Starting phenix.real_space_refine on Fri Aug 7 06:33:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lt_77144/08_2026/13lt_77144.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lt_77144/08_2026/13lt_77144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13lt_77144/08_2026/13lt_77144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lt_77144/08_2026/13lt_77144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13lt_77144/08_2026/13lt_77144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lt_77144/08_2026/13lt_77144.map" } resolution = 3.25 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= 0.009 sd= 0.029 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 120 5.16 5 C 12714 2.51 5 N 3168 2.21 5 O 3422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19430 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4725 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 11, 'TRANS': 565} Chain breaks: 2 Chain: "B" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4834 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 17, 'TRANS': 573} Chain breaks: 3 Chain: "C" Number of atoms: 4725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4725 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 11, 'TRANS': 565} Chain breaks: 2 Chain: "D" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4834 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 17, 'TRANS': 573} Chain breaks: 3 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.95, per 1000 atoms: 0.20 Number of scatterers: 19430 At special positions: 0 Unit cell: (126.549, 132.435, 121.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 6 15.00 O 3422 8.00 N 3168 7.00 C 12714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.55 Conformation dependent library (CDL) restraints added in 770.2 milliseconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 60.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.728A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 145 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.850A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.581A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.581A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.779A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.583A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.556A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.576A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 removed outlier: 3.671A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.565A pdb=" N THR A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.708A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.658A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.772A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 434 removed outlier: 4.106A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 461 removed outlier: 3.631A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.614A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 541 removed outlier: 4.091A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.512A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.778A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.705A pdb=" N MET A 578 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 603 removed outlier: 3.529A pdb=" N ASP A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 594 " --> pdb=" O PHE A 590 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 676 removed outlier: 3.568A pdb=" N PHE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 671 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 688 Processing helix chain 'A' and resid 689 through 707 removed outlier: 3.869A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 738 through 748 Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.722A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.567A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.770A pdb=" N ARG B 149 " --> pdb=" O CYS B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 153 through 162 removed outlier: 4.146A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.511A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 229 through 238 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.901A pdb=" N GLY B 258 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.527A pdb=" N LEU B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.559A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 329 removed outlier: 3.613A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.514A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.638A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 431 removed outlier: 4.255A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 447 removed outlier: 3.704A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.821A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.710A pdb=" N LEU B 485 " --> pdb=" O TRP B 481 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 542 removed outlier: 3.844A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.909A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 removed outlier: 3.551A pdb=" N LEU B 563 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.755A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 598 removed outlier: 3.864A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.704A pdb=" N LEU B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.545A pdb=" N MET B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 removed outlier: 4.041A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 703 removed outlier: 3.701A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'C' and resid 119 through 129 removed outlier: 3.668A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 Processing helix chain 'C' and resid 153 through 162 removed outlier: 3.850A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.582A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.580A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.780A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 228 through 238 removed outlier: 3.583A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.557A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.577A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.672A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 