residues: 93.1132 Evaluate side-chains 246 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 114 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 204 optimal weight: 50.0000 chunk 30 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 388 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN A1215 ASN A1493 ASN B 43 GLN B 388 ASN ** B 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1215 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.112065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083385 restraints weight = 84679.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.079078 restraints weight = 66893.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.079982 restraints weight = 59423.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.080010 restraints weight = 42400.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080484 restraints weight = 40832.667| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22972 Z= 0.173 Angle : 0.616 11.998 31186 Z= 0.313 Chirality : 0.043 0.171 3574 Planarity : 0.004 0.048 3936 Dihedral : 4.879 19.138 3088 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.15), residues: 2832 helix: -0.87 (0.11), residues: 1744 sheet: -0.72 (0.39), residues: 152 loop : -1.57 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1299 TYR 0.021 0.002 TYR B 369 PHE 0.012 0.002 PHE A1020 TRP 0.014 0.001 TRP B 260 HIS 0.002 0.001 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00380 (22970) covalent geometry : angle 0.61560 (31182) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.50819 ( 4) hydrogen bonds : bond 0.05431 ( 984) hydrogen bonds : angle 5.06535 ( 2874) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.9525 (mt) cc_final: 0.9216 (pp) REVERT: A 365 MET cc_start: 0.8161 (ttm) cc_final: 0.7491 (ttm) REVERT: A 384 LEU cc_start: 0.9593 (mt) cc_final: 0.9144 (tp) REVERT: A 455 LEU cc_start: 0.9120 (tt) cc_final: 0.8768 (tp) REVERT: A 463 MET cc_start: 0.8877 (mmp) cc_final: 0.8665 (tpp) REVERT: A 476 LYS cc_start: 0.9236 (tttt) cc_final: 0.8988 (ttpt) REVERT: A 481 MET cc_start: 0.9103 (tpp) cc_final: 0.8571 (tpp) REVERT: A 485 LEU cc_start: 0.9523 (mt) cc_final: 0.9149 (mt) REVERT: A 509 ASP cc_start: 0.9307 (m-30) cc_final: 0.9044 (m-30) REVERT: A 570 LEU cc_start: 0.8935 (mt) cc_final: 0.8484 (tt) REVERT: A 746 GLN cc_start: 0.8908 (tp40) cc_final: 0.8630 (tp-100) REVERT: A 750 MET cc_start: 0.9095 (mmm) cc_final: 0.8683 (mmm) REVERT: A 912 GLN cc_start: 0.8844 (tt0) cc_final: 0.8640 (mt0) REVERT: A 979 TYR cc_start: 0.8152 (t80) cc_final: 0.7864 (t80) REVERT: A 1022 LYS cc_start: 0.9092 (tttt) cc_final: 0.8805 (tppt) REVERT: A 1087 MET cc_start: 0.8985 (mtp) cc_final: 0.8782 (mtp) REVERT: A 1132 PHE cc_start: 0.8486 (m-80) cc_final: 0.8105 (m-10) REVERT: A 1146 ARG cc_start: 0.8641 (mtt90) cc_final: 0.7664 (ttt180) REVERT: A 1425 PHE cc_start: 0.2895 (m-80) cc_final: 0.2301 (m-80) REVERT: B 114 LEU cc_start: 0.9531 (mt) cc_final: 0.9223 (pp) REVERT: B 365 MET cc_start: 0.8237 (ttm) cc_final: 0.7557 (ttm) REVERT: B 384 LEU cc_start: 0.9598 (mt) cc_final: 0.9146 (tp) REVERT: B 463 MET cc_start: 0.8871 (mmp) cc_final: 0.8652 (tpp) REVERT: B 476 LYS cc_start: 0.9240 (tttt) cc_final: 0.8985 (ttpt) REVERT: B 481 MET cc_start: 0.9102 (tpp) cc_final: 0.8581 (tpp) REVERT: B 485 LEU cc_start: 0.9518 (mt) cc_final: 0.9151 (mt) REVERT: B 509 ASP cc_start: 0.9316 (m-30) cc_final: 0.9046 (m-30) REVERT: B 570 LEU cc_start: 0.8916 (mt) cc_final: 0.8452 (tt) REVERT: B 746 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8656 (tp-100) REVERT: B 750 MET cc_start: 0.9089 (mmm) cc_final: 0.8668 (mmm) REVERT: B 912 GLN cc_start: 0.8852 (tt0) cc_final: 0.8638 (mt0) REVERT: B 1132 PHE cc_start: 0.8485 (m-80) cc_final: 0.8108 (m-10) REVERT: B 1146 ARG cc_start: 0.8664 (mtt90) cc_final: 0.7675 (ttt180) REVERT: B 1425 PHE cc_start: 0.2898 (m-80) cc_final: 0.2306 (m-80) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1561 time to fit residues: 79.3244 Evaluate side-chains 238 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 181 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 395 GLN A 746 GLN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN B 43 GLN B 395 GLN ** B 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.114049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.084774 restraints weight = 84448.