Starting phenix.real_space_refine on Thu Feb 5 16:31:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vim_65093/02_2026/9vim_65093.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vim_65093/02_2026/9vim_65093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vim_65093/02_2026/9vim_65093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vim_65093/02_2026/9vim_65093.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vim_65093/02_2026/9vim_65093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vim_65093/02_2026/9vim_65093.map" } resolution = 3.41 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 12042 2.51 5 N 3039 2.21 5 O 3213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18404 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 4931 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 23, 'TRANS': 635} Chain breaks: 2 Chain: "B" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4551 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 2 Chain: "C" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4459 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 20, 'TRANS': 580} Chain breaks: 2 Chain: "D" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4459 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 20, 'TRANS': 580} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'URE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.22 Number of scatterers: 18404 At special positions: 0 Unit cell: (120, 163.2, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 3213 8.00 N 3039 7.00 C 12042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 28 " distance=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS B 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 28 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 28 " distance=2.03 Simple disulfide: pdb=" SG CYS D 272 " - pdb=" SG CYS D 283 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4438 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 0 sheets defined 70.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 42 through 52 removed outlier: 4.114A pdb=" N GLY A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.854A pdb=" N PHE A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.669A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 117 removed outlier: 3.654A pdb=" N ALA A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.524A pdb=" N ARG A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 167 through 197 removed outlier: 3.833A pdb=" N ALA A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.606A pdb=" N LEU A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.853A pdb=" N GLY A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 247 removed outlier: 3.634A pdb=" N VAL A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.755A pdb=" N ASP A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.863A pdb=" N SER A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.831A pdb=" N ILE A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.982A pdb=" N TRP A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.561A pdb=" N GLY A 343 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.753A pdb=" N LEU A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.658A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.623A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 removed outlier: 3.985A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 removed outlier: 3.911A pdb=" N ARG A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 462 removed outlier: 3.562A pdb=" N LEU A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.509A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.792A pdb=" N VAL A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 516 removed outlier: 3.782A pdb=" N VAL A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 4.009A pdb=" N TYR A 520 " --> pdb=" O ALA A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.797A pdb=" N GLY A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 547 through 554 Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.847A pdb=" N HIS A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.573A pdb=" N TRP A 595 " --> pdb=" O HIS A 591 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 596' Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.911A pdb=" N PHE A 603 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 616 removed outlier: 3.609A pdb=" N VAL A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 639 removed outlier: 3.694A pdb=" N THR A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET A 628 " --> pdb=" O GLY A 624 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 Processing helix chain 'A' and resid 652 through 664 removed outlier: 3.635A pdb=" N LYS A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 687 removed outlier: 3.687A pdb=" N ARG A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 680 " --> pdb=" O MET A 676 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET A 687 " --> pdb=" O ILE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 700 removed outlier: 4.047A pdb=" N GLU A 691 " --> pdb=" O MET A 687 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.102A pdb=" N GLY B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 72 removed outlier: 3.670A pdb=" N PHE B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 removed outlier: 4.903A pdb=" N TRP B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 127 through 147 removed outlier: 3.994A pdb=" N ILE B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 166 through 196 removed outlier: 3.917A pdb=" N CYS B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 removed outlier: 4.405A pdb=" N VAL B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.093A pdb=" N SER B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.942A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 299 through 319 removed outlier: 3.580A pdb=" N PHE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 327 Processing helix chain 'B' and resid 331 through 364 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 382 through 387 removed outlier: 4.147A pdb=" N MET B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 404 removed outlier: 3.626A pdb=" N VAL B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.642A pdb=" N TYR B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 451 removed outlier: 3.614A pdb=" N CYS B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.724A pdb=" N LEU B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.555A pdb=" N LEU B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.648A pdb=" N LEU B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 516 removed outlier: 3.794A pdb=" N ALA B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B 516 " --> pdb=" O TRP B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 556 removed outlier: 3.841A pdb=" N MET B 534 " --> pdb=" O ARG B 530 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 537 " --> pdb=" O PRO B 533 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 639 Processing helix chain 'B' and resid 646 through 652 Processing helix chain 'B' and resid 652 through 665 removed outlier: 3.790A pdb=" N CYS B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 684 removed outlier: 3.631A pdb=" N TYR B 670 " --> pdb=" O ASN B 666 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 675 " --> pdb=" O GLU B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 701 removed outlier: 3.756A pdb=" N GLU B 691 " --> pdb=" O MET B 687 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 692 " --> pdb=" O PRO B 688 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N MET B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 698 " --> pdb=" O TYR B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 removed outlier: 4.028A pdb=" N GLY C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 72 removed outlier: 3.520A pdb=" N PHE C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.662A pdb=" N SER C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 100' Processing helix chain 'C' and resid 109 through 118 removed outlier: 3.736A pdb=" N ALA C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 