removed outlier: 3.565A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.708A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.658A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.772A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 removed outlier: 4.106A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 461 removed outlier: 3.631A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.615A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 541 removed outlier: 4.091A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.513A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.777A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 578 removed outlier: 3.705A pdb=" N MET C 578 " --> pdb=" O TYR C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 603 removed outlier: 3.529A pdb=" N ASP C 586 " --> pdb=" O VAL C 582 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 598 " --> pdb=" O TYR C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 676 removed outlier: 3.568A pdb=" N PHE C 654 " --> pdb=" O TYR C 650 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 663 " --> pdb=" O ILE C 659 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 665 " --> pdb=" O TYR C 661 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 688 Processing helix chain 'C' and resid 689 through 707 removed outlier: 3.869A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 738 through 748 Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.722A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.568A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.770A pdb=" N ARG D 149 " --> pdb=" O CYS D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 153 through 162 removed outlier: 4.146A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.510A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 229 through 238 Processing helix chain 'D' and resid 254 through 258 removed outlier: 3.901A pdb=" N GLY D 258 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.528A pdb=" N LEU D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.559A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.613A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.514A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.639A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 431 removed outlier: 4.254A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 447 removed outlier: 3.704A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.821A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 457 " --> pdb=" O ILE D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.710A pdb=" N LEU D 485 " --> pdb=" O TRP D 481 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 542 removed outlier: 3.843A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.908A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.552A pdb=" N LEU D 563 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 583 Processing helix chain 'D' and resid 583 through 591 removed outlier: 3.754A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 598 removed outlier: 3.864A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 660 removed outlier: 3.704A pdb=" N LEU D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 676 removed outlier: 3.544A pdb=" N MET D 672 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 removed outlier: 4.041A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 703 removed outlier: 3.701A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 381 removed outlier: 6.880A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 729 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 73 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 3.520A pdb=" N LEU B 389 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 729 " --> pdb=" O CYS B 721 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 381 removed outlier: 6.880A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 729 " --> pdb=" O CYS C 721 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG D 73 " --> pdb=" O LYS C 722 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 3.520A pdb=" N LEU D 389 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 729 " --> pdb=" O CYS D 721 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2124 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: 3.17 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3260 1.32 - 1.44: 5195 1.44 - 1.57: 11177 1.57 - 1.69: 12 1.69 - 1.81: 202 Bond restraints: 19846 Sorted by residual: bond pdb=" CA SER C 387 " pdb=" CB SER C 387 " ideal model delta sigma weight residual 1.528 1.461 0.066 1.39e-02 5.18e+03 2.26e+01 bond pdb=" CA SER A 387 " pdb=" CB SER A 387 " ideal model delta sigma weight residual 1.528 1.462 0.065 1.39e-02 5.18e+03 2.21e+01 bond pdb=" CA SER B 387 " pdb=" CB SER B 387 " ideal model delta sigma weight residual 1.529 1.478 0.050 1.34e-02 5.57e+03 1.41e+01 bond pdb=" CA SER D 387 " pdb=" CB SER D 387 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.34e-02 5.57e+03 1.40e+01 bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.337 1.378 -0.041 1.11e-02 8.12e+03 1.39e+01 ... (remaining 19841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 25030 2.08 - 4.15: 1459 4.15 - 6.23: 217 6.23 - 8.31: 56 8.31 - 10.39: 28 Bond angle restraints: 26790 Sorted by residual: angle pdb=" C ASP D 153 " pdb=" N VAL D 154 " pdb=" CA VAL D 154 " ideal model delta sigma weight residual 120.24 125.00 -4.76 6.30e-01 2.52e+00 5.70e+01 angle pdb=" C ASP B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta sigma weight residual 120.24 124.99 -4.75 6.30e-01 2.52e+00 5.67e+01 angle pdb=" CA ASP B 151 " pdb=" C ASP B 151 " pdb=" N GLU B 152 " ideal model delta sigma weight residual 118.43 125.11 -6.68 1.33e+00 5.65e-01 2.53e+01 angle pdb=" CA ASP D 151 " pdb=" C ASP D 151 " pdb=" N GLU D 152 " ideal model delta sigma weight residual 118.43 125.09 -6.66 1.33e+00 5.65e-01 2.51e+01 angle pdb=" C GLU C 725 " pdb=" N ASP C 726 " pdb=" CA ASP C 726 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 ... (remaining 26785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.60: 11667 34.60 - 69.20: 184 69.20 - 