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.081250 restraints weight = 57761.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.081751 restraints weight = 55721.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081872 restraints weight = 39662.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.082552 restraints weight = 37902.866| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22972 Z= 0.108 Angle : 0.548 9.128 31186 Z= 0.274 Chirality : 0.040 0.183 3574 Planarity : 0.003 0.044 3936 Dihedral : 4.547 17.039 3088 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 2832 helix: -0.25 (0.12), residues: 1714 sheet: -0.54 (0.38), residues: 162 loop : -1.27 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 785 TYR 0.023 0.001 TYR A 369 PHE 0.020 0.001 PHE B 934 TRP 0.016 0.001 TRP B 241 HIS 0.002 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00224 (22970) covalent geometry : angle 0.54780 (31182) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.24642 ( 4) hydrogen bonds : bond 0.04407 ( 984) hydrogen bonds : angle 4.49614 ( 2874) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.9539 (mt) cc_final: 0.9200 (pp) REVERT: A 242 MET cc_start: 0.8801 (mmm) cc_final: 0.8069 (mmm) REVERT: A 463 MET cc_start: 0.8750 (mmp) cc_final: 0.8439 (mmt) REVERT: A 476 LYS cc_start: 0.9239 (tttt) cc_final: 0.9014 (ttpt) REVERT: A 481 MET cc_start: 0.9133 (tpp) cc_final: 0.8514 (tpp) REVERT: A 485 LEU cc_start: 0.9469 (mt) cc_final: 0.9100 (mt) REVERT: A 746 GLN cc_start: 0.8935 (tp-100) cc_final: 0.7859 (tp-100) REVERT: A 750 MET cc_start: 0.9131 (mmm) cc_final: 0.8217 (mmm) REVERT: A 755 TYR cc_start: 0.8450 (t80) cc_final: 0.8238 (t80) REVERT: A 794 LEU cc_start: 0.9176 (pp) cc_final: 0.8866 (mm) REVERT: A 979 TYR cc_start: 0.8109 (t80) cc_final: 0.7305 (t80) REVERT: A 980 TRP cc_start: 0.7277 (m100) cc_final: 0.7060 (m100) REVERT: A 1024 LEU cc_start: 0.8709 (tp) cc_final: 0.8402 (tt) REVERT: A 1087 MET cc_start: 0.9094 (mtp) cc_final: 0.8823 (mtp) REVERT: A 1126 MET cc_start: 0.8894 (tpt) cc_final: 0.8618 (tpp) REVERT: A 1132 PHE cc_start: 0.8293 (m-80) cc_final: 0.7874 (m-10) REVERT: A 1146 ARG cc_start: 0.8668 (mtt90) cc_final: 0.7290 (ttt180) REVERT: A 1425 PHE cc_start: 0.2645 (m-80) cc_final: 0.2369 (m-80) REVERT: B 114 LEU cc_start: 0.9550 (mt) cc_final: 0.9211 (pp) REVERT: B 242 MET cc_start: 0.8902 (mmm) cc_final: 0.8352 (mmm) REVERT: B 455 LEU cc_start: 0.8978 (tp) cc_final: 0.8472 (tt) REVERT: B 463 MET cc_start: 0.8765 (mmp) cc_final: 0.8453 (mmt) REVERT: B 476 LYS cc_start: 0.9243 (tttt) cc_final: 0.9011 (ttpt) REVERT: B 481 MET cc_start: 0.9114 (tpp) cc_final: 0.8497 (tpp) REVERT: B 485 LEU cc_start: 0.9460 (mt) cc_final: 0.9096 (mt) REVERT: B 528 ILE cc_start: 0.8978 (tp) cc_final: 0.8763 (tp) REVERT: B 746 GLN cc_start: 0.8893 (tp-100) cc_final: 0.7802 (tp-100) REVERT: B 750 MET cc_start: 0.9110 (mmm) cc_final: 0.8184 (mmm) REVERT: B 755 TYR cc_start: 0.8422 (t80) cc_final: 0.8211 (t80) REVERT: B 794 LEU cc_start: 0.9184 (pp) cc_final: 0.8880 (mm) REVERT: B 1024 LEU cc_start: 0.8688 (tp) cc_final: 0.8428 (tt) REVERT: B 1132 PHE cc_start: 0.8290 (m-80) cc_final: 0.7912 (m-10) REVERT: B 1146 ARG cc_start: 0.8658 (mtt90) cc_final: 0.7625 (ttt180) REVERT: B 1425 PHE cc_start: 0.2645 (m-80) cc_final: 0.2358 (m-80) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1530 time to fit residues: 84.0025 Evaluate side-chains 251 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 9 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 165 optimal weight: 0.3980 chunk 222 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 415 GLN A 697 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN B 43 GLN B 415 GLN B 697 ASN ** B 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.111526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.083179 restraints weight = 83893.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.078998 restraints weight = 62557.