127 through 147 removed outlier: 3.704A pdb=" N ILE C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 removed outlier: 4.130A pdb=" N ARG C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 196 removed outlier: 4.367A pdb=" N CYS C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 removed outlier: 4.585A pdb=" N VAL C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 247 removed outlier: 3.827A pdb=" N SER C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 239 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 removed outlier: 3.826A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS C 259 " --> pdb=" O PRO C 255 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 299 through 319 removed outlier: 3.647A pdb=" N PHE C 305 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN C 309 " --> pdb=" O PHE C 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 327 Processing helix chain 'C' and resid 331 through 364 Proline residue: C 350 - end of helix removed outlier: 3.638A pdb=" N LEU C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 removed outlier: 3.715A pdb=" N ALA C 383 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 404 removed outlier: 3.562A pdb=" N VAL C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 402 " --> pdb=" O MET C 398 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 420 Processing helix chain 'C' and resid 434 through 458 removed outlier: 3.856A pdb=" N GLY C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 453 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 476 removed outlier: 3.749A pdb=" N LEU C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY C 473 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 475 " --> pdb=" O ALA C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.750A pdb=" N LEU C 487 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 516 removed outlier: 3.935A pdb=" N ALA C 497 " --> pdb=" O ASN C 493 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 516 " --> pdb=" O TRP C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 547 removed outlier: 3.705A pdb=" N MET C 534 " --> pdb=" O ARG C 530 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 537 " --> pdb=" O PRO C 533 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 544 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 639 Processing helix chain 'C' and resid 646 through 652 Processing helix chain 'C' and resid 652 through 665 removed outlier: 3.644A pdb=" N CYS C 660 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 684 removed outlier: 3.829A pdb=" N GLU C 675 " --> pdb=" O GLU C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 694 removed outlier: 3.640A pdb=" N GLU C 691 " --> pdb=" O MET C 687 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C 692 " --> pdb=" O PRO C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 701 removed outlier: 3.835A pdb=" N GLN C 698 " --> pdb=" O TYR C 694 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 701 " --> pdb=" O MET C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 removed outlier: 4.083A pdb=" N GLY D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 72 removed outlier: 3.621A pdb=" N PHE D 60 " --> pdb=" O PHE D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.676A pdb=" N SER D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 109 through 118 removed outlier: 3.699A pdb=" N ALA D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 127 through 147 removed outlier: 3.725A pdb=" N ILE D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 134 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 145 " --> pdb=" O ILE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 161 removed outlier: 3.893A pdb=" N ARG D 158 " --> pdb=" O CYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 187 removed outlier: 3.509A pdb=" N PHE D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 196 removed outlier: 3.630A pdb=" N VAL D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 218 removed outlier: 3.573A pdb=" N GLY D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 246 removed outlier: 3.702A pdb=" N SER D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 239 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.771A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS D 259 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 299 through 319 removed outlier: 3.583A pdb=" N PHE D 305 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE D 307 " --> pdb=" O LEU D 303 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN D 309 " --> pdb=" O PHE D 305 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 316 " --> pdb=" O GLY D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 327 Processing helix chain 'D' and resid 331 through 364 removed outlier: 3.548A pdb=" N LYS D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 369 through 375 removed outlier: 4.047A pdb=" N ALA D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 4.094A pdb=" N ALA D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR D 384 " --> pdb=" O ALA D 380 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 386 " --> pdb=" O THR D 382 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 404 removed outlier: 3.875A pdb=" N ALA D 402 " --> pdb=" O MET D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 420 removed outlier: 3.628A pdb=" N TYR D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 458 removed outlier: 3.550A pdb=" N CYS D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 456 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 476 removed outlier: 3.705A pdb=" N LEU D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 470 " --> pdb=" O GLY D 466 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY D 473 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.797A pdb=" N LEU D 487 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 516 removed outlier: 3.896A pdb=" N ALA D 497 " --> pdb=" O ASN D 493 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 516 " --> pdb=" O TRP D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 547 removed outlier: 3.804A pdb=" N MET D 534 " --> pdb=" O ARG D 530 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 544 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY D 545 " --> pdb=" O SER D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 639 Processing helix chain 'D' and resid 646 through 652 Processing helix chain 'D' and resid 652 through 665 removed outlier: 3.736A pdb=" N CYS D 660 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 684 removed outlier: 3.637A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 675 " --> pdb=" O GLU D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 701 removed outlier: 3.620A pdb=" N GLU D 691 " --> pdb=" O MET D 687 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 692 " --> pdb=" O PRO D 688 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN D 695 " --> pdb=" O GLU D 691 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 698 " --> pdb=" O TYR D 694 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2880 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: 3.39 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2873 1.32 - 1.45: 5246 1.45 - 1.58: 10542 1.58 - 1.70: 0 1.70 - 1.83: 174 Bond restraints: 18835 Sorted by residual: bond pdb=" CA ARG A 158 " pdb=" C ARG A 158 " ideal model delta sigma weight residual 1.524 1.449 0.075 1.24e-02 6.50e+03 3.66e+01 bond pdb=" CA GLU D 661 " pdb=" C GLU D 661 " ideal model delta sigma weight residual 1.524 1.448 0.075 1.29e-02 6.01e+03 3.42e+01 bond pdb=" CA GLU C 661 " pdb=" C GLU C 661 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.27e-02 6.20e+03 2.33e+01 bond pdb=" CA GLY D 662 " pdb=" C GLY D 662 " ideal model delta sigma weight residual 1.516 1.466 0.050 1.09e-02 8.42e+03 2.09e+01 bond pdb=" C VAL D 659 " pdb=" O VAL D 659 " ideal model delta sigma weight residual 1.236 1.288 -0.052 1.35e-02 5.49e+03 1.47e+01 ... (remaining 18830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 25178 2.23 - 4.46: 439 4.46 - 6.69: 70 6.69 - 8.92: 12 8.92 - 11.15: 5 Bond angle restraints: 25704 Sorted by residual: angle pdb=" N ARG A 158 " pdb=" CA ARG A 158 " pdb=" C ARG A 158 " ideal model delta sigma weight residual 111.03 101.39 9.64 1.11e+00 8.12e-01 7.54e+01 angle pdb=" N MET B 663 " pdb=" CA MET B 663 " pdb=" C MET B 663 " ideal model delta sigma weight residual 111.24 122.39 -11.15 1.29e+00 6.01e-01 7.47e+01 angle pdb=" N MET D 663 " pdb=" CA MET D 663 " pdb=" C MET D 663 " ideal model delta sigma weight residual 112.23 122.81 -10.58 1.26e+00 6.30e-01 7.04e+01 angle pdb=" N ALA A 159 " pdb=" CA ALA A 159 " pdb=" C ALA A 159 " ideal model delta sigma weight residual 109.96 98.91 11.05 1.49e+00 4.50e-01 5.50e+01 angle pdb=" N MET C 663 " pdb=" CA MET C 663 " pdb=" C MET C 663 " ideal model delta sigma weight residual 112.89 121.14 -8.25 1.24e+00 6.50e-01 4.43e+01 ... (remaining 25699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 9827 17.50 - 35.01: 814 35.01 - 52.51: 121 52.51 - 70.01: 20 70.01 - 87.52: 10 Dihedral angle restraints: 10792 sinusoidal: 3806 harmonic: 6986 Sorted by residual: dihedral pdb=" CB CYS A 272 " pdb=" SG CYS A 272 " pdb=" SG CYS A 283 " pdb=" CB CYS A 283 " ideal model delta sinusoidal sigma weight residual 93.00 31.24 61.76 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CA VAL A 518 " pdb=" C VAL A 518 " pdb=" N GLN A 519 " pdb=" CA GLN A 519 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA TRP A 489 " pdb=" C TRP A 489 " pdb=" N ARG A 490 " pdb=" CA ARG A 490 " ideal model delta harmonic sigma weight residual -180.00 -157.04 -22.96 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 10789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2895 0.082 - 0.164: 170 0.164 - 0.246: 1 0.246 - 0.329: 2 0.329 - 0.411: 2 Chirality restraints: 3070 Sorted by residual: chirality pdb=" CA MET D 663 " pdb=" N MET D 663 " pdb=" C MET D 663 " pdb=" CB MET D 663 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA TRP A 161 " pdb=" N TRP A 161 " pdb=" C TRP A 161 " pdb=" CB TRP A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA MET C 663 " pdb=" N MET C 663 " pdb=" C MET C 663 " pdb=" CB MET C 663 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 3067 not shown) Planarity restraints: 3158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 349 " 0.059 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO D 350 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 350 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 350 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 349 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO B 350 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 350 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 350 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 349 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO C 350 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 350 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 350 " -0.048 5.00e-02 4.00e+02 ... (remaining 3155 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 181 2.63 - 3.20: 17299 3.20 - 3.76: 27838 3.76 - 4.33: 38315 4.33 - 4.90: 60618 Nonbonded interactions: 144251 Sorted by model distance: nonbonded pdb=" O ALA B 330 " pdb=" OG1 THR B 335 " model vdw 2.061 3.040 nonbonded pdb=" O ALA D 330 " pdb=" OG1 THR D 335 " model vdw 2.128 3.040 nonbonded pdb=" O ALA C 330 " pdb=" OG1 THR C 335 " model vdw 2.152 3.040 nonbonded pdb=" OD1 ASN B 289 " pdb=" OG SER B 299 " model vdw 2.165 3.040 nonbonded pdb=" O VAL B 40 " pdb=" NZ LYS B 389 " model vdw 2.202 3.120 ... (remaining 144246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 73 or resid 93 through 547 or resid 622 through \ 701)) selection = (chain 'B' and (resid 8 through 547 or resid 622 through 701)) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.650 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.050 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.004 0.075 18843 Z= 0.218 Angle : 0.724 11.152 25720 Z= 0.414 Chirality : 0.044 0.411 3070 Planarity : 0.005 0.088 3158 Dihedral : 13.203 87.517 6330 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.88 % Favored : 90.04 % Rotamer: Outliers : 0.21 % Allowed : 0.37 % Favored : 99.42 % 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: -2.79 (0.16), residues: 2450 helix: -1.30 (0.13), residues: 1664 sheet: None (None), residues: 0 loop : -2.84 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 594 TYR 0.017 0.001 TYR B 339 PHE 0.027 0.001 PHE B 305 TRP 0.031 0.002 TRP B 489 HIS 0.006 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00388 (18835) covalent geometry : angle 0.72376 (25704) SS BOND : bond 0.00147 ( 8) SS BOND : angle 1.08137 ( 16) hydrogen bonds : bond 0.25041 ( 970) hydrogen bonds : angle 7.84262 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 460 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8328 (tt) cc_final: 0.8062 (tt) REVERT: A 49 VAL cc_start: 0.8132 (t) cc_final: 0.7928 (m) REVERT: A 57 PHE cc_start: 0.7977 (t80) cc_final: 0.7695 (t80) REVERT: A 69 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8377 (tttp) REVERT: A 127 SER cc_start: 0.8169 (m) cc_final: 0.7768 (t) REVERT: A 245 VAL cc_start: 0.8357 (t) cc_final: 0.8010 (p) REVERT: A 328 ILE cc_start: 0.8504 (mm) cc_final: 0.8233 (mt) REVERT: A 450 LEU cc_start: 0.8184 (tp) cc_final: 0.7977 (tt) REVERT: A 451 MET cc_start: 0.8264 (mmp) cc_final: 0.7569 (mmp) REVERT: A 593 LYS cc_start: 0.7259 (mtmt) cc_final: 0.7030 (mtmt) REVERT: A 658 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8163 (ttmm) REVERT: A 691 GLU cc_start: 0.7201 (tp30) cc_final: 0.6811 (tp30) REVERT: A 692 GLU cc_start: 0.7354 (mp0) cc_final: 0.6925 (mp0) REVERT: B 56 PHE cc_start: 0.7809 (t80) cc_final: 0.7558 (t80) REVERT: B 69 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7794 (ttmm) REVERT: B 138 VAL cc_start: 0.8035 (t) cc_final: 0.7778 (m) REVERT: B 139 MET cc_start: 0.6981 (ttm) cc_final: 0.6563 (ttm) REVERT: B 142 GLU cc_start: 0.7646 (tp30) cc_final: 0.7360 (tp30) REVERT: B 324 TRP cc_start: 0.8418 (m100) cc_final: 0.7594 (m100) REVERT: B 352 SER cc_start: 0.7465 (m) cc_final: 0.7254 (t) REVERT: B 421 ASP cc_start: 0.7124 (t0) cc_final: 0.6801 (t0) REVERT: B 458 LEU cc_start: 0.8318 (mt) cc_final: 0.8084 (mt) REVERT: B 520 TYR cc_start: 0.7435 (m-80) cc_final: 0.7224 (m-80) REVERT: B 628 MET cc_start: 0.5913 (mmp) cc_final: 0.5578 (mmp) REVERT: B 661 GLU cc_start: 0.6879 (tp30) cc_final: 0.6518 (tp30) REVERT: B 681 LYS cc_start: 0.8355 (mttt) cc_final: 0.8019 (mtpp) REVERT: B 695 GLN cc_start: 0.8515 (mm110) cc_final: 0.7995 (mm110) REVERT: B 697 MET cc_start: 0.8149 (mmt) cc_final: 0.7943 (mmm) REVERT: B 700 GLU cc_start: 0.7967 (tp30) cc_final: 0.7748 (tp30) REVERT: C 70 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7908 (ttt90) REVERT: C 96 VAL cc_start: 0.8557 (m) cc_final: 0.8281 (t) REVERT: C 123 PHE cc_start: 0.8137 (t80) cc_final: 0.7761 (t80) REVERT: C 191 VAL cc_start: 0.8509 (p) cc_final: 0.8183 (t) REVERT: C 212 VAL cc_start: 0.8298 (p) cc_final: 0.7882 (t) REVERT: C 214 TYR cc_start: 0.7788 (t80) cc_final: 0.7548 (t80) REVERT: C 394 LEU cc_start: 0.7957 (mt) cc_final: 0.7630 (mm) REVERT: C 465 LEU cc_start: 0.8087 (tp) cc_final: 0.6648 (mt) REVERT: C 467 TRP cc_start: 0.7405 (t60) cc_final: 0.6801 (t60) REVERT: C 632 ILE cc_start: 0.7247 (tp) cc_final: 0.7042 (tp) REVERT: C 656 ILE cc_start: 0.8637 (pt) cc_final: 0.8382 (mt) REVERT: C 666 ASN cc_start: 0.8309 (p0) cc_final: 0.7989 (p0) REVERT: C 683 ILE cc_start: 0.8078 (mt) cc_final: 0.6639 (tp) REVERT: D 65 VAL cc_start: 0.7888 (p) cc_final: 0.7627 (t) REVERT: D 139 MET cc_start: 0.7061 (ttm) cc_final: 0.6832 (ttm) REVERT: D 148 PRO cc_start: 0.8798 (Cg_endo) cc_final: 0.8509 (Cg_exo) REVERT: D 169 PHE cc_start: 0.7897 (m-80) cc_final: 0.7501 (m-80) REVERT: D 206 LEU cc_start: 0.7863 (mt) cc_final: 0.7648 (mm) REVERT: D 209 LEU cc_start: 0.7550 (mt) cc_final: 0.7191 (mt) REVERT: D 232 VAL cc_start: 0.7938 (t) cc_final: 0.7722 (t) REVERT: D 305 PHE cc_start: 0.6824 (t80) cc_final: 0.6550 (t80) REVERT: D 387 MET cc_start: 0.7153 (ttp) cc_final: 0.6735 (ttp) REVERT: D 527 SER cc_start: 0.8397 (m) cc_final: 0.8001 (t) REVERT: D 651 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6888 (tm-30) REVERT: D 671 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7003 (tm-30) REVERT: D 691 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6358 (tm-30) outliers start: 4 outliers final: 3 residues processed: 462 average time/residue: 0.1363 time to fit residues: 97.4793 Evaluate side-chains 404 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 401 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 321 ASN A 428 ASN B 177 ASN ** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.171752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139760 restraints weight = 31864.947| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.81 r_work: 0.3659 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18843 Z= 0.162 Angle : 0.699 12.424 25720 Z= 0.364 Chirality : 0.043 0.241 3070 Planarity : 0.005 0.061 3158 Dihedral : 5.146 27.347 2634 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.43 % Favored : 90.53 % Rotamer: Outliers : 1.37 % Allowed : 10.11 % Favored : 88.53 % 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: -2.34 (0.17), residues: 2450 helix: -0.86 (0.13), residues: 1681 sheet: None (None), residues: 0 loop : -2.96 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 679 TYR 0.019 0.001 TYR B 339 PHE 0.026 0.002 PHE B 136 TRP 0.021 0.002 TRP A 103 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00344 (18835) covalent geometry : angle 0.69891 (25704) SS BOND : bond 0.00211 ( 8) SS BOND : angle 1.26224 ( 16) hydrogen bonds : bond 0.05761 ( 970) hydrogen bonds : angle 5.16204 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 397 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8306 (tt) cc_final: 0.7965 (tt) REVERT: A 49 VAL cc_start: 0.8108 (t) cc_final: 0.7799 (m) REVERT: A 69 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8373 (tttp) REVERT: A 127 SER cc_start: 0.8287 (m) cc_final: 0.7906 (t) REVERT: A 142 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 145 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7582 (ptm-80) REVERT: A 245 VAL cc_start: 0.8298 (t) cc_final: 0.7910 (p) REVERT: A 328 ILE cc_start: 0.8488 (mm) cc_final: 0.8120 (mt) REVERT: A 437 LEU cc_start: 0.7914 (tp) cc_final: 0.7538 (tt) REVERT: A 485 LEU cc_start: 0.7526 (mt) cc_final: 0.7324 (mt) REVERT: A 515 VAL cc_start: 0.8570 (t) cc_final: 0.8271 (t) REVERT: A 658 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8157 (ttmm) REVERT: A 691 GLU cc_start: 0.7138 (tp30) cc_final: 0.6719 (tp30) REVERT: A 692 GLU cc_start: 0.7336 (mp0) cc_final: 0.6925 (mp0) REVERT: B 56 PHE cc_start: 0.7842 (t80) cc_final: 0.7562 (t80) REVERT: B 142 GLU cc_start: 0.7625 (tp30) cc_final: 0.7327 (tp30) REVERT: B 148 PRO cc_start: 0.8154 (Cg_endo) cc_final: 0.7787 (Cg_exo) REVERT: B 244 LEU cc_start: 0.7650 (tp) cc_final: 0.7365 (tt) REVERT: B 324 TRP cc_start: 0.8370 (m100) cc_final: 0.7690 (m100) REVERT: B 352 SER cc_start: 0.7488 (m) cc_final: 0.7274 (t) REVERT: B 458 LEU cc_start: 0.8287 (mt) cc_final: 0.8085 (mt) REVERT: B 628 MET cc_start: 0.5995 (mmp) cc_final: 0.5674 (mmp) REVERT: B 661 GLU cc_start: 0.6744 (tp30) cc_final: 0.6281 (tp30) REVERT: B 674 ASP cc_start: 0.8213 (p0) cc_final: 0.7776 (p0) REVERT: B 681 LYS cc_start: 0.8315 (mttt) cc_final: 0.8032 (mtpp) REVERT: B 695 GLN cc_start: 0.8493 (mm110) cc_final: 0.7464 (mm110) REVERT: C 96 VAL cc_start: 0.8502 (m) cc_final: 0.8265 (t) REVERT: C 191 VAL cc_start: 0.8144 (p) cc_final: 0.7845 (t) REVERT: C 394 LEU cc_start: 0.8045 (mt) cc_final: 0.7720 (mm) REVERT: C 404 THR cc_start: 0.7681 (p) cc_final: 0.6895 (m) REVERT: C 467 TRP cc_start: 0.7478 (t60) cc_final: 0.6908 (t60) REVERT: C 632 ILE cc_start: 0.7055 (tp) cc_final: 0.6827 (tp) REVERT: C 656 ILE cc_start: 0.8472 (pt) cc_final: 0.8205 (mt) REVERT: C 666 ASN cc_start: 0.7724 (p0) cc_final: 0.7497 (p0) REVERT: C 677 ASN cc_start: 0.8075 (t0) cc_final: 0.7789 (t0) REVERT: D 69 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7969 (ttmm) REVERT: D 131 ILE cc_start: 0.6867 (mm) cc_final: 0.6567 (mt) REVERT: D 139 MET cc_start: 0.7036 (ttm) cc_final: 0.6648 (ttm) REVERT: D 225 LEU cc_start: 0.7102 (tp) cc_final: 0.6795 (tt) REVERT: D 387 MET cc_start: 0.7388 (ttp) cc_final: 0.6803 (ttp) REVERT: D 475 ILE cc_start: 0.6914 (pt) cc_final: 0.6165 (mp) REVERT: D 522 ARG cc_start: 0.6968 (ptm-80) cc_final: 0.6504 (ptm-80) REVERT: D 527 SER cc_start: 0.8232 (m) cc_final: 0.7862 (t) REVERT: D 677 ASN cc_start: 0.8130 (t0) cc_final: 0.7925 (t0) REVERT: D 691 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6415 (tm-30) outliers start: 26 outliers final: 12 residues processed: 409 average time/residue: 0.1324 time to fit residues: 83.7046 Evaluate side-chains 392 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 379 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 480 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 110 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 172 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 157 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 261 HIS ** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 261 HIS ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.169325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135877 restraints weight = 31948.086| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.73 r_work: 0.3629 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18843 Z= 0.180 Angle : 0.680 8.826 25720 Z= 0.356 Chirality : 0.043 0.159 3070 Planarity : 0.005 0.060 3158 Dihedral : 5.154 27.302 2627 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.84 % Favored : 90.12 % Rotamer: Outliers : 2.32 % Allowed : 13.89 % Favored : 83.79 % 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: -2.28 (0.17), residues: 2450 helix: -0.80 (0.13), residues: 1692 sheet: None (None), residues: 0 loop : -3.01 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 441 TYR 0.029 0.002 TYR B 117 PHE 0.029 0.002 PHE A 60 TRP 0.022 0.002 TRP D 115 HIS 0.009 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00393 (18835) covalent geometry : angle 0.67922 (25704) SS BOND : bond 0.00228 ( 8) SS BOND : angle 1.27700 ( 16) hydrogen bonds : bond 0.05569 ( 970) hydrogen bonds : angle 4.94648 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 393 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8311 (tt) cc_final: 0.7987 (tt) REVERT: A 49 VAL cc_start: 0.8063 (t) cc_final: 0.7733 (m) REVERT: A 69 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8358 (tttp) REVERT: A 245 VAL cc_start: 0.8351 (t) cc_final: 0.7977 (p) REVERT: A 328 ILE cc_start: 0.8506 (mm) cc_final: 0.8222 (mt) REVERT: A 389 LYS cc_start: 0.7766 (mmtp) cc_final: 0.7513 (mmtp) REVERT: A 399 LEU cc_start: 0.8153 (tp) cc_final: 0.7872 (tt) REVERT: A 437 LEU cc_start: 0.7987 (tp) cc_final: 0.7640 (tt) REVERT: A 485 LEU cc_start: 0.7621 (mt) cc_final: 0.7355 (mt) REVERT: A 515 VAL cc_start: 0.8583 (t) cc_final: 0.8291 (t) REVERT: A 639 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7819 (p) REVERT: A 658 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8232 (ttmm) REVERT: A 689 GLU cc_start: 0.8149 (tp30) cc_final: 0.7932 (tp30) REVERT: A 691 GLU cc_start: 0.7205 (tp30) cc_final: 0.6817 (tp30) REVERT: A 699 LYS cc_start: 0.7947 (pttm) cc_final: 0.7655 (pttm) REVERT: B 56 PHE cc_start: 0.7935 (t80) cc_final: 0.7620 (t80) REVERT: B 142 GLU cc_start: 0.7637 (tp30) cc_final: 0.7379 (tp30) REVERT: B 225 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7262 (tt) REVERT: B 401 MET cc_start: 0.7680 (tpp) cc_final: 0.7412 (tpp) REVERT: B 628 MET cc_start: 0.6017 (mmp) cc_final: 0.5731 (mmp) REVERT: B 661 GLU cc_start: 0.6822 (tp30) cc_final: 0.6350 (tp30) REVERT: B 681 LYS cc_start: 0.8338 (mttt) cc_final: 0.8060 (mtpp) REVERT: B 695 GLN cc_start: 0.8578 (mm110) cc_final: 0.7731 (mm110) REVERT: C 69 LYS cc_start: 0.8261 (ttmm) cc_final: 0.8046 (ttmm) REVERT: C 96 VAL cc_start: 0.8542 (m) cc_final: 0.8305 (t) REVERT: C 212 VAL cc_start: 0.8355 (p) cc_final: 0.7976 (t) REVERT: C 394 LEU cc_start: 0.8167 (mt) cc_final: 0.7825 (mm) REVERT: C 404 THR cc_start: 0.7618 (p) cc_final: 0.6832 (m) REVERT: C 467 TRP cc_start: 0.7630 (t60) cc_final: 0.7191 (t60) REVERT: C 632 ILE cc_start: 0.7152 (tp) cc_final: 0.6921 (tp) REVERT: C 656 ILE cc_start: 0.8501 (pt) cc_final: 0.8195 (mt) REVERT: C 666 ASN cc_start: 0.7642 (p0) cc_final: 0.7409 (p0) REVERT: C 677 ASN cc_start: 0.8190 (t0) cc_final: 0.7941 (t0) REVERT: D 139 MET cc_start: 0.7058 (ttm) cc_final: 0.6669 (ttm) REVERT: D 161 TRP cc_start: 0.5619 (m-10) cc_final: 0.5276 (m-90) REVERT: D 183 MET cc_start: 0.7023 (mmm) cc_final: 0.6789 (mmm) REVERT: D 387 MET cc_start: 0.7408 (ttp) cc_final: 0.6767 (ttp) REVERT: D 475 ILE cc_start: 0.7083 (pt) cc_final: 0.6363 (mt) REVERT: D 522 ARG cc_start: 0.6937 (ptm-80) cc_final: 0.6493 (ptm-80) REVERT: D 677 ASN cc_start: 0.8202 (t0) cc_final: 0.7961 (t0) REVERT: D 691 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6693 (tm-30) REVERT: D 693 ARG cc_start: 0.8392 (tmm-80) cc_final: 0.7894 (ttp80) outliers start: 44 outliers final: 23 residues processed: 413 average time/residue: 0.1311 time to fit residues: 83.5036 Evaluate side-chains 405 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 380 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 480 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 62 optimal weight: 0.3980 chunk 229 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 175 optimal weight: 0.0980 chunk 145 optimal weight: 0.0070 chunk 206 optimal weight: 0.6980 chunk 239 optimal weight: 0.8980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 261 HIS ** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 HIS D 261 HIS D 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.171881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138726 restraints weight = 32073.308| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.76 r_work: 0.3674 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18843 Z= 0.124 Angle : 0.635 9.230 25720 Z= 0.325 Chirality : 0.040 0.177 3070 Planarity : 0.004 0.059 3158 Dihedral : 4.958 28.045 2627 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.63 % Favored : 90.33 % Rotamer: Outliers : 2.26 % Allowed : 17.00 % Favored : 80.74 % 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: -2.00 (0.17), residues: 2450 helix: -0.61 (0.13), residues: 1718 sheet: None (None), residues: 0 loop : -2.90 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 441 TYR 0.020 0.001 TYR B 117 PHE 0.030 0.001 PHE A 60 TRP 0.023 0.001 TRP D 115 HIS 0.007 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00262 (18835) covalent geometry : angle 0.63410 (25704) SS BOND : bond 0.00266 ( 8) SS BOND : angle 1.30888 ( 16) hydrogen bonds : bond 0.04250 ( 970) hydrogen bonds : angle 4.66505 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 376 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8335 (tt) cc_final: 0.7991 (tt) REVERT: A 49 VAL cc_start: 0.8101 (t) cc_final: 0.7711 (m) REVERT: A 69 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8361 (tttp) REVERT: A 323 TYR cc_start: 0.7335 (m-80) cc_final: 0.6758 (m-80) REVERT: A 328 ILE cc_start: 0.8450 (mm) cc_final: 0.8113 (mt) REVERT: A 389 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7425 (mmtp) REVERT: A 485 LEU cc_start: 0.7560 (mt) cc_final: 0.7343 (mt) REVERT: A 515 VAL cc_start: 0.8629 (t) cc_final: 0.8336 (t) REVERT: A 535 LEU cc_start: 0.7858 (tt) cc_final: 0.7624 (tp) REVERT: A 658 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8241 (ttmm) REVERT: A 691 GLU cc_start: 0.7173 (tp30) cc_final: 0.6746 (tp30) REVERT: A 692 GLU cc_start: 0.7124 (mp0) cc_final: 0.6891 (mp0) REVERT: A 699 LYS cc_start: 0.7917 (pttm) cc_final: 0.7643 (pttm) REVERT: B 56 PHE cc_start: 0.7935 (t80) cc_final: 0.7619 (t80) REVERT: B 71 TYR cc_start: 0.8485 (m-80) cc_final: 0.8278 (m-80) REVERT: B 142 GLU cc_start: 0.7593 (tp30) cc_final: 0.7330 (tp30) REVERT: B 201 TYR cc_start: 0.7717 (m-10) cc_final: 0.7458 (m-10) REVERT: B 225 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7148 (tt) REVERT: B 395 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7816 (tp) REVERT: B 401 MET cc_start: 0.7617 (tpp) cc_final: 0.7325 (tpp) REVERT: B 628 MET cc_start: 0.6050 (mmp) cc_final: 0.5747 (mmp) REVERT: B 661 GLU cc_start: 0.6844 (tp30) cc_final: 0.6358 (tp30) REVERT: B 674 ASP cc_start: 0.8187 (p0) cc_final: 0.7835 (p0) REVERT: B 681 LYS cc_start: 0.8270 (mttt) cc_final: 0.7805 (ttmm) REVERT: B 695 GLN cc_start: 0.8561 (mm110) cc_final: 0.8050 (mm110) REVERT: C 69 LYS cc_start: 0.8276 (ttmm) cc_final: 0.8056 (ttmm) REVERT: C 96 VAL cc_start: 0.8502 (m) cc_final: 0.8265 (t) REVERT: C 117 TYR cc_start: 0.7684 (m-80) cc_final: 0.7185 (m-80) REVERT: C 212 VAL cc_start: 0.8285 (p) cc_final: 0.7902 (t) REVERT: C 213 VAL cc_start: 0.7694 (t) cc_final: 0.7250 (t) REVERT: C 404 THR cc_start: 0.7337 (p) cc_final: 0.6599 (m) REVERT: C 467 TRP cc_start: 0.7567 (t60) cc_final: 0.7126 (t60) REVERT: C 632 ILE cc_start: 0.7114 (tp) cc_final: 0.6856 (tp) REVERT: C 656 ILE cc_start: 0.8462 (pt) cc_final: 0.8133 (mt) REVERT: C 666 ASN cc_start: 0.7349 (p0) cc_final: 0.7142 (p0) REVERT: C 677 ASN cc_start: 0.8214 (t0) cc_final: 0.7878 (t0) REVERT: D 139 MET cc_start: 0.7041 (ttm) cc_final: 0.6597 (ttm) REVERT: D 344 LEU cc_start: 0.6936 (pt) cc_final: 0.6662 (pt) REVERT: D 387 MET cc_start: 0.7466 (ttp) cc_final: 0.6860 (ttp) REVERT: D 475 ILE cc_start: 0.6711 (pt) cc_final: 0.5895 (mt) REVERT: D 522 ARG cc_start: 0.6857 (ptm-80) cc_final: 0.6464 (ptm-80) REVERT: D 636 TRP cc_start: 0.6865 (OUTLIER) cc_final: 0.6249 (t-100) REVERT: D 677 ASN cc_start: 0.8227 (t0) cc_final: 0.7969 (t0) REVERT: D 691 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6725 (tm-30) REVERT: D 693 ARG cc_start: 0.8393 (tmm-80) cc_final: 0.8040 (ttp-170) outliers start: 43 outliers final: 25 residues processed: 394 average time/residue: 0.1357 time to fit residues: 82.0646 Evaluate side-chains 395 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 367 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 636 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 212 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 261 HIS C 100 GLN C 459 ASN C 538 ASN D 261 HIS D 666 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.169293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135805 restraints weight = 31647.526| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.73 r_work: 0.3629 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18843 Z= 0.154 Angle : 0.653 11.785 25720 Z= 0.336 Chirality : 0.041 0.166 3070 Planarity : 0.004 0.060 3158 Dihedral : 4.998 27.488 2627 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.04 % Favored : 89.92 % Rotamer: Outliers : 2.79 % Allowed : 18.11 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.90 (0.17), residues: 2450 helix: -0.52 (0.13), residues: 1715 sheet: None (None), residues: 0 loop : -2.91 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 441 TYR 0.013 0.001 TYR B 117 PHE 0.031 0.001 PHE A 60 TRP 0.021 0.001 TRP D 115 HIS 0.007 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00336 (18835) covalent geometry : angle 0.65237 (25704) SS BOND : bond 0.00230 ( 8) SS BOND : angle 1.51824 ( 16) hydrogen bonds : bond 0.04773 ( 970) hydrogen bonds : angle 4.61999 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 382 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8354 (tt) cc_final: 0.8020 (tt) REVERT: A 49 VAL cc_start: 0.8095 (t) cc_final: 0.7738 (m) REVERT: A 69 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8364 (tttp) REVERT: A 323 TYR cc_start: 0.7378 (m-80) cc_final: 0.6774 (m-80) REVERT: A 328 ILE cc_start: 0.8467 (mm) cc_final: 0.8189 (mt) REVERT: A 451 MET cc_start: 0.8280 (mmp) cc_final: 0.7845 (mmp) REVERT: A 515 VAL cc_start: 0.8573 (t) cc_final: 0.8303 (t) REVERT: A 658 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8216 (ttmm) REVERT: A 663 MET cc_start: 0.7959 (ttt) cc_final: 0.7747 (mtp) REVERT: A 691 GLU cc_start: 0.7222 (tp30) cc_final: 0.6796 (tp30) REVERT: A 692 GLU cc_start: 0.7137 (mp0) cc_final: 0.6883 (mp0) REVERT: A 699 LYS cc_start: 0.7930 (pttm) cc_final: 0.7705 (pttm) REVERT: B 111 SER cc_start: 0.8563 (p) cc_final: 0.8344 (p) REVERT: B 142 GLU cc_start: 0.7647 (tp30) cc_final: 0.7387 (tp30) REVERT: B 201 TYR cc_start: 0.7825 (m-10) cc_final: 0.7375 (m-80) REVERT: B 225 