103.80: 23 103.80 - 138.40: 10 138.40 - 173.00: 6 Dihedral angle restraints: 11890 sinusoidal: 4992 harmonic: 6898 Sorted by residual: dihedral pdb=" CA LEU B 422 " pdb=" C LEU B 422 " pdb=" N GLU B 423 " pdb=" CA GLU B 423 " ideal model delta harmonic sigma weight residual -180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA LEU D 422 " pdb=" C LEU D 422 " pdb=" N GLU D 423 " pdb=" CA GLU D 423 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU C 422 " pdb=" C LEU C 422 " pdb=" N GLU C 423 " pdb=" CA GLU C 423 " ideal model delta harmonic sigma weight residual 180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 11887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2369 0.058 - 0.116: 562 0.116 - 0.174: 66 0.174 - 0.231: 6 0.231 - 0.289: 19 Chirality restraints: 3022 Sorted by residual: chirality pdb=" CG LEU C 676 " pdb=" CB LEU C 676 " pdb=" CD1 LEU C 676 " pdb=" CD2 LEU C 676 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU A 676 " pdb=" CB LEU A 676 " pdb=" CD1 LEU A 676 " pdb=" CD2 LEU A 676 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CG LEU D 535 " pdb=" CB LEU D 535 " pdb=" CD1 LEU D 535 " pdb=" CD2 LEU D 535 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 3019 not shown) Planarity restraints: 3300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " -0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO B 181 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO D 181 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 574 " 0.014 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C MET D 574 " -0.046 2.00e-02 2.50e+03 pdb=" O MET D 574 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR D 575 " 0.015 2.00e-02 2.50e+03 ... (remaining 3297 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6066 2.83 - 3.35: 17117 3.35 - 3.87: 29430 3.87 - 4.38: 35764 4.38 - 4.90: 60194 Nonbonded interactions: 148571 Sorted by model distance: nonbonded pdb=" OD1 ASN D 298 " pdb=" ND1 HIS D 301 " model vdw 2.314 3.120 nonbonded pdb=" OD1 ASN B 298 " pdb=" ND1 HIS B 301 " model vdw 2.314 3.120 nonbonded pdb=" O THR C 680 " pdb=" OG1 THR C 680 " model vdw 2.320 3.040 nonbonded pdb=" O THR C 167 " pdb=" OG1 THR C 209 " model vdw 2.336 3.040 nonbonded pdb=" OD1 ASN C 298 " pdb=" ND1 HIS C 301 " model vdw 2.336 3.120 ... (remaining 148566 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.320 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.850 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.007 0.087 19846 Z= 0.323 Angle : 1.154 10.387 26790 Z= 0.684 Chirality : 0.052 0.289 3022 Planarity : 0.006 0.069 3300 Dihedral : 14.028 172.996 7402 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.54 % Favored : 91.03 % Rotamer: Outliers : 0.77 % Allowed : 5.38 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.45 (0.11), residues: 2308 helix: -4.70 (0.05), residues: 1394 sheet: -2.76 (0.44), residues: 100 loop : -3.24 (0.18), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 416 TYR 0.025 0.002 TYR A 594 PHE 0.040 0.003 PHE D 445 TRP 0.033 0.002 TRP D 692 HIS 0.011 0.002 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.32 (19846) covalent geometry : angle 1.15398 / 0.68 (26790) hydrogen bonds : bond 0.32682 / 21.09 ( 724) hydrogen bonds : angle 9.61857 / 6.62 ( 2124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 376 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7762 (pp20) cc_final: 0.7225 (pp20) REVERT: A 323 MET cc_start: 0.8537 (ttm) cc_final: 0.8129 (ttm) REVERT: A 484 LEU cc_start: 0.4719 (OUTLIER) cc_final: 0.3785 (tm) REVERT: A 488 MET cc_start: 0.6501 (mpm) cc_final: 0.5712 (tpp) REVERT: A 491 LEU cc_start: 0.7596 (tp) cc_final: 0.7349 (tp) REVERT: A 495 MET cc_start: 0.7189 (mmm) cc_final: 0.6935 (tmm) REVERT: A 555 MET cc_start: 0.6497 (mtm) cc_final: 0.6023 (mpp) REVERT: A 563 LEU cc_start: 0.8342 (mt) cc_final: 0.8103 (pp) REVERT: A 572 MET cc_start: 0.1565 (mtm) cc_final: 0.0191 (ptt) REVERT: B 140 VAL cc_start: 0.9211 (t) cc_final: 0.8310 (t) REVERT: B 320 MET cc_start: 0.9136 (mmt) cc_final: 0.8899 (mmt) REVERT: B 657 LEU cc_start: 0.8254 (mm) cc_final: 0.7698 (tt) REVERT: B 743 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8233 (pttp) REVERT: C 211 GLU cc_start: 0.7686 (pp20) cc_final: 0.7264 (pp20) REVERT: C 323 MET cc_start: 0.8396 (ttm) cc_final: 0.8005 (ttm) REVERT: C 484 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4140 (tm) REVERT: C 488 MET cc_start: 0.6610 (mpm) cc_final: 0.5698 (tpp) REVERT: C 491 LEU cc_start: 0.7597 (tp) cc_final: 0.7322 (tp) REVERT: C 493 TRP cc_start: 0.6414 (t-100) cc_final: 0.6173 (t-100) REVERT: C 495 MET cc_start: 0.7149 (mmm) cc_final: 0.6806 (tmm) REVERT: C 572 MET cc_start: 0.1495 (mtm) cc_final: 0.0146 (ptt) REVERT: D 140 VAL cc_start: 0.9270 (t) cc_final: 0.8487 (t) REVERT: D 657 LEU cc_start: 0.8182 (mm) cc_final: 0.7610 (tt) REVERT: D 743 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8257 (pttp) outliers start: 16 outliers final: 4 residues processed: 390 average time/residue: 0.1486 time to fit residues: 86.3172 Evaluate side-chains 229 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 223 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 576 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 284 HIS A 286 GLN A 412 ASN A 417 HIS A 585 HIS A 683 ASN A 750 ASN B 74 GLN B 220 ASN B 251 ASN B 410 ASN B 570 GLN B 683 ASN B 750 ASN C 220 ASN C 284 HIS C 286 GLN C 412 ASN C 417 HIS C 585 HIS C 683 ASN C 750 ASN D 74 GLN D 220 ASN D 251 ASN D 410 ASN D 570 GLN D 683 ASN D 750 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111891 restraints weight = 28117.318| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.01 r_work: 0.3206 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19846 Z= 0.124 Angle : 0.629 11.897 26790 Z= 0.323 Chirality : 0.038 0.149 3022 Planarity : 0.004 0.056 3300 Dihedral : 14.269 169.956 2808 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 2.02 % Allowed : 8.12 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.14), residues: 2308 helix: -2.85 (0.10), residues: 1420 sheet: -2.07 (0.47), residues: 100 loop : -3.06 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 202 TYR 0.017 0.001 TYR C 547 PHE 0.018 0.001 PHE C 538 