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079722 restraints weight = 57938.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079778 restraints weight = 40958.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.080275 restraints weight = 39383.527| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22972 Z= 0.172 Angle : 0.589 9.384 31186 Z= 0.296 Chirality : 0.042 0.158 3574 Planarity : 0.003 0.043 3936 Dihedral : 4.473 17.129 3088 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.16), residues: 2832 helix: -0.06 (0.12), residues: 1752 sheet: -0.47 (0.38), residues: 162 loop : -1.16 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1316 TYR 0.020 0.002 TYR B 709 PHE 0.016 0.001 PHE A 958 TRP 0.017 0.002 TRP A 260 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00379 (22970) covalent geometry : angle 0.58884 (31182) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.57566 ( 4) hydrogen bonds : bond 0.04351 ( 984) hydrogen bonds : angle 4.55513 ( 2874) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.947 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 39 LEU cc_start: 0.8529 (tp) cc_final: 0.7939 (tt) REVERT: A 114 LEU cc_start: 0.9578 (mt) cc_final: 0.9195 (pp) REVERT: A 125 MET cc_start: 0.8754 (ttt) cc_final: 0.8364 (mmm) REVERT: A 242 MET cc_start: 0.9012 (mmm) cc_final: 0.8660 (mmm) REVERT: A 463 MET cc_start: 0.8833 (mmp) cc_final: 0.8470 (mmt) REVERT: A 476 LYS cc_start: 0.9267 (tttt) cc_final: 0.9033 (ttpt) REVERT: A 481 MET cc_start: 0.9071 (tpp) cc_final: 0.8430 (tpp) REVERT: A 485 LEU cc_start: 0.9449 (mt) cc_final: 0.9009 (mt) REVERT: A 588 LYS cc_start: 0.8723 (mttt) cc_final: 0.8408 (tptt) REVERT: A 591 GLU cc_start: 0.8987 (pt0) cc_final: 0.8783 (pp20) REVERT: A 746 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8705 (tp-100) REVERT: A 750 MET cc_start: 0.9143 (mmm) cc_final: 0.8751 (mmm) REVERT: A 755 TYR cc_start: 0.8505 (t80) cc_final: 0.8240 (t80) REVERT: A 794 LEU cc_start: 0.9231 (pp) cc_final: 0.8929 (mm) REVERT: A 912 GLN cc_start: 0.9029 (pt0) cc_final: 0.8817 (pt0) REVERT: A 1039 MET cc_start: 0.9420 (mmm) cc_final: 0.9184 (mmp) REVERT: A 1126 MET cc_start: 0.8837 (tpt) cc_final: 0.8599 (tpp) REVERT: A 1132 PHE cc_start: 0.8527 (m-80) cc_final: 0.8172 (m-10) REVERT: A 1146 ARG cc_start: 0.8615 (mtt90) cc_final: 0.7378 (ttt-90) REVERT: B 39 LEU cc_start: 0.8502 (tp) cc_final: 0.7920 (tt) REVERT: B 114 LEU cc_start: 0.9590 (mt) cc_final: 0.9211 (pp) REVERT: B 125 MET cc_start: 0.8785 (ttt) cc_final: 0.8418 (mmm) REVERT: B 242 MET cc_start: 0.9027 (mmm) cc_final: 0.8485 (mmm) REVERT: B 463 MET cc_start: 0.8827 (mmp) cc_final: 0.8351 (mmt) REVERT: B 476 LYS cc_start: 0.9278 (tttt) cc_final: 0.9027 (ttpt) REVERT: B 481 MET cc_start: 0.9069 (tpp) cc_final: 0.8422 (tpp) REVERT: B 485 LEU cc_start: 0.9455 (mt) cc_final: 0.9013 (mt) REVERT: B 588 LYS cc_start: 0.8721 (mttt) cc_final: 0.8407 (tptt) REVERT: B 746 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8697 (tp-100) REVERT: B 750 MET cc_start: 0.9145 (mmm) cc_final: 0.8751 (mmm) REVERT: B 755 TYR cc_start: 0.8489 (t80) cc_final: 0.8222 (t80) REVERT: B 794 LEU cc_start: 0.9225 (pp) cc_final: 0.8938 (mm) REVERT: B 912 GLN cc_start: 0.9035 (pt0) cc_final: 0.8819 (pt0) REVERT: B 979 TYR cc_start: 0.8062 (t80) cc_final: 0.7818 (t80) REVERT: B 1039 MET cc_start: 0.9380 (mmm) cc_final: 0.9139 (mmp) REVERT: B 1132 PHE cc_start: 0.8617 (m-80) cc_final: 0.8327 (m-10) REVERT: B 1146 ARG cc_start: 0.8628 (mtt90) cc_final: 0.7365 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1523 time to fit residues: 76.7118 Evaluate side-chains 229 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 123 optimal weight: 30.0000 chunk 181 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN B 43 GLN B 912 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.113747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083798 restraints weight = 83983.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080545 restraints weight = 56492.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.081131 restraints weight = 54272.