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7252 (tt) REVERT: B 324 TRP cc_start: 0.8350 (m100) cc_final: 0.7746 (m100) REVERT: B 421 ASP cc_start: 0.7539 (t70) cc_final: 0.7307 (t70) REVERT: B 628 MET cc_start: 0.6051 (mmp) cc_final: 0.5754 (mmp) REVERT: B 661 GLU cc_start: 0.6799 (tp30) cc_final: 0.6282 (tp30) REVERT: B 674 ASP cc_start: 0.8212 (p0) cc_final: 0.7819 (p0) REVERT: B 681 LYS cc_start: 0.8322 (mttt) cc_final: 0.7852 (ttmm) REVERT: B 693 ARG cc_start: 0.8007 (ptm160) cc_final: 0.7785 (ptm160) REVERT: B 695 GLN cc_start: 0.8559 (mm110) cc_final: 0.7706 (mm110) REVERT: C 69 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8151 (ttmm) REVERT: C 96 VAL cc_start: 0.8513 (m) cc_final: 0.8270 (t) REVERT: C 117 TYR cc_start: 0.7809 (m-80) cc_final: 0.7429 (m-80) REVERT: C 152 THR cc_start: 0.7822 (t) cc_final: 0.7567 (t) REVERT: C 212 VAL cc_start: 0.8421 (p) cc_final: 0.8041 (t) REVERT: C 224 PHE cc_start: 0.6609 (t80) cc_final: 0.6350 (t80) REVERT: C 316 THR cc_start: 0.7236 (p) cc_final: 0.6941 (m) REVERT: C 467 TRP cc_start: 0.7754 (t60) cc_final: 0.7295 (t60) REVERT: C 632 ILE cc_start: 0.7202 (tp) cc_final: 0.6945 (tp) REVERT: C 656 ILE cc_start: 0.8484 (pt) cc_final: 0.8205 (mt) REVERT: D 38 LYS cc_start: 0.5809 (ptmm) cc_final: 0.5458 (ptmm) REVERT: D 139 MET cc_start: 0.6972 (ttm) cc_final: 0.6556 (ttm) REVERT: D 161 TRP cc_start: 0.5806 (m-10) cc_final: 0.5589 (m-90) REVERT: D 305 PHE cc_start: 0.6938 (t80) cc_final: 0.6552 (t80) REVERT: D 344 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6671 (pt) REVERT: D 522 ARG cc_start: 0.6834 (ptm-80) cc_final: 0.6463 (ptm-80) REVERT: D 636 TRP cc_start: 0.7032 (OUTLIER) cc_final: 0.6391 (t-100) REVERT: D 677 ASN cc_start: 0.8265 (t0) cc_final: 0.7990 (t0) REVERT: D 691 GLU cc_start: 0.7511 (tm-30) cc_final: 0.6877 (tm-30) REVERT: D 693 ARG cc_start: 0.8447 (tmm-80) cc_final: 0.8090 (ttp-170) outliers start: 53 outliers final: 32 residues processed: 406 average time/residue: 0.1290 time to fit residues: 79.6986 Evaluate side-chains 412 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 377 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 636 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 197 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 198 optimal weight: 0.0970 chunk 43 optimal weight: 0.9990 chunk 208 optimal weight: 0.0010 chunk 235 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 261 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN D 177 ASN ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS D 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.170305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136962 restraints weight = 31624.887| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.72 r_work: 0.3641 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18843 Z= 0.136 Angle : 0.645 10.499 25720 Z= 0.330 Chirality : 0.040 0.201 3070 Planarity : 0.004 0.063 3158 Dihedral : 4.904 27.857 2627 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.43 % Favored : 90.53 % Rotamer: Outliers : 2.42 % Allowed : 18.89 % Favored : 78.68 % 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: -1.81 (0.17), residues: 2450 helix: -0.44 (0.13), residues: 1721 sheet: None (None), residues: 0 loop : -2.91 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 158 TYR 0.024 0.001 TYR B 117 PHE 0.032 0.001 PHE A 60 TRP 0.025 0.001 TRP D 115 HIS 0.007 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00297 (18835) covalent geometry : angle 0.64394 (25704) SS BOND : bond 0.00305 ( 8) SS BOND : angle 1.58562 ( 16) hydrogen bonds : bond 0.04317 ( 970) hydrogen bonds : angle 4.52092 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8340 (tt) cc_final: 0.8014 (tt) REVERT: A 49 VAL cc_start: 0.8117 (t) cc_final: 0.7702 (m) REVERT: A 69 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8376 (tttp) REVERT: A 273 SER cc_start: 0.8110 (p) cc_final: 0.7817 (p) REVERT: A 323 TYR cc_start: 0.7379 (m-80) cc_final: 0.6730 (m-80) REVERT: A 328 ILE cc_start: 0.8473 (mm) cc_final: 0.8169 (mt) REVERT: A 515 VAL cc_start: 0.8571 (t) cc_final: 0.8300 (t) REVERT: A 658 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8218 (ttmm) REVERT: A 691 GLU cc_start: 0.7226 (tp30) cc_final: 0.6788 (tp30) REVERT: A 692 GLU cc_start: 0.7143 (mp0) cc_final: 0.6881 (mp0) REVERT: A 699 LYS cc_start: 0.7932 (pttm) cc_final: 0.7711 (pttm) REVERT: B 71 TYR cc_start: 0.8543 (m-80) cc_final: 0.8329 (m-80) REVERT: B 111 SER cc_start: 0.8542 (p) cc_final: 0.8330 (p) REVERT: B 142 GLU cc_start: 0.7632 (tp30) cc_final: 0.7391 (tp30) REVERT: B 225 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7201 (tt) REVERT: B 324 TRP cc_start: 0.8321 (m100) cc_final: 0.7666 (m100) REVERT: B 395 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7863 (tp) REVERT: B 628 MET cc_start: 0.6059 (mmp) cc_final: 0.5732 (mmp) REVERT: B 661 GLU cc_start: 0.6638 (tp30) cc_final: 0.6079 (tp30) REVERT: B 674 ASP cc_start: 0.8200 (p0) cc_final: 0.7817 (p0) REVERT: B 681 LYS cc_start: 0.8286 (mttt) cc_final: 0.7825 (ttmm) REVERT: B 693 ARG cc_start: 0.8009 (ptm160) cc_final: 0.7793 (ptm160) REVERT: B 695 GLN cc_start: 0.8562 (mm110) cc_final: 0.8158 (mm110) REVERT: C 69 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8147 (ttmm) REVERT: C 96 VAL cc_start: 0.8486 (m) cc_final: 0.8248 (t) REVERT: C 117 TYR cc_start: 0.7798 (m-80) cc_final: 0.7447 (m-80) REVERT: C 139 MET cc_start: 0.6721 (ttm) cc_final: 0.6420 (ttm) REVERT: C 212 VAL cc_start: 0.8420 (p) cc_final: 0.8042 (t) REVERT: C 316 THR cc_start: 0.7198 (p) cc_final: 0.6893 (m) REVERT: C 467 TRP cc_start: 0.7744 (t60) cc_final: 0.7318 (t60) REVERT: C 632 ILE cc_start: 0.7206 (tp) cc_final: 0.6948 (tp) REVERT: C 656 ILE cc_start: 0.8480 (pt) cc_final: 0.8196 (mt) REVERT: D 38 LYS cc_start: 0.5735 (ptmm) cc_final: 0.5324 (ptmm) REVERT: D 139 MET cc_start: 0.6996 (ttm) cc_final: 0.6580 (ttm) REVERT: D 179 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.5913 (tp) REVERT: D 297 MET cc_start: 0.4457 (tpp) cc_final: 0.3872 (tpp) REVERT: D 305 PHE cc_start: 0.6907 (t80) cc_final: 0.6487 (t80) REVERT: D 344 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6744 (pt) REVERT: D 522 ARG cc_start: 0.6914 (ptm-80) cc_final: 0.6496 (ptm-80) REVERT: D 636 TRP cc_start: 0.6970 (OUTLIER) cc_final: 0.6328 (t-100) REVERT: D 677 ASN cc_start: 0.8249 (t0) cc_final: 0.7964 (t0) REVERT: D 691 GLU cc_start: 0.7527 (tm-30) cc_final: 0.6811 (tm-30) REVERT: D 693 ARG cc_start: 0.8454 (tmm-80) cc_final: 0.8156 (ttp-170) outliers start: 46 outliers final: 28 residues processed: 398 average time/residue: 0.1329 time to fit residues: 80.6229 Evaluate side-chains 405 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 372 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 636 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 44 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 221 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 261 HIS D 261 HIS D 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.168237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134731 restraints weight = 31852.145| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.72 r_work: 0.3617 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18843 Z= 0.154 Angle : 0.665 9.623 25720 Z= 0.341 Chirality : 0.041 0.204 3070 Planarity : 0.004 0.066 3158 Dihedral : 4.963 27.650 2627 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.00 % Favored : 89.96 % Rotamer: Outliers : 2.68 % Allowed : 19.89 % Favored : 77.42 % 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: -1.81 (0.17), residues: 2450 helix: -0.42 (0.13), residues: 1721 sheet: None (None), residues: 0 loop : -2.98 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 251 TYR 0.027 0.001 TYR B 117 PHE 0.034 0.002 PHE A 60 TRP 0.026 0.001 TRP D 115 HIS 0.008 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00338 (18835) covalent geometry : angle 0.66409 (25704) SS BOND : bond 0.00255 ( 8) SS BOND : angle 1.35101 ( 16) hydrogen bonds : bond 0.04623 ( 970) hydrogen bonds : angle 4.55455 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 382 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8339 (tt) cc_final: 0.8022 (tt) REVERT: A 49 VAL cc_start: 0.8116 (t) cc_final: 0.7679 (m) REVERT: A 69 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8382 (tttp) REVERT: A 323 TYR cc_start: 0.7391 (m-80) cc_final: 0.6766 (m-80) REVERT: A 328 ILE cc_start: 0.8513 (mm) cc_final: 0.8220 (mt) REVERT: A 399 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7877 (tt) REVERT: A 450 LEU cc_start: 0.8171 (tt) cc_final: 0.7967 (tp) REVERT: A 515 VAL cc_start: 0.8577 (t) cc_final: 0.8310 (t) REVERT: A 593 LYS cc_start: 0.7522 (mtmt) cc_final: 0.7261 (mtmt) REVERT: A 658 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8231 (ttmm) REVERT: A 663 MET cc_start: 0.7975 (ttt) cc_final: 0.7756 (mtp) REVERT: A 691 GLU cc_start: 0.7261 (tp30) cc_final: 0.6808 (tp30) REVERT: A 692 GLU cc_start: 0.7165 (mp0) cc_final: 0.6891 (mp0) REVERT: A 699 LYS cc_start: 0.7949 (pttm) cc_final: 0.7701 (pttm) REVERT: B 71 TYR cc_start: 0.8580 (m-80) cc_final: 0.8354 (m-80) REVERT: B 111 SER cc_start: 0.8609 (p) cc_final: 0.8383 (p) REVERT: B 142 GLU cc_start: 0.7663 (tp30) cc_final: 0.7382 (tp30) REVERT: B 148 PRO cc_start: 0.8115 (Cg_endo) cc_final: 0.7834 (Cg_exo) REVERT: B 225 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7285 (tt) REVERT: B 324 TRP cc_start: 0.8273 (m100) cc_final: 0.7688 (m100) REVERT: B 628 MET cc_start: 0.6100 (mmp) cc_final: 0.5802 (mmp) REVERT: B 661 GLU cc_start: 0.6707 (tp30) cc_final: 0.6128 (tp30) REVERT: B 674 ASP cc_start: 0.8213 (p0) cc_final: 0.7838 (p0) REVERT: B 681 LYS cc_start: 0.8309 (mttt) cc_final: 0.7869 (ttmm) REVERT: B 695 GLN cc_start: 0.8542 (mm110) cc_final: 0.8053 (mm110) REVERT: C 96 VAL cc_start: 0.8498 (m) cc_final: 0.8232 (t) REVERT: C 117 TYR cc_start: 0.7847 (m-80) cc_final: 0.7502 (m-80) REVERT: C 124 TRP cc_start: 0.7285 (m100) cc_final: 0.6928 (m100) REVERT: C 139 MET cc_start: 0.6725 (ttm) cc_final: 0.6395 (ttm) REVERT: C 212 VAL cc_start: 0.8453 (p) cc_final: 0.8076 (t) REVERT: C 443 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7758 (t) REVERT: C 467 TRP cc_start: 0.7741 (t60) cc_final: 0.7350 (t60) REVERT: C 632 ILE cc_start: 0.7266 (tp) cc_final: 0.6999 (tp) REVERT: C 656 ILE cc_start: 0.8492 (pt) cc_final: 0.8218 (mt) REVERT: D 38 LYS cc_start: 0.5750 (ptmm) cc_final: 0.5202 (ptmm) REVERT: D 139 MET cc_start: 0.7007 (ttm) cc_final: 0.6614 (ttm) REVERT: D 179 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6064 (tt) REVERT: D 297 MET cc_start: 0.4520 (tpp) cc_final: 0.4312 (tpp) REVERT: D 305 PHE cc_start: 0.7059 (t80) cc_final: 0.6621 (t80) REVERT: D 344 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6780 (pt) REVERT: D 387 MET cc_start: 0.7327 (ttp) cc_final: 0.6797 (ttp) REVERT: D 397 ILE cc_start: 0.7807 (tt) cc_final: 0.7457 (tp) REVERT: D 636 TRP cc_start: 0.7024 (OUTLIER) cc_final: 0.6393 (t-100) REVERT: D 677 ASN cc_start: 0.8271 (t0) cc_final: 0.7974 (t0) REVERT: D 678 LEU cc_start: 0.8389 (mm) cc_final: 0.8032 (mm) REVERT: D 691 GLU cc_start: 0.7580 (tm-30) cc_final: 0.6769 (tm-30) REVERT: D 693 ARG cc_start: 0.8481 (tmm-80) cc_final: 0.8158 (ttp-170) outliers start: 51 outliers final: 33 residues processed: 403 average time/residue: 0.1320 time to fit residues: 81.0567 Evaluate side-chains 415 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 376 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 636 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 240 optimal weight: 0.0970 chunk 102 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 230 HIS B 261 HIS D 230 HIS ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.168758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135344 restraints weight = 31616.488| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.71 r_work: 0.3626 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18843 Z= 0.146 Angle : 0.666 11.475 25720 Z= 0.341 Chirality : 0.041 0.215 3070 Planarity : 0.004 0.068 3158 Dihedral : 4.933 27.878 2627 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.63 % Favored : 90.33 % Rotamer: Outliers : 2.53 % Allowed : 20.89 % Favored : 76.58 % 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: -1.75 (0.17), residues: 2450 helix: -0.36 (0.13), residues: 1721 sheet: None (None), residues: 0 loop : -2.99 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 158 TYR 0.029 0.001 TYR B 117 PHE 0.035 0.001 PHE C 314 TRP 0.027 0.001 TRP D 115 HIS 0.007 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00318 (18835) covalent geometry : angle 0.66498 (25704) SS BOND : bond 0.00256 ( 8) SS BOND : angle 1.34211 ( 16) hydrogen bonds : bond 0.04414 ( 970) hydrogen bonds : angle 4.51126 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 375 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8350 (tt) cc_final: 0.8015 (tt) REVERT: A 49 VAL cc_start: 0.8126 (t) cc_final: 0.7696 (m) REVERT: A 69 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8381 (tttp) REVERT: A 245 VAL cc_start: 0.8257 (t) cc_final: 0.7936 (p) REVERT: A 323 TYR cc_start: 0.7389 (m-80) cc_final: 0.6763 (m-80) REVERT: A 328 ILE cc_start: 0.8502 (mm) cc_final: 0.8202 (mt) REVERT: A 450 LEU cc_start: 0.8186 (tt) cc_final: 0.7981 (tp) REVERT: A 515 VAL cc_start: 0.8578 (t) cc_final: 0.8310 (t) REVERT: A 593 LYS cc_start: 0.7477 (mtmt) cc_final: 0.7103 (mtmt) REVERT: A 658 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8228 (ttmm) REVERT: A 691 GLU cc_start: 0.7239 (tp30) cc_final: 0.6829 (tp30) REVERT: A 692 GLU cc_start: 0.7152 (mp0) cc_final: 0.6831 (mp0) REVERT: A 699 LYS cc_start: 0.7924 (pttm) cc_final: 0.7702 (pttm) REVERT: B 71 TYR cc_start: 0.8553 (m-80) cc_final: 0.8325 (m-80) REVERT: B 111 SER cc_start: 0.8600 (p) cc_final: 0.8376 (p) REVERT: B 142 GLU cc_start: 0.7638 (tp30) cc_final: 0.7394 (tp30) REVERT: B 225 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7182 (tt) REVERT: B 324 TRP cc_start: 0.8203 (m100) cc_final: 0.7696 (m100) REVERT: B 534 MET cc_start: 0.7496 (ttm) cc_final: 0.7211 (mmm) REVERT: B 628 MET cc_start: 0.6154 (mmp) cc_final: 0.5814 (mmp) REVERT: B 661 GLU cc_start: 0.6702 (tp30) cc_final: 0.6116 (tp30) REVERT: B 674 ASP cc_start: 0.8208 (p0) cc_final: 0.7857 (p0) REVERT: B 681 LYS cc_start: 0.8294 (mttt) cc_final: 0.7854 (ttmm) REVERT: B 695 GLN cc_start: 0.8513 (mm110) cc_final: 0.7678 (mm110) REVERT: C 96 VAL cc_start: 0.8480 (m) cc_final: 0.8231 (t) REVERT: C 117 TYR cc_start: 0.7848 (m-80) cc_final: 0.7507 (m-80) REVERT: C 124 TRP cc_start: 0.7360 (m100) cc_final: 0.6977 (m100) REVERT: C 139 MET cc_start: 0.6681 (ttm) cc_final: 0.6354 (ttm) REVERT: C 212 VAL cc_start: 0.8438 (p) cc_final: 0.8063 (t) REVERT: C 443 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7738 (t) REVERT: C 467 TRP cc_start: 0.7798 (t60) cc_final: 0.7385 (t60) REVERT: C 632 ILE cc_start: 0.7291 (tp) cc_final: 0.6998 (tp) REVERT: C 656 ILE cc_start: 0.8498 (pt) cc_final: 0.8222 (mt) REVERT: C 664 PHE cc_start: 0.7741 (m-80) cc_final: 0.7277 (m-80) REVERT: C 681 LYS cc_start: 0.8704 (mttt) cc_final: 0.8303 (ttmm) REVERT: D 38 LYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5231 (ptmm) REVERT: D 179 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6061 (tt) REVERT: D 297 MET cc_start: 0.4522 (tpp) cc_final: 0.4294 (tpp) REVERT: D 305 PHE cc_start: 0.7099 (t80) cc_final: 0.6744 (t80) REVERT: D 324 TRP cc_start: 0.8068 (m100) cc_final: 0.7832 (m100) REVERT: D 344 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6828 (pt) REVERT: D 397 ILE cc_start: 0.7827 (tt) cc_final: 0.7119 (tp) REVERT: D 401 MET cc_start: 0.7010 (tpp) cc_final: 0.6392 (mpp) REVERT: D 636 TRP cc_start: 0.7025 (OUTLIER) cc_final: 0.6399 (t-100) REVERT: D 677 ASN cc_start: 0.8257 (t0) cc_final: 0.7972 (t0) REVERT: D 691 GLU cc_start: 0.7590 (tm-30) cc_final: 0.6743 (tm-30) REVERT: D 693 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8194 (ttp-170) outliers start: 48 outliers final: 36 residues processed: 393 average time/residue: 0.1260 time to fit residues: 74.8206 Evaluate side-chains 413 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 628 MET Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 636 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 121 optimal weight: 0.5980 chunk 209 