TRP 0.025 0.001 TRP D 692 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19846) covalent geometry : angle 0.62870 / 0.32 (26790) hydrogen bonds : bond 0.04225 / 2.72 ( 724) hydrogen bonds : angle 4.59561 / 3.17 ( 2124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.494 Fit side-chains REVERT: A 211 GLU cc_start: 0.8408 (pp20) cc_final: 0.7379 (pp20) REVERT: A 323 MET cc_start: 0.8321 (ttm) cc_final: 0.7945 (ttm) REVERT: A 336 THR cc_start: 0.8811 (m) cc_final: 0.8344 (p) REVERT: A 488 MET cc_start: 0.6772 (mpm) cc_final: 0.6030 (tpp) REVERT: A 495 MET cc_start: 0.7548 (mmm) cc_final: 0.6977 (tmm) REVERT: A 563 LEU cc_start: 0.8506 (mt) cc_final: 0.8148 (pp) REVERT: A 572 MET cc_start: 0.1048 (mtm) cc_final: -0.0167 (ptt) REVERT: A 601 PHE cc_start: 0.7775 (m-10) cc_final: 0.7403 (m-80) REVERT: B 484 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7926 (mp) REVERT: B 544 TYR cc_start: 0.6046 (m-10) cc_final: 0.5534 (m-80) REVERT: B 657 LEU cc_start: 0.7798 (mm) cc_final: 0.7262 (tt) REVERT: B 692 TRP cc_start: 0.4550 (t60) cc_final: 0.4305 (t60) REVERT: B 743 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8251 (pttp) REVERT: C 211 GLU cc_start: 0.8462 (pp20) cc_final: 0.7443 (pp20) REVERT: C 323 MET cc_start: 0.8336 (ttm) cc_final: 0.8044 (ttm) REVERT: C 336 THR cc_start: 0.8802 (m) cc_final: 0.8324 (p) REVERT: C 488 MET cc_start: 0.6735 (mpm) cc_final: 0.6049 (tpp) REVERT: C 495 MET cc_start: 0.7522 (mmm) cc_final: 0.6906 (tmm) REVERT: C 572 MET cc_start: 0.0816 (mtm) cc_final: -0.0380 (ptt) REVERT: C 601 PHE cc_start: 0.7747 (m-10) cc_final: 0.7469 (m-80) REVERT: D 173 MET cc_start: 0.8436 (mtm) cc_final: 0.8201 (mtm) REVERT: D 484 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7893 (mp) REVERT: D 656 PHE cc_start: 0.7142 (t80) cc_final: 0.6887 (t80) REVERT: D 657 LEU cc_start: 0.7818 (mm) cc_final: 0.7254 (tt) REVERT: D 743 LYS cc_start: 0.8925 (ptpt) cc_final: 0.8272 (pttp) outliers start: 42 outliers final: 16 residues processed: 259 average time/residue: 0.1261 time to fit residues: 51.0805 Evaluate side-chains 218 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS A 735 ASN B 514 GLN C 585 HIS C 735 ASN D 514 GLN D 695 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.159154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110668 restraints weight = 28487.738| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.95 r_work: 0.3164 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19846 Z= 0.141 Angle : 0.602 9.800 26790 Z= 0.302 Chirality : 0.038 0.145 3022 Planarity : 0.004 0.051 3300 Dihedral : 13.537 170.100 2802 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.76 % Favored : 92.07 % Rotamer: Outliers : 1.59 % Allowed : 10.82 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.16), residues: 2308 helix: -1.80 (0.12), residues: 1444 sheet: -1.82 (0.45), residues: 100 loop : -2.89 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.014 0.001 TYR D 208 PHE 0.016 0.001 PHE D 445 TRP 0.018 0.001 TRP D 692 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (19846) covalent geometry : angle 0.60215 / 0.30 (26790) hydrogen bonds : bond 0.03525 / 2.26 ( 724) hydrogen bonds : angle 4.04552 / 2.80 ( 2124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.712 Fit side-chains REVERT: A 211 GLU cc_start: 0.8476 (pp20) cc_final: 0.7602 (pp20) REVERT: A 286 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: A 323 MET cc_start: 0.8467 (ttm) cc_final: 0.8100 (ttm) REVERT: A 336 THR cc_start: 0.8837 (m) cc_final: 0.8346 (p) REVERT: A 488 MET cc_start: 0.6661 (mpm) cc_final: 0.6089 (tpp) REVERT: A 495 MET cc_start: 0.7623 (mmm) cc_final: 0.7168 (tmm) REVERT: A 514 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5647 (mp10) REVERT: A 563 LEU cc_start: 0.8472 (mt) cc_final: 0.8111 (pp) REVERT: A 572 MET cc_start: 0.1225 (mtm) cc_final: -0.0047 (ptt) REVERT: A 601 PHE cc_start: 0.7828 (m-10) cc_final: 0.7448 (m-80) REVERT: B 460 TYR cc_start: 0.7117 (t80) cc_final: 0.6405 (t80) REVERT: B 484 LEU cc_start: 0.8598 (tt) cc_final: 0.7966 (mp) REVERT: B 657 LEU cc_start: 0.7840 (mm) cc_final: 0.7290 (tt) REVERT: B 743 LYS cc_start: 0.8922 (ptpt) cc_final: 0.8326 (pttp) REVERT: C 211 GLU cc_start: 0.8496 (pp20) cc_final: 0.7585 (pp20) REVERT: C 323 MET cc_start: 0.8442 (ttm) cc_final: 0.8137 (ttm) REVERT: C 336 THR cc_start: 0.8824 (m) cc_final: 0.8330 (p) REVERT: C 488 MET cc_start: 0.6732 (mpm) cc_final: 0.6127 (tpp) REVERT: C 495 MET cc_start: 0.7559 (mmm) cc_final: 0.6967 (tmm) REVERT: C 514 GLN cc_start: 0.5965 (OUTLIER) cc_final: 0.5607 (mp10) REVERT: C 572 MET cc_start: 0.1086 (mtm) cc_final: -0.0099 (ptt) REVERT: C 701 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7430 (mt) REVERT: D 188 ARG cc_start: 0.8688 (mtt-85) cc_final: 0.8194 (ttm-80) REVERT: D 484 LEU cc_start: 0.8459 (tt) cc_final: 0.7808 (mp) REVERT: D 488 MET cc_start: 0.8251 (tpp) cc_final: 0.8046 (tpp) REVERT: D 524 PHE cc_start: 0.7655 (m-80) cc_final: 0.7049 (t80) REVERT: D 555 MET cc_start: 0.6346 (tpp) cc_final: 0.5893 (mmp) REVERT: D 657 LEU cc_start: 0.7885 (mm) cc_final: 0.7347 (tt) REVERT: D 743 LYS cc_start: 0.8931 (ptpt) cc_final: 0.8369 (pttp) outliers start: 33 outliers final: 17 residues processed: 231 average time/residue: 0.1266 time to fit residues: 46.8457 Evaluate side-chains 225 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 126 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 167 optimal weight: 0.2980 chunk 34 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 483 GLN A 585 HIS C 286 GLN C 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.160616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108937 restraints weight = 28514.075| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.84 r_work: 0.3188 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19846 Z= 0.111 Angle : 0.542 7.846 26790 Z= 0.273 Chirality : 0.037 0.139 3022 Planarity : 0.003 0.049 3300 Dihedral : 12.842 165.450 2802 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.85 % Rotamer: Outliers : 2.31 % Allowed : 11.06 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.17), residues: 2308 helix: -1.03 (0.13), residues: 1462 sheet: -1.45 (0.49), residues: 100 loop : -2.74 