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.081438 restraints weight = 39466.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.082011 restraints weight = 36778.815| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22972 Z= 0.100 Angle : 0.547 9.620 31186 Z= 0.268 Chirality : 0.040 0.198 3574 Planarity : 0.003 0.043 3936 Dihedral : 4.287 17.237 3088 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2832 helix: 0.21 (0.13), residues: 1748 sheet: -0.40 (0.38), residues: 162 loop : -1.03 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1316 TYR 0.021 0.001 TYR A 709 PHE 0.022 0.001 PHE B 968 TRP 0.017 0.001 TRP A 260 HIS 0.003 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00205 (22970) covalent geometry : angle 0.54724 (31182) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.32796 ( 4) hydrogen bonds : bond 0.03946 ( 984) hydrogen bonds : angle 4.16858 ( 2874) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.881 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 39 LEU cc_start: 0.8447 (tp) cc_final: 0.7862 (tt) REVERT: A 114 LEU cc_start: 0.9570 (mt) cc_final: 0.9169 (pp) REVERT: A 125 MET cc_start: 0.8713 (ttt) cc_final: 0.8501 (mmm) REVERT: A 242 MET cc_start: 0.8990 (mmm) cc_final: 0.8728 (mmm) REVERT: A 444 ILE cc_start: 0.9139 (mp) cc_final: 0.8805 (tt) REVERT: A 476 LYS cc_start: 0.9267 (tttt) cc_final: 0.9020 (ttpt) REVERT: A 481 MET cc_start: 0.9013 (tpp) cc_final: 0.8379 (tpp) REVERT: A 485 LEU cc_start: 0.9368 (mt) cc_final: 0.8992 (mt) REVERT: A 588 LYS cc_start: 0.8730 (mttt) cc_final: 0.8398 (tptt) REVERT: A 591 GLU cc_start: 0.8844 (pt0) cc_final: 0.8578 (pp20) REVERT: A 746 GLN cc_start: 0.8877 (tp-100) cc_final: 0.8587 (tp-100) REVERT: A 750 MET cc_start: 0.9106 (mmm) cc_final: 0.8663 (mmm) REVERT: A 755 TYR cc_start: 0.8510 (t80) cc_final: 0.8250 (t80) REVERT: A 794 LEU cc_start: 0.9205 (pp) cc_final: 0.8940 (mm) REVERT: A 1024 LEU cc_start: 0.8702 (tp) cc_final: 0.8442 (tt) REVERT: A 1109 ILE cc_start: 0.9607 (mt) cc_final: 0.9319 (tp) REVERT: A 1126 MET cc_start: 0.8769 (tpt) cc_final: 0.8491 (tpp) REVERT: A 1132 PHE cc_start: 0.8484 (m-80) cc_final: 0.8022 (m-10) REVERT: A 1146 ARG cc_start: 0.8666 (mtt90) cc_final: 0.7682 (ttt180) REVERT: B 39 LEU cc_start: 0.8432 (tp) cc_final: 0.7922 (tt) REVERT: B 114 LEU cc_start: 0.9581 (mt) cc_final: 0.9185 (pp) REVERT: B 242 MET cc_start: 0.8902 (mmm) cc_final: 0.8394 (mmm) REVERT: B 375 LEU cc_start: 0.9153 (pp) cc_final: 0.8833 (tp) REVERT: B 444 ILE cc_start: 0.9164 (mp) cc_final: 0.8830 (tt) REVERT: B 476 LYS cc_start: 0.9266 (tttt) cc_final: 0.9020 (ttpt) REVERT: B 481 MET cc_start: 0.9035 (tpp) cc_final: 0.8384 (tpp) REVERT: B 485 LEU cc_start: 0.9377 (mt) cc_final: 0.8992 (mt) REVERT: B 746 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8603 (tp-100) REVERT: B 750 MET cc_start: 0.9111 (mmm) cc_final: 0.8660 (mmm) REVERT: B 755 TYR cc_start: 0.8508 (t80) cc_final: 0.8237 (t80) REVERT: B 794 LEU cc_start: 0.9212 (pp) cc_final: 0.8948 (mm) REVERT: B 1024 LEU cc_start: 0.8708 (tp) cc_final: 0.8455 (tt) REVERT: B 1039 MET cc_start: 0.9447 (mmm) cc_final: 0.9246 (mmp) REVERT: B 1109 ILE cc_start: 0.9613 (mt) cc_final: 0.9313 (tp) REVERT: B 1132 PHE cc_start: 0.8566 (m-80) cc_final: 0.8220 (m-10) REVERT: B 1146 ARG cc_start: 0.8700 (mtt90) cc_final: 0.7719 (ttt180) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1521 time to fit residues: 79.4203 Evaluate side-chains 243 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 261 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 131 optimal weight: 50.0000 chunk 78 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 912 GLN B 43 GLN B 912 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.113141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.084077 restraints weight = 84458.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.081288 restraints weight = 64182.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.082247 restraints weight = 61702.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.082152 restraints weight = 44867.