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.021 0.001 TYR B 540 PHE 0.016 0.001 PHE C 592 TRP 0.013 0.001 TRP A 692 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (19846) covalent geometry : angle 0.54185 / 0.27 (26790) hydrogen bonds : bond 0.02755 / 1.77 ( 724) hydrogen bonds : angle 3.61573 / 2.49 ( 2124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8421 (pp20) cc_final: 0.7473 (pp20) REVERT: A 336 THR cc_start: 0.8803 (m) cc_final: 0.8286 (p) REVERT: A 488 MET cc_start: 0.6582 (mpm) cc_final: 0.6198 (tpp) REVERT: A 495 MET cc_start: 0.7642 (mmm) cc_final: 0.7314 (tmm) REVERT: A 514 GLN cc_start: 0.5777 (OUTLIER) cc_final: 0.5366 (mp10) REVERT: A 562 MET cc_start: 0.8132 (mmt) cc_final: 0.7900 (tpp) REVERT: A 563 LEU cc_start: 0.8486 (mt) cc_final: 0.8126 (pp) REVERT: A 572 MET cc_start: 0.1088 (mtm) cc_final: -0.0099 (ptt) REVERT: B 188 ARG cc_start: 0.8759 (mtt-85) cc_final: 0.8392 (ttm-80) REVERT: B 290 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8673 (t) REVERT: B 484 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7895 (mp) REVERT: B 541 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.5363 (mm) REVERT: B 544 TYR cc_start: 0.6135 (m-10) cc_final: 0.5701 (m-80) REVERT: B 657 LEU cc_start: 0.7683 (mm) cc_final: 0.7185 (tt) REVERT: B 717 MET cc_start: 0.8240 (mtp) cc_final: 0.7893 (mtt) REVERT: B 743 LYS cc_start: 0.8912 (ptpt) cc_final: 0.8329 (pttp) REVERT: C 195 GLU cc_start: 0.9260 (tt0) cc_final: 0.9056 (tm-30) REVERT: C 211 GLU cc_start: 0.8454 (pp20) cc_final: 0.7487 (pp20) REVERT: C 336 THR cc_start: 0.8800 (m) cc_final: 0.8284 (p) REVERT: C 488 MET cc_start: 0.6658 (mpm) cc_final: 0.6310 (tpp) REVERT: C 495 MET cc_start: 0.7561 (mmm) cc_final: 0.7181 (tmm) REVERT: C 514 GLN cc_start: 0.5763 (OUTLIER) cc_final: 0.5352 (mp10) REVERT: C 572 MET cc_start: 0.1015 (mtm) cc_final: -0.0099 (ptt) REVERT: C 601 PHE cc_start: 0.7771 (m-10) cc_final: 0.7394 (m-80) REVERT: D 188 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.8247 (ttm-80) REVERT: D 484 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7922 (mp) REVERT: D 541 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5549 (mm) REVERT: D 555 MET cc_start: 0.6178 (tpp) cc_final: 0.5798 (mmp) REVERT: D 657 LEU cc_start: 0.7771 (mm) cc_final: 0.7181 (tt) REVERT: D 717 MET cc_start: 0.8243 (mtp) cc_final: 0.7850 (mtt) REVERT: D 743 LYS cc_start: 0.8935 (ptpt) cc_final: 0.8312 (pttp) outliers start: 48 outliers final: 25 residues processed: 258 average time/residue: 0.1256 time to fit residues: 51.1324 Evaluate side-chains 233 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 201 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 585 HIS C 286 GLN C 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108287 restraints weight = 28144.629| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.02 r_work: 0.3165 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19846 Z= 0.127 Angle : 0.550 9.334 26790 Z= 0.275 Chirality : 0.038 0.187 3022 Planarity : 0.003 0.047 3300 Dihedral : 12.528 158.727 2802 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.24 % Favored : 92.59 % Rotamer: Outliers : 2.26 % Allowed : 11.78 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.17), residues: 2308 helix: -0.66 (0.14), residues: 1466 sheet: -1.37 (0.49), residues: 100 loop : -2.75 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.024 0.001 TYR B 540 PHE 0.016 0.001 PHE C 592 TRP 0.011 0.001 TRP C 692 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (19846) covalent geometry : angle 0.55017 / 0.28 (26790) hydrogen bonds : bond 0.02725 / 1.74 ( 724) hydrogen bonds : angle 3.53382 / 2.43 ( 2124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.618 Fit side-chains REVERT: A 211 GLU cc_start: 0.8477 (pp20) cc_final: 0.7595 (pp20) REVERT: A 336 THR cc_start: 0.8793 (m) cc_final: 0.8261 (p) REVERT: A 488 MET cc_start: 0.6600 (mpm) cc_final: 0.6309 (tpp) REVERT: A 493 TRP cc_start: 0.6057 (m100) cc_final: 0.5815 (m100) REVERT: A 495 MET cc_start: 0.7549 (mmm) cc_final: 0.7236 (tmm) REVERT: A 514 GLN cc_start: 0.5771 (OUTLIER) cc_final: 0.5391 (mp10) REVERT: A 562 MET cc_start: 0.8112 (mmt) cc_final: 0.7851 (tpp) REVERT: A 563 LEU cc_start: 0.8502 (mt) cc_final: 0.8140 (pp) REVERT: A 572 MET cc_start: 0.1233 (mtm) cc_final: 0.0060 (ptt) REVERT: A 601 PHE cc_start: 0.7738 (m-80) cc_final: 0.7273 (m-80) REVERT: A 685 SER cc_start: 0.7333 (t) cc_final: 0.6938 (p) REVERT: B 188 ARG cc_start: 0.8755 (mtt-85) cc_final: 0.8438 (ttm-80) REVERT: B 290 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8682 (t) REVERT: B 322 ASP cc_start: 0.8848 (t0) cc_final: 0.8588 (t70) REVERT: B 484 LEU cc_start: 0.8568 (tt) cc_final: 0.7962 (mp) REVERT: B 541 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5397 (mm) REVERT: B 572 MET cc_start: 0.5672 (tpt) cc_final: 0.5255 (tpt) REVERT: B 657 LEU cc_start: 0.7725 (mm) cc_final: 0.7231 (tt) REVERT: B 717 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7936 (mtt) REVERT: B 743 LYS cc_start: 0.8913 (ptpt) cc_final: 0.8331 (pttp) REVERT: C 211 GLU cc_start: 0.8492 (pp20) cc_final: 0.7580 (pp20) REVERT: C 320 MET cc_start: 0.8561 (mtp) cc_final: 0.7884 (mmm) REVERT: C 336 THR cc_start: 0.8783 (m) cc_final: 0.8250 (p) REVERT: C 488 MET cc_start: 0.6800 (mpm) cc_final: 0.6009 (tpp) REVERT: C 493 TRP cc_start: 0.6173 (m100) cc_final: 0.5914 (m100) REVERT: C 495 MET cc_start: 0.7628 (mmm) cc_final: 0.7280 (tmm) REVERT: C 514 GLN cc_start: 0.5733 (OUTLIER) cc_final: 0.5314 (mp10) REVERT: C 572 MET cc_start: 0.1119 (mtm) cc_final: -0.0065 (ptt) REVERT: C 601 PHE cc_start: 0.7726 (m-80) cc_final: 0.7320 (m-80) REVERT: D 188 ARG cc_start: 0.8723 (mtt-85) cc_final: 0.8338 (ttm-80) REVERT: D 322 ASP cc_start: 0.8813 (t0) cc_final: 0.8538 (t70) REVERT: D 484 LEU cc_start: 0.8486 (tt) cc_final: 0.7915 (mp) REVERT: D 524 PHE cc_start: 0.7707 (m-80) cc_final: 0.7074 (t80) REVERT: D 555 MET cc_start: 0.6249 (tpp) cc_final: 0.5883 (mmp) REVERT: D 657 LEU cc_start: 0.7704 (mm) cc_final: 0.7139 (tt) REVERT: D 717 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7899 (mtt) REVERT: D 743 LYS cc_start: 0.8928 (ptpt) cc_final: 0.8293 (pttp) outliers start: 47 outliers final: 25 residues