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.082282 restraints weight = 39366.432| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22972 Z= 0.120 Angle : 0.562 12.464 31186 Z= 0.277 Chirality : 0.041 0.145 3574 Planarity : 0.003 0.042 3936 Dihedral : 4.264 20.089 3088 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2832 helix: 0.42 (0.13), residues: 1746 sheet: -0.36 (0.38), residues: 162 loop : -0.86 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 785 TYR 0.018 0.001 TYR A 709 PHE 0.027 0.001 PHE B 968 TRP 0.018 0.001 TRP A 260 HIS 0.002 0.000 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00263 (22970) covalent geometry : angle 0.56177 (31182) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.50553 ( 4) hydrogen bonds : bond 0.03801 ( 984) hydrogen bonds : angle 4.13341 ( 2874) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.778 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 39 LEU cc_start: 0.8452 (tp) cc_final: 0.7825 (tt) REVERT: A 90 PHE cc_start: 0.8864 (m-80) cc_final: 0.8388 (m-10) REVERT: A 114 LEU cc_start: 0.9565 (mt) cc_final: 0.9197 (pp) REVERT: A 155 MET cc_start: 0.9020 (tpp) cc_final: 0.8763 (mmm) REVERT: A 242 MET cc_start: 0.9005 (mmm) cc_final: 0.8163 (mmm) REVERT: A 455 LEU cc_start: 0.9061 (tp) cc_final: 0.8801 (tt) REVERT: A 476 LYS cc_start: 0.9250 (tttt) cc_final: 0.9048 (ttpt) REVERT: A 481 MET cc_start: 0.9002 (tpp) cc_final: 0.8353 (tpp) REVERT: A 485 LEU cc_start: 0.9377 (mt) cc_final: 0.8982 (mt) REVERT: A 746 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8549 (tp-100) REVERT: A 750 MET cc_start: 0.8986 (mmm) cc_final: 0.8560 (mmm) REVERT: A 755 TYR cc_start: 0.8375 (t80) cc_final: 0.8125 (t80) REVERT: A 794 LEU cc_start: 0.9080 (pp) cc_final: 0.8736 (tt) REVERT: A 1109 ILE cc_start: 0.9563 (mt) cc_final: 0.9284 (tp) REVERT: A 1126 MET cc_start: 0.8705 (tpt) cc_final: 0.8443 (tpp) REVERT: A 1132 PHE cc_start: 0.8564 (m-80) cc_final: 0.8100 (m-10) REVERT: A 1146 ARG cc_start: 0.8758 (mtt90) cc_final: 0.7417 (ttt180) REVERT: B 39 LEU cc_start: 0.8419 (tp) cc_final: 0.8207 (tt) REVERT: B 44 LEU cc_start: 0.9645 (mt) cc_final: 0.9410 (pp) REVERT: B 90 PHE cc_start: 0.8879 (m-80) cc_final: 0.8421 (m-10) REVERT: B 114 LEU cc_start: 0.9571 (mt) cc_final: 0.9199 (pp) REVERT: B 125 MET cc_start: 0.8390 (mmm) cc_final: 0.7786 (mmm) REVERT: B 155 MET cc_start: 0.9011 (tpp) cc_final: 0.8754 (mmm) REVERT: B 242 MET cc_start: 0.8889 (mmm) cc_final: 0.8466 (mmm) REVERT: B 375 LEU cc_start: 0.9138 (pp) cc_final: 0.8832 (tp) REVERT: B 476 LYS cc_start: 0.9275 (tttt) cc_final: 0.9059 (ttpt) REVERT: B 481 MET cc_start: 0.8991 (tpp) cc_final: 0.8349 (tpp) REVERT: B 485 LEU cc_start: 0.9378 (mt) cc_final: 0.9023 (mt) REVERT: B 746 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8549 (tp-100) REVERT: B 750 MET cc_start: 0.9002 (mmm) cc_final: 0.8565 (mmm) REVERT: B 755 TYR cc_start: 0.8367 (t80) cc_final: 0.8110 (t80) REVERT: B 794 LEU cc_start: 0.9094 (pp) cc_final: 0.8751 (tt) REVERT: B 1064 MET cc_start: 0.8045 (mmt) cc_final: 0.7789 (mmt) REVERT: B 1109 ILE cc_start: 0.9556 (mt) cc_final: 0.9274 (tp) REVERT: B 1132 PHE cc_start: 0.8499 (m-80) cc_final: 0.8197 (m-10) REVERT: B 1146 ARG cc_start: 0.8770 (mtt90) cc_final: 0.7541 (ttt180) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1466 time to fit residues: 73.1233 Evaluate side-chains 231 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 0.0770 chunk 231 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.113945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.084120 restraints weight = 83337.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081118 restraints weight = 53664.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.081592 restraints weight = 52815.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081918 restraints weight = 38436.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.083648 restraints weight = 35528.144| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 22972 Z= 0.099 Angle : 0.549 12.406 31186 Z= 0.267 Chirality : 0.041 0.273 3574 Planarity : 0.003 0.043 3936 Dihedral : 4.153 19.742 3088 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2832 helix: 0.65 (0.13), residues: 1728 sheet: -0.29 (0.39), residues: 162 loop : -0.73 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1316 TYR 0.019 0.001 TYR A 369 PHE 0.028 0.001 PHE A 90 TRP 0.018 0.001 TRP A 260 HIS 0.003 0.000 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00214 (22970) covalent geometry : angle 0.54917 (31182) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.38146 ( 4) hydrogen bonds : bond 0.03540 ( 984) hydrogen bonds : angle 3.96198 ( 2874) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.885 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: A 39 LEU cc_start: 0.8422 (tp) cc_final: 0.7818 (tt) REVERT: A 90 PHE cc_start: 0.8735 (m-80) cc_final: 0.8341 (m-10) REVERT: A 114 LEU cc_start: 0.9592 (mt) cc_final: 0.9169 (pp) REVERT: A 125 MET cc_start: 0.8422 (mpp) cc_final: 0.7971 (tpt) REVERT: A 155 MET cc_start: 0.9061 (tpp) cc_final: 0.8833 (mmm) REVERT: A 444 ILE cc_start: 0.9261 (mp) cc_final: 0.8975 (tt) REVERT: A 476 LYS cc_start: 0.9292 (tttt) cc_final: 0.9067 (ttpt) REVERT: A 481 MET cc_start: 0.9149 (tpp) cc_final: 0.8513 (tpp) REVERT: A 485 LEU cc_start: 0.9347 (mt) cc_final: 0.9015 (mt) REVERT: A 521 LEU cc_start: 0.9049 (tp) cc_final: 0.8847 (mm) REVERT: A 746 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8589 (tp-100) REVERT: A 750 MET cc_start: 0.9123 (mmm) cc_final: 0.8676 (mmm) REVERT: A 755 TYR cc_start: 0.8532 (t80) cc_final: 0.8282 (t80) REVERT: A 794 LEU cc_start: 0.9258 (pp) cc_final: 0.8961 (tt) REVERT: A 1064 MET cc_start: 0.7819 (mmt) cc_final: 0.7436 (mmt) REVERT: A 1126 MET cc_start: 0.8784 (tpt) cc_final: 0.8470 (tpp) REVERT: A 1132 PHE cc_start: 0.8500 (m-80) cc_final: 0.8041 (m-10) REVERT: A 1146 ARG cc_start: 0.8715 (mtt90) cc_final: 0.7367 (ttt180) REVERT: B 39 LEU cc_start: 0.8472 (tp) cc_final: 0.8036 (tt) REVERT: B 90 PHE cc_start: 0.8920 (m-80) cc_final: 0.8597 (m-10) REVERT: B 114 LEU cc_start: 0.9593 (mt) cc_final: 0.9156 (pp) REVERT: B 125 MET cc_start: 0.8470 (mmm) cc_final: 0.7923 (mmm) REVERT: B 155 MET cc_start: 0.9054 (tpp) cc_final: 0.8830 (mmm) REVERT: B 375 LEU cc_start: 0.9159 (pp) cc_final: 0.8918 (tp) REVERT: B 444 ILE cc_start: 0.9242 (mp) cc_final: 0.8971 (tt) REVERT: B 481 MET cc_start: 0.9125 (tpp) cc_final: 0.8492 (tpp) REVERT: B 485 LEU cc_start: 0.9338 (mt) cc_final: 0.9002 (mt) REVERT: B 746 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8595 (tp-100) REVERT: B 750 MET cc_start: 0.9126 (mmm) cc_final: 0.8678 (mmm) REVERT: B 755 TYR cc_start: 0.8519 (t80) cc_final: 0.8269 (t80) REVERT: B 794 LEU cc_start: 0.9259 (pp) cc_final: 0.8956 (tt) REVERT: B 1024 LEU cc_start: 0.8662 (tp) cc_final: 0.8439 (tt) REVERT: B 1064 MET cc_start: 0.7889 (mmt) cc_final: 0.7599 (mmt) REVERT: B 1126 MET cc_start: 0.8781 (tpt) cc_final: 0.8490 (tpp) REVERT: B 1132 PHE cc_start: 0.8514 (m-80) cc_final: 0.8156 (m-10) REVERT: B 1146 ARG cc_start: 0.8538 (mtt90) cc_final: 0.7374 (ttt180) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.1425 time to fit residues: 73.0974 Evaluate side-chains 237 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 280 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 993 HIS B 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.113398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.083167 restraints weight = 84284.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.080640 restraints weight = 54701.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.081115 restraints weight = 51155.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081374 restraints weight = 38209.