processed: 249 average time/residue: 0.1213 time to fit residues: 48.3336 Evaluate side-chains 239 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Chi-restraints excluded: chain D residue 717 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 115 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN C 286 GLN D 695 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106743 restraints weight = 28030.845| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.76 r_work: 0.3146 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19846 Z= 0.147 Angle : 0.560 10.269 26790 Z= 0.279 Chirality : 0.038 0.212 3022 Planarity : 0.003 0.048 3300 Dihedral : 12.329 147.272 2802 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.29 % Rotamer: Outliers : 2.40 % Allowed : 12.26 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.17), residues: 2308 helix: -0.46 (0.14), residues: 1468 sheet: -1.13 (0.53), residues: 86 loop : -2.64 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 696 TYR 0.022 0.001 TYR B 540 PHE 0.016 0.001 PHE C 592 TRP 0.012 0.001 TRP A 692 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (19846) covalent geometry : angle 0.55991 / 0.28 (26790) hydrogen bonds : bond 0.02796 / 1.80 ( 724) hydrogen bonds : angle 3.54558 / 2.43 ( 2124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8513 (pp20) cc_final: 0.7572 (pp20) REVERT: A 336 THR cc_start: 0.8768 (m) cc_final: 0.8223 (p) REVERT: A 488 MET cc_start: 0.6658 (mpm) cc_final: 0.6070 (tpp) REVERT: A 495 MET cc_start: 0.7570 (mmm) cc_final: 0.7354 (tmm) REVERT: A 514 GLN cc_start: 0.5773 (OUTLIER) cc_final: 0.5386 (mp10) REVERT: A 563 LEU cc_start: 0.8454 (mt) cc_final: 0.8108 (pp) REVERT: A 572 MET cc_start: 0.1348 (mtm) cc_final: 0.0118 (ptt) REVERT: A 601 PHE cc_start: 0.7750 (m-80) cc_final: 0.7276 (m-80) REVERT: A 685 SER cc_start: 0.7276 (t) cc_final: 0.6854 (p) REVERT: B 138 LEU cc_start: 0.8302 (mt) cc_final: 0.7941 (mt) REVERT: B 188 ARG cc_start: 0.8750 (mtt-85) cc_final: 0.8446 (ttm-80) REVERT: B 322 ASP cc_start: 0.8829 (t0) cc_final: 0.8544 (t70) REVERT: B 484 LEU cc_start: 0.8538 (tt) cc_final: 0.7932 (mp) REVERT: B 541 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.5357 (mm) REVERT: B 544 TYR cc_start: 0.5841 (m-10) cc_final: 0.5606 (m-80) REVERT: B 572 MET cc_start: 0.6058 (tpt) cc_final: 0.5751 (tpt) REVERT: B 657 LEU cc_start: 0.7637 (mm) cc_final: 0.7097 (tt) REVERT: B 717 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: B 743 LYS cc_start: 0.8923 (ptpt) cc_final: 0.8253 (pttp) REVERT: C 211 GLU cc_start: 0.8454 (pp20) cc_final: 0.7495 (pp20) REVERT: C 336 THR cc_start: 0.8766 (m) cc_final: 0.8220 (p) REVERT: C 488 MET cc_start: 0.6909 (mpm) cc_final: 0.6146 (tpp) REVERT: C 493 TRP cc_start: 0.6147 (m100) cc_final: 0.5940 (m100) REVERT: C 495 MET cc_start: 0.7615 (mmm) cc_final: 0.7353 (tmm) REVERT: C 514 GLN cc_start: 0.5755 (OUTLIER) cc_final: 0.5373 (mp10) REVERT: C 572 MET cc_start: 0.1113 (mtm) cc_final: 0.0149 (ptt) REVERT: C 601 PHE cc_start: 0.7713 (m-80) cc_final: 0.7331 (m-80) REVERT: C 685 SER cc_start: 0.7318 (t) cc_final: 0.6920 (p) REVERT: D 188 ARG cc_start: 0.8729 (mtt-85) cc_final: 0.8389 (ttm-80) REVERT: D 322 ASP cc_start: 0.8876 (t0) cc_final: 0.8619 (t70) REVERT: D 484 LEU cc_start: 0.8478 (tt) cc_final: 0.7920 (mp) REVERT: D 519 ASP cc_start: 0.7005 (m-30) cc_final: 0.6554 (m-30) REVERT: D 555 MET cc_start: 0.6222 (tpp) cc_final: 0.5859 (mmp) REVERT: D 657 LEU cc_start: 0.7602 (mm) cc_final: 0.7004 (tt) REVERT: D 717 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8113 (mtp) REVERT: D 743 LYS cc_start: 0.8938 (ptpt) cc_final: 0.8296 (pttp) outliers start: 50 outliers final: 31 residues processed: 246 average time/residue: 0.1156 time to fit residues: 45.8988 Evaluate side-chains 243 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Chi-restraints excluded: chain D residue 717 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 189 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN C 286 GLN C 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108959 restraints weight = 28152.730| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.77 r_work: 0.3188 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19846 Z= 0.098 Angle : 0.526 10.600 26790 Z= 0.261 Chirality : 0.037 0.228 3022 Planarity : 0.003 0.046 3300 Dihedral : 11.955 139.760 2802 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.21 % Allowed : 12.26 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2308 helix: -0.21 (0.14), residues: 1468 sheet: -0.87 (0.54), residues: 86 loop : -2.51 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 462 TYR 0.023 0.001 TYR C 460 PHE 0.012 0.001 PHE C 538 TRP 0.015 0.001 TRP D 692 HIS 0.004 0.001 HIS C 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (19846) covalent geometry : angle 0.52575 / 0.26 (26790) hydrogen bonds : bond 0.02385 / 1.52 ( 724) hydrogen bonds : angle 3.37787 / 2.32 ( 2124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.521 Fit side-chains REVERT: A 211 GLU cc_start: 0.8463 (pp20) cc_final: 0.7572 (pp20) REVERT: A 336 THR cc_start: 0.8787 (m) cc_final: 0.8248 (p) REVERT: A 488 MET cc_start: 0.6665 (mpm) cc_final: 0.6102 (tpp) REVERT: A 514 GLN cc_start: 0.5560 (OUTLIER) cc_final: 0.5202 (mp10) REVERT: A 563 LEU cc_start: 0.8483 (mt) cc_final: 0.8144 (pp) REVERT: A 572 MET cc_start: 0.1438 (mtm) cc_final: 0.0420 (ptt) REVERT: A 601 PHE cc_start: 0.7715 (m-80) cc_final: 0.7226 (m-80) REVERT: A 685 SER cc_start: 0.7318 (t) cc_final: 0.6911 (p) REVERT: B 138 LEU cc_start: 0.8301 (mt) cc_final: 0.7949 (mt) REVERT: B 188 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8471 (ttm-80) REVERT: B 322 ASP cc_start: 0.8866 (t0) cc_final: 0.8607 (t70) REVERT: B 484 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7961 (mp) REVERT: B 541 LEU cc_start: 0.5613 (OUTLIER) cc_final: 0.5372 (mm) REVERT: B 657 LEU cc_start: 0.7555 (mm) cc_final: 0.7004 (tt) REVERT: B 696 ARG cc_start: 0.7027 (tpp80) cc_final: 0.6683 (mmm-85) REVERT: B 743 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8344 (pttp) REVERT: C 211 GLU cc_start: 0.8487 (pp20) cc_final: 0.7577 (pp20) REVERT: C 336 THR cc_start: 0.8784 (m) cc_final: 0.8248 (p) REVERT: C 488 MET cc_start: 