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.081929 restraints weight = 35421.779| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22972 Z= 0.114 Angle : 0.559 10.791 31186 Z= 0.272 Chirality : 0.041 0.144 3574 Planarity : 0.003 0.041 3936 Dihedral : 4.120 19.905 3088 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2832 helix: 0.77 (0.13), residues: 1718 sheet: -0.18 (0.39), residues: 162 loop : -0.62 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1316 TYR 0.018 0.001 TYR A 369 PHE 0.018 0.001 PHE A 90 TRP 0.019 0.001 TRP A 260 HIS 0.002 0.000 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00251 (22970) covalent geometry : angle 0.55912 (31182) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.56124 ( 4) hydrogen bonds : bond 0.03535 ( 984) hydrogen bonds : angle 3.99484 ( 2874) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8437 (tp) cc_final: 0.7901 (tt) REVERT: A 90 PHE cc_start: 0.8610 (m-80) cc_final: 0.8200 (m-10) REVERT: A 114 LEU cc_start: 0.9575 (mt) cc_final: 0.9150 (pp) REVERT: A 125 MET cc_start: 0.8414 (mpp) cc_final: 0.7932 (tpp) REVERT: A 155 MET cc_start: 0.9044 (tpp) cc_final: 0.8835 (mmm) REVERT: A 242 MET cc_start: 0.8720 (mmm) cc_final: 0.8033 (mmm) REVERT: A 375 LEU cc_start: 0.9190 (pp) cc_final: 0.8856 (tp) REVERT: A 481 MET cc_start: 0.9106 (tpp) cc_final: 0.8630 (tpp) REVERT: A 485 LEU cc_start: 0.9328 (mt) cc_final: 0.9033 (mt) REVERT: A 588 LYS cc_start: 0.8654 (mttt) cc_final: 0.8184 (tptt) REVERT: A 590 LEU cc_start: 0.9336 (mt) cc_final: 0.8745 (mt) REVERT: A 746 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8043 (tm-30) REVERT: A 750 MET cc_start: 0.9054 (mmm) cc_final: 0.7997 (mmm) REVERT: A 755 TYR cc_start: 0.8434 (t80) cc_final: 0.8229 (t80) REVERT: A 794 LEU cc_start: 0.9158 (pp) cc_final: 0.8837 (tt) REVERT: A 1064 MET cc_start: 0.7968 (mmt) cc_final: 0.7569 (mmt) REVERT: A 1126 MET cc_start: 0.8701 (tpt) cc_final: 0.8462 (tpp) REVERT: A 1132 PHE cc_start: 0.8538 (m-80) cc_final: 0.8097 (m-10) REVERT: A 1146 ARG cc_start: 0.8683 (mtt90) cc_final: 0.7503 (ttt180) REVERT: B 39 LEU cc_start: 0.8455 (tp) cc_final: 0.8104 (tt) REVERT: B 90 PHE cc_start: 0.8763 (m-80) cc_final: 0.8460 (m-10) REVERT: B 114 LEU cc_start: 0.9581 (mt) cc_final: 0.9152 (pp) REVERT: B 125 MET cc_start: 0.8514 (mmm) cc_final: 0.8038 (mmm) REVERT: B 155 MET cc_start: 0.9024 (tpp) cc_final: 0.8808 (mmm) REVERT: B 375 LEU cc_start: 0.9151 (pp) cc_final: 0.8857 (tp) REVERT: B 481 MET cc_start: 0.9058 (tpp) cc_final: 0.8589 (tpp) REVERT: B 485 LEU cc_start: 0.9332 (mt) cc_final: 0.9060 (mt) REVERT: B 532 ILE cc_start: 0.9445 (mm) cc_final: 0.9218 (mm) REVERT: B 588 LYS cc_start: 0.8874 (mttt) cc_final: 0.8423 (tptt) REVERT: B 746 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8046 (tm-30) REVERT: B 750 MET cc_start: 0.9065 (mmm) cc_final: 0.8002 (mmm) REVERT: B 755 TYR cc_start: 0.8465 (t80) cc_final: 0.8250 (t80) REVERT: B 794 LEU cc_start: 0.9166 (pp) cc_final: 0.8845 (tt) REVERT: B 1064 MET cc_start: 0.8032 (mmt) cc_final: 0.7674 (mmt) REVERT: B 1126 MET cc_start: 0.8743 (tpt) cc_final: 0.8504 (tpp) REVERT: B 1132 PHE cc_start: 0.8595 (m-80) cc_final: 0.8285 (m-10) REVERT: B 1146 ARG cc_start: 0.8499 (mtt90) cc_final: 0.7598 (ttt180) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1300 time to fit residues: 64.0989 Evaluate side-chains 225 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 125 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 283 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 202 optimal weight: 40.0000 chunk 98 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 739 ASN A1356 HIS B 43 GLN B 739 ASN B1356 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.112316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.082658 restraints weight = 84390.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.079606 restraints weight = 59349.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.080401 restraints weight = 53834.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080457 restraints weight = 38979.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.080896 restraints weight = 37619.125| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22972 Z= 0.143 Angle : 0.605 11.117 31186 Z= 0.292 Chirality : 0.042 0.144 3574 Planarity : 0.003 0.042 3936 Dihedral : 4.164 19.903 3088 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2832 helix: 0.83 (0.13), residues: 1706 sheet: -0.10 (0.39), residues: 162 loop : -0.52 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1092 TYR 0.023 0.001 TYR A1096 PHE 0.016 0.001 PHE A 90 TRP 0.024 0.001 TRP A 260 HIS 0.004 0.001 HIS B 720 Details of bonding type rmsd covalent geometry : bond 0.00322 (22970) covalent geometry : angle 