0.6881 (mpm) cc_final: 0.6192 (tpp) REVERT: C 495 MET cc_start: 0.7648 (mmm) cc_final: 0.7404 (tmm) REVERT: C 514 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5266 (mp10) REVERT: C 572 MET cc_start: 0.1248 (mtm) cc_final: 0.0267 (ptt) REVERT: C 601 PHE cc_start: 0.7635 (m-80) cc_final: 0.7274 (m-80) REVERT: C 685 SER cc_start: 0.7352 (t) cc_final: 0.6953 (p) REVERT: D 157 PHE cc_start: 0.8781 (t80) cc_final: 0.8537 (t80) REVERT: D 188 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8438 (ttm-80) REVERT: D 322 ASP cc_start: 0.8872 (t0) cc_final: 0.8598 (t70) REVERT: D 484 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7958 (mp) REVERT: D 555 MET cc_start: 0.6226 (tpp) cc_final: 0.5900 (mmp) REVERT: D 657 LEU cc_start: 0.7613 (mm) cc_final: 0.7026 (tt) REVERT: D 692 TRP cc_start: 0.4714 (t60) cc_final: 0.4387 (t60) REVERT: D 743 LYS cc_start: 0.8966 (ptpt) cc_final: 0.8376 (pttp) outliers start: 46 outliers final: 28 residues processed: 244 average time/residue: 0.1200 time to fit residues: 46.5129 Evaluate side-chains 235 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 226 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 224 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN C 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.159224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110245 restraints weight = 28169.835| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.22 r_work: 0.3164 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19846 Z= 0.117 Angle : 0.555 12.555 26790 Z= 0.272 Chirality : 0.039 0.373 3022 Planarity : 0.003 0.046 3300 Dihedral : 11.673 138.463 2802 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.12 % Allowed : 12.60 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.38 (0.18), residues: 2308 helix: -0.11 (0.14), residues: 1474 sheet: -0.78 (0.56), residues: 84 loop : -2.47 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.025 0.001 TYR B 540 PHE 0.018 0.001 PHE C 592 TRP 0.016 0.001 TRP D 692 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (19846) covalent geometry : angle 0.55535 / 0.27 (26790) hydrogen bonds : bond 0.02518 / 1.62 ( 724) hydrogen bonds : angle 3.40722 / 2.34 ( 2124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.750 Fit side-chains REVERT: A 211 GLU cc_start: 0.8529 (pp20) cc_final: 0.7600 (pp20) REVERT: A 336 THR cc_start: 0.8784 (m) cc_final: 0.8244 (p) REVERT: A 488 MET cc_start: 0.6745 (mpm) cc_final: 0.6192 (tpp) REVERT: A 514 GLN cc_start: 0.5573 (OUTLIER) cc_final: 0.5191 (mp10) REVERT: A 563 LEU cc_start: 0.8478 (mt) cc_final: 0.8133 (pp) REVERT: A 572 MET cc_start: 0.1433 (mtm) cc_final: 0.0380 (ptt) REVERT: A 601 PHE cc_start: 0.7792 (m-80) cc_final: 0.7267 (m-80) REVERT: A 685 SER cc_start: 0.7334 (t) cc_final: 0.6913 (p) REVERT: B 138 LEU cc_start: 0.8302 (mt) cc_final: 0.7944 (mt) REVERT: B 188 ARG cc_start: 0.8737 (mtt-85) cc_final: 0.8473 (ttm-80) REVERT: B 322 ASP cc_start: 0.8876 (t0) cc_final: 0.8624 (t70) REVERT: B 484 LEU cc_start: 0.8513 (tt) cc_final: 0.7923 (mp) REVERT: B 541 LEU cc_start: 0.5636 (OUTLIER) cc_final: 0.5385 (mm) REVERT: B 657 LEU cc_start: 0.7581 (mm) cc_final: 0.7028 (tt) REVERT: B 743 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8337 (pttp) REVERT: C 211 GLU cc_start: 0.8487 (pp20) cc_final: 0.7526 (pp20) REVERT: C 336 THR cc_start: 0.8786 (m) cc_final: 0.8243 (p) REVERT: C 488 MET cc_start: 0.6876 (mpm) cc_final: 0.6224 (tpp) REVERT: C 495 MET cc_start: 0.7665 (mmm) cc_final: 0.7414 (tmm) REVERT: C 514 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5241 (mp10) REVERT: C 601 PHE cc_start: 0.7611 (m-80) cc_final: 0.7271 (m-80) REVERT: C 685 SER cc_start: 0.7317 (t) cc_final: 0.6900 (p) REVERT: D 157 PHE cc_start: 0.8759 (t80) cc_final: 0.8545 (t80) REVERT: D 188 ARG cc_start: 0.8736 (mtt-85) cc_final: 0.8439 (ttm-80) REVERT: D 322 ASP cc_start: 0.8881 (t0) cc_final: 0.8620 (t70) REVERT: D 484 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7941 (mp) REVERT: D 555 MET cc_start: 0.6214 (tpp) cc_final: 0.5885 (mmp) REVERT: D 657 LEU cc_start: 0.7486 (mm) cc_final: 0.6939 (tt) REVERT: D 692 TRP cc_start: 0.4603 (t60) cc_final: 0.4320 (t60) REVERT: D 743 LYS cc_start: 0.8968 (ptpt) cc_final: 0.8369 (pttp) outliers start: 44 outliers final: 32 residues processed: 243 average time/residue: 0.1260 time to fit residues: 48.7160 Evaluate side-chains 238 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 43 optimal weight: 0.0470 chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN C 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.159153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110343 restraints weight = 27954.344| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.03 r_work: 0.3173 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19846 Z= 0.116 Angle : 0.564 12.838 26790 Z= 0.275 Chirality : 0.038 0.318 3022 Planarity : 0.003 0.046 3300 Dihedral : 11.364 137.503 2802 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.12 % Allowed : 12.74 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2308 helix: -0.01 (0.14), residues: 1474 sheet: -0.57 (0.58), residues: 84 loop : -2.40 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 693 TYR 0.024 0.001 TYR B 540 PHE 0.012 0.001 PHE B 445 TRP 0.017 0.001 TRP D 692 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (19846) covalent geometry : angle 0.56435 / 0.28 (26790) hydrogen bonds : bond 0.02525 / 1.62 ( 724) hydrogen bonds : angle 3.41792 / 2.34 ( 2124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8472 (pp20) cc_final: 0.7576 (pp20) REVERT: A 336 THR cc_start: 0.8783 (m) cc_final: 0.8243 (p) REVERT: A 488 MET cc_start: 0.6770 (mpm) cc_final: 0.6253 (tpp) REVERT: A 514 GLN cc_start: 0.5621 (OUTLIER) cc_final: 0.5229 (mp10) REVERT: A 563 LEU cc_start: 0.8474 (mt) cc_final: 0.8130 (pp) REVERT: A 572 MET cc_start: 0.1361 (mtm) cc_final: 0.0324 (ptt) REVERT: A 601 PHE cc_start: 0.7779 (m-80) cc_final: 0.7231 (m-80) REVERT: A 685 SER cc_start: 0.7372 (t) cc_final: 0.6949 (p) REVERT: B 138 LEU cc_start: 0.8310 (mt) cc_final: 0.7940 (mt) REVERT: B 188 ARG cc_start: 0.8729 (mtt-85) cc_final: 0.8516 (ttm-80) REVERT: B 322 ASP cc_start: 0.8877 (t0) cc_final: 0.8621 (t70) REVERT: B 484 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 541 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5363 (mm) REVERT: B 657 LEU cc_start: 0.7501 (mm) cc_final: 0.6943 (tt) REVERT: B 743 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8354 (pttp) REVERT: C 211 GLU cc_start: 0.8547 (pp20) cc_final: 0.7604 (pp20) REVERT: C 336 THR cc_start: 0.8785 (m) cc_final: 0.8245 (p) REVERT: C 488 MET cc_start: 0.6898 (mpm) cc_final: 0.6250 (tpp) REVERT: C 495 MET cc_start: 0.7671 (mmm) cc_final: 0.7435 (tmm) REVERT: C 514 GLN cc_start: 0.5582 (OUTLIER) cc_final: 0.5185 (mp10) REVERT: C 601 PHE cc_start: 0.7587 (m-80) cc_final: 0.7243 (m-80) REVERT: C 685 SER cc_start: 0.7326 (t) cc_final: 0.6908 (p) REVERT: D 60 SER cc_start: 0.8317 (m) cc_final: 0.7479 (p) REVERT: D 157 PHE cc_start: 0.8789 (t80) cc_final: 0.8564 (t80) REVERT: D 188 ARG cc_start: 0.8745 (mtt-85) cc_final: 0.8476 (ttm-80) REVERT: D 322 ASP cc_start: 0.8881 (t0) cc_final: 0.8616 (t70) REVERT: D 417 HIS cc_start: 0.7333 (p-80) cc_final: 0.7032 (t70) REVERT: D 484 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7886 (mp) REVERT: D 555 MET cc_start: 0.6227 (tpp) cc_final: 0.5911 (mmp) REVERT: D 657 LEU cc_start: 0.7472 (mm) cc_final: 0.6927 (tt) REVERT: D 692 TRP cc_start: 0.4617 (t60) cc_final: 0.4396 (t60) REVERT: D 743 LYS cc_start: 0.8974 (ptpt) cc_final: 0.8385 (pttp) outliers start: 44 outliers final: 35 residues processed: 245 average time/residue: 0.1150 time to fit residues: 45.0315 Evaluate side-chains 246 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 215 optimal weight: 0.0020 chunk 222 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN C 286 GLN C 430 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109937 restraints weight = 28000.780| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.75 r_work: 0.3203 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19846 Z= 0.093 Angle : 0.549 13.134 26790 Z= 0.267 Chirality : 0.038 0.295 3022 Planarity : 0.003 0.046 3300 Dihedral : 10.926 135.941 2802 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.92 % Allowed : 13.08 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2308 helix: 0.15 (0.14), residues: 1472 sheet: -0.37 (0.60), residues: 84 loop : -2.37 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 693 TYR 0.023 0.001 TYR B 540 PHE 0.019 0.001 PHE C 592 TRP 0.015 0.001 TRP D 692 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (19846) covalent geometry : angle 0.54909 / 0.27 (26790) hydrogen bonds : bond 0.02280 / 1.46 ( 724) hydrogen bonds : angle 3.32925 / 2.27 ( 2124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8510 (pp20) cc_final: 0.7595 (pp20) REVERT: A 336 THR cc_start: 0.8796 (m) cc_final: 0.8265 (p) REVERT: A 488 MET cc_start: 0.6819 (mpm) cc_final: 0.6338 (tpp) REVERT: A 514 GLN cc_start: 0.5493 (OUTLIER) cc_final: 0.5141 (tm-30) REVERT: A 563 LEU cc_start: 0.8433 (mt) cc_final: 0.8018 (pp) REVERT: A 572 MET cc_start: 0.1103 (mtm) cc_final: 0.0103 (ptt) REVERT: A 601 PHE cc_start: 0.7695 (m-80) cc_final: 0.7178 (m-80) REVERT: A 685 SER cc_start: 0.7384 (t) cc_final: 0.6960 (p) REVERT: A 717 MET cc_start: 0.7631 (ttm) cc_final: 0.7201 (pmm) REVERT: B 68 MET cc_start: 0.8849 (ttm) cc_final: 0.8452 (mtt) REVERT: B 138 LEU cc_start: 0.8320 (mt) cc_final: 0.7967 (mt) REVERT: B 417 HIS cc_start: 0.7303 (p-80) cc_final: 0.6986 (t70) REVERT: B 484 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 541 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5358 (mm) REVERT: B 594 TYR cc_start: 0.5952 (OUTLIER) cc_final: 0.4609 (t80) REVERT: B 657 LEU cc_start: 0.7436 (mm) cc_final: 0.6927 (tt) REVERT: B 743 LYS cc_start: 0.8950 (ptpt) cc_final: 0.8367 (pttp) REVERT: C 211 GLU cc_start: 0.8516 (pp20) cc_final: 0.7579 (pp20) REVERT: C 336 THR cc_start: 0.8792 (m) cc_final: 0.8263 (p) REVERT: C 488 MET cc_start: 0.6920 (mpm) cc_final: 0.6386 (tpp) REVERT: C 495 MET cc_start: 0.7666 (mmm) cc_final: 0.7425 (tmm) REVERT: C 514 GLN cc_start: 0.5317 (OUTLIER) cc_final: 0.4971 (tm-30) REVERT: C 601 PHE cc_start: 0.7447 (m-80) cc_final: 0.7121 (m-80) REVERT: C 685 SER cc_start: 0.7375 (t) cc_final: 0.6950 (p) REVERT: C 717 MET cc_start: 0.7528 (ttm) cc_final: 0.7236 (ptp) REVERT: D 60 SER cc_start: 0.8243 (m) cc_final: 0.7430 (p) REVERT: D 138 LEU cc_start: 0.8272 (mt) cc_final: 0.7898 (mt) REVERT: D 157 PHE cc_start: 0.8798 (t80) cc_final: 0.8574 (t80) REVERT: D 322 ASP cc_start: 0.8889 (t0) cc_final: 0.8615 (t70) REVERT: D 417 HIS cc_start: 0.7316 (p-80) cc_final: 0.7017 (t70) REVERT: D 484 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7900 (mp) REVERT: D 555 MET cc_start: 0.6384 (tpp) cc_final: 0.6091 (mmp) REVERT: D 657 LEU cc_start: 0.7416 (mm) cc_final: 0.6951 (tt) REVERT: D 743 LYS cc_start: 0.8966 (ptpt) cc_final: 0.8401 (pttp) outliers start: 40 outliers final: 33 residues processed: 249 average time/residue: 0.1104 time to fit residues: 44.0290 Evaluate side-chains 246 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 594 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 594 TYR Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 40 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 HIS A 286 GLN C 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109523 restraints weight = 28107.984| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.13 r_work: 0.3168 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19846 Z= 0.128 Angle : 0.580 13.197 26790 Z= 0.282 Chirality : 0.039 0.292 3022 Planarity : 0.003 0.071 3300 Dihedral : 10.787 133.767 2802 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.12 % Allowed : 13.17 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2308 helix: 0.13 (0.14), residues: 1472 sheet: -0.28 (0.61), residues: 84 loop : -2.34 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 188 TYR 0.024 0.001 TYR B 540 PHE 0.017 0.001 PHE C 538 TRP 0.016 0.001 TRP B 692 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (19846) covalent geometry : angle 0.57950 / 0.28 (26790) hydrogen bonds : bond 0.02555 / 1.64 ( 724) hydrogen bonds : angle 3.40173 / 2.32 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4420.20 seconds wall clock time: 76 minutes 17.99 seconds (4577.99 seconds total)