0.60481 (31182) SS BOND : bond 0.00181 ( 2) SS BOND : angle 0.61328 ( 4) hydrogen bonds : bond 0.03632 ( 984) hydrogen bonds : angle 4.10392 ( 2874) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.946 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: A 39 LEU cc_start: 0.8499 (tp) cc_final: 0.7972 (tt) REVERT: A 90 PHE cc_start: 0.8777 (m-80) cc_final: 0.8132 (m-10) REVERT: A 114 LEU cc_start: 0.9578 (mt) cc_final: 0.9155 (pp) REVERT: A 125 MET cc_start: 0.8470 (mpp) cc_final: 0.7943 (tpp) REVERT: A 242 MET cc_start: 0.8773 (mmm) cc_final: 0.8273 (ttm) REVERT: A 375 LEU cc_start: 0.9193 (pp) cc_final: 0.8857 (tp) REVERT: A 481 MET cc_start: 0.9091 (tpp) cc_final: 0.8413 (tpp) REVERT: A 485 LEU cc_start: 0.9332 (mt) cc_final: 0.8993 (mt) REVERT: A 588 LYS cc_start: 0.8599 (mttt) cc_final: 0.8264 (tptt) REVERT: A 746 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8061 (tm-30) REVERT: A 750 MET cc_start: 0.9081 (mmm) cc_final: 0.8013 (mmm) REVERT: A 794 LEU cc_start: 0.9197 (pp) cc_final: 0.8866 (tt) REVERT: A 1126 MET cc_start: 0.8703 (tpt) cc_final: 0.8472 (tpp) REVERT: A 1132 PHE cc_start: 0.8585 (m-80) cc_final: 0.8207 (m-10) REVERT: A 1137 MET cc_start: 0.8278 (tpp) cc_final: 0.8035 (tpt) REVERT: A 1146 ARG cc_start: 0.8731 (mtt90) cc_final: 0.7783 (ttt180) REVERT: A 1294 GLU cc_start: 0.7189 (mm-30) cc_final: 0.5673 (pp20) REVERT: B 39 LEU cc_start: 0.8495 (tp) cc_final: 0.8107 (tt) REVERT: B 90 PHE cc_start: 0.8936 (m-80) cc_final: 0.8432 (m-10) REVERT: B 114 LEU cc_start: 0.9580 (mt) cc_final: 0.9156 (pp) REVERT: B 125 MET cc_start: 0.8587 (mmm) cc_final: 0.8169 (mmt) REVERT: B 375 LEU cc_start: 0.9182 (pp) cc_final: 0.8891 (tp) REVERT: B 481 MET cc_start: 0.9107 (tpp) cc_final: 0.8431 (tpp) REVERT: B 485 LEU cc_start: 0.9342 (mt) cc_final: 0.9004 (mt) REVERT: B 588 LYS cc_start: 0.8872 (mttt) cc_final: 0.8384 (tptt) REVERT: B 746 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8016 (tm-30) REVERT: B 750 MET cc_start: 0.9062 (mmm) cc_final: 0.7990 (mmm) REVERT: B 1064 MET cc_start: 0.7990 (mmt) cc_final: 0.7548 (mmt) REVERT: B 1126 MET cc_start: 0.8777 (tpt) cc_final: 0.8547 (tpp) REVERT: B 1132 PHE cc_start: 0.8577 (m-80) cc_final: 0.8320 (m-10) REVERT: B 1146 ARG cc_start: 0.8775 (mtt90) cc_final: 0.7795 (ttt180) REVERT: B 1294 GLU cc_start: 0.7188 (mm-30) cc_final: 0.5659 (pp20) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1312 time to fit residues: 63.4540 Evaluate side-chains 218 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 212 optimal weight: 5.9990 chunk 263 optimal weight: 0.0770 chunk 86 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 152 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 205 optimal weight: 0.0870 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 43 GLN B 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.114197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.083668 restraints weight = 83300.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.081551 restraints weight = 53351.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.082362 restraints weight = 45585.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.082650 restraints weight = 34492.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.082754 restraints weight = 32721.106| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22972 Z= 0.098 Angle : 0.574 11.006 31186 Z= 0.273 Chirality : 0.041 0.190 3574 Planarity : 0.003 0.041 3936 Dihedral : 4.046 19.254 3088 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2832 helix: 0.98 (0.13), residues: 1682 sheet: 0.02 (0.40), residues: 162 loop : -0.53 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 589 TYR 0.022 0.001 TYR A1096 PHE 0.016 0.001 PHE B1265 TRP 0.024 0.001 TRP B 241 HIS 0.003 0.000 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00205 (22970) covalent geometry : angle 0.57389 (31182) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.45022 ( 4) hydrogen bonds : bond 0.03378 ( 984) hydrogen bonds : angle 3.89408 ( 2874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.27 seconds wall clock time: 63 minutes 57.90 seconds (3837.90 seconds total)