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 116 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 HIS B 261 HIS ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.168372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135000 restraints weight = 31568.494| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.71 r_work: 0.3617 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18843 Z= 0.149 Angle : 0.680 11.190 25720 Z= 0.348 Chirality : 0.041 0.218 3070 Planarity : 0.004 0.071 3158 Dihedral : 4.956 27.914 2627 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.88 % Favored : 90.08 % Rotamer: Outliers : 2.26 % Allowed : 21.58 % Favored : 76.16 % 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: -1.77 (0.17), residues: 2450 helix: -0.37 (0.13), residues: 1718 sheet: None (None), residues: 0 loop : -3.00 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 158 TYR 0.030 0.001 TYR B 117 PHE 0.039 0.001 PHE C 314 TRP 0.028 0.001 TRP D 115 HIS 0.007 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00325 (18835) covalent geometry : angle 0.67900 (25704) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.25484 ( 16) hydrogen bonds : bond 0.04506 ( 970) hydrogen bonds : angle 4.56082 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 378 time to evaluate : 0.639 Fit side-chains REVERT: A 14 LEU cc_start: 0.8358 (tt) cc_final: 0.8027 (tt) REVERT: A 69 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8378 (tttp) REVERT: A 245 VAL cc_start: 0.8272 (t) cc_final: 0.7994 (p) REVERT: A 323 TYR cc_start: 0.7379 (m-80) cc_final: 0.6754 (m-80) REVERT: A 328 ILE cc_start: 0.8502 (mm) cc_final: 0.8207 (mt) REVERT: A 450 LEU cc_start: 0.8197 (tt) cc_final: 0.7986 (tp) REVERT: A 515 VAL cc_start: 0.8572 (t) cc_final: 0.8302 (t) REVERT: A 593 LYS cc_start: 0.7546 (mtmt) cc_final: 0.7298 (mtmt) REVERT: A 658 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8219 (ttmm) REVERT: A 663 MET cc_start: 0.8002 (ttt) cc_final: 0.7747 (mtp) REVERT: A 691 GLU cc_start: 0.7273 (tp30) cc_final: 0.6869 (tp30) REVERT: B 57 PHE cc_start: 0.7960 (t80) cc_final: 0.7427 (t80) REVERT: B 71 TYR cc_start: 0.8559 (m-80) cc_final: 0.8336 (m-80) REVERT: B 111 SER cc_start: 0.8614 (p) cc_final: 0.8385 (p) REVERT: B 135 LEU cc_start: 0.7168 (mt) cc_final: 0.6901 (mt) REVERT: B 142 GLU cc_start: 0.7651 (tp30) cc_final: 0.7378 (tp30) REVERT: B 148 PRO cc_start: 0.8088 (Cg_endo) cc_final: 0.7780 (Cg_exo) REVERT: B 225 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7188 (tt) REVERT: B 324 TRP cc_start: 0.8224 (m100) cc_final: 0.7696 (m100) REVERT: B 489 TRP cc_start: 0.7104 (t60) cc_final: 0.6704 (t60) REVERT: B 534 MET cc_start: 0.7588 (ttm) cc_final: 0.7282 (mmm) REVERT: B 628 MET cc_start: 0.6068 (mmp) cc_final: 0.5725 (mmp) REVERT: B 661 GLU cc_start: 0.6654 (tp30) cc_final: 0.6098 (tp30) REVERT: B 674 ASP cc_start: 0.8202 (p0) cc_final: 0.7866 (p0) REVERT: B 681 LYS cc_start: 0.8302 (mttt) cc_final: 0.7857 (ttmm) REVERT: B 695 GLN cc_start: 0.8433 (mm110) cc_final: 0.8037 (mm110) REVERT: C 96 VAL cc_start: 0.8522 (m) cc_final: 0.8273 (t) REVERT: C 117 TYR cc_start: 0.7853 (m-80) cc_final: 0.7520 (m-80) REVERT: C 124 TRP cc_start: 0.7415 (m100) cc_final: 0.7000 (m100) REVERT: C 139 MET cc_start: 0.6713 (ttm) cc_final: 0.6387 (ttm) REVERT: C 212 VAL cc_start: 0.8464 (p) cc_final: 0.8086 (t) REVERT: C 443 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7754 (t) REVERT: C 467 TRP cc_start: 0.7831 (t60) cc_final: 0.7426 (t60) REVERT: C 632 ILE cc_start: 0.7308 (tp) cc_final: 0.7008 (tp) REVERT: C 656 ILE cc_start: 0.8491 (pt) cc_final: 0.8225 (mt) REVERT: C 664 PHE cc_start: 0.7605 (m-80) cc_final: 0.7162 (m-80) REVERT: C 681 LYS cc_start: 0.8716 (mttt) cc_final: 0.8314 (ttmm) REVERT: D 38 LYS cc_start: 0.5747 (OUTLIER) cc_final: 0.5183 (ptmm) REVERT: D 179 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6120 (tp) REVERT: D 180 VAL cc_start: 0.8121 (t) cc_final: 0.7717 (m) REVERT: D 305 PHE cc_start: 0.7204 (t80) cc_final: 0.6917 (t80) REVERT: D 344 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6914 (pt) REVERT: D 397 ILE cc_start: 0.7833 (tt) cc_final: 0.7130 (tp) REVERT: D 401 MET cc_start: 0.7061 (tpp) cc_final: 0.6450 (mpp) REVERT: D 636 TRP cc_start: 0.7045 (OUTLIER) cc_final: 0.6443 (t-100) REVERT: D 677 ASN cc_start: 0.8261 (t0) cc_final: 0.7980 (t0) REVERT: D 691 GLU cc_start: 0.7612 (tm-30) cc_final: 0.6734 (tm-30) REVERT: D 693 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.8165 (ttp-170) outliers start: 43 outliers final: 27 residues processed: 392 average time/residue: 0.1320 time to fit residues: 78.8048 Evaluate side-chains 406 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 373 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 628 MET Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 636 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 51 optimal weight: 0.5980 chunk 171 optimal weight: 0.0060 chunk 165 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 129 optimal weight: 0.2980 chunk 128 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN A 538 ASN B 230 HIS B 261 HIS C 309 ASN C 313 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.169485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136096 restraints weight = 31724.843| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.74 r_work: 0.3638 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18843 Z= 0.133 Angle : 0.680 10.895 25720 Z= 0.347 Chirality : 0.041 0.149 3070 Planarity : 0.004 0.071 3158 Dihedral : 4.894 28.272 2627 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.51 % Favored : 90.45 % Rotamer: Outliers : 2.11 % Allowed : 22.32 % Favored : 75.58 % 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: -1.69 (0.17), residues: 2450 helix: -0.33 (0.13), residues: 1723 sheet: None (None), residues: 0 loop : -2.96 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 251 TYR 0.029 0.001 TYR B 117 PHE 0.045 0.001 PHE C 314 TRP 0.038 0.001 TRP D 324 HIS 0.007 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00286 (18835) covalent geometry : angle 0.67918 (25704) SS BOND : bond 0.00237 ( 8) SS BOND : angle 1.21586 ( 16) hydrogen bonds : bond 0.04215 ( 970) hydrogen bonds : angle 4.50752 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 374 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8368 (tt) cc_final: 0.8035 (tt) REVERT: A 69 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8379 (tttp) REVERT: A 256 ARG cc_start: 0.7902 (tpp-160) cc_final: 0.7673 (tpp-160) REVERT: A 323 TYR cc_start: 0.7344 (m-80) cc_final: 0.6742 (m-80) REVERT: A 328 ILE cc_start: 0.8495 (mm) cc_final: 0.8184 (mt) REVERT: A 450 LEU cc_start: 0.8205 (tt) cc_final: 0.7982 (tp) REVERT: A 515 VAL cc_start: 0.8571 (t) cc_final: 0.8285 (t) REVERT: A 593 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7251 (mtmt) REVERT: A 691 GLU cc_start: 0.7237 (tp30) cc_final: 0.6841 (tp30) REVERT: A 692 GLU cc_start: 0.7349 (mp0) cc_final: 0.7070 (mp0) REVERT: B 57 PHE cc_start: 0.7982 (t80) cc_final: 0.7454 (t80) REVERT: B 71 TYR cc_start: 0.8525 (m-80) cc_final: 0.8302 (m-80) REVERT: B 111 SER cc_start: 0.8593 (p) cc_final: 0.8381 (p) REVERT: B 148 PRO cc_start: 0.8083 (Cg_endo) cc_final: 0.7765 (Cg_exo) REVERT: B 225 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7094 (tt) REVERT: B 324 TRP cc_start: 0.8179 (m100) cc_final: 0.7718 (m100) REVERT: B 489 TRP cc_start: 0.7063 (t60) cc_final: 0.6646 (t60) REVERT: B 534 MET cc_start: 0.7559 (ttm) cc_final: 0.7195 (mmm) REVERT: B 628 MET cc_start: 0.6074 (mmp) cc_final: 0.5719 (mmp) REVERT: B 661 GLU cc_start: 0.6647 (tp30) cc_final: 0.6078 (tp30) REVERT: B 674 ASP cc_start: 0.8203 (p0) cc_final: 0.7870 (p0) REVERT: B 681 LYS cc_start: 0.8330 (mttt) cc_final: 0.7831 (ttmm) REVERT: B 695 GLN cc_start: 0.8428 (mm110) cc_final: 0.8062 (mm110) REVERT: C 70 ARG cc_start: 0.8419 (ttt90) cc_final: 0.8131 (ttt90) REVERT: C 96 VAL cc_start: 0.8499 (m) cc_final: 0.8262 (t) REVERT: C 115 TRP cc_start: 0.8446 (t60) cc_final: 0.8231 (t60) REVERT: C 117 TYR cc_start: 0.7842 (m-80) cc_final: 0.7518 (m-80) REVERT: C 124 TRP cc_start: 0.7382 (m100) cc_final: 0.6949 (m100) REVERT: C 139 MET cc_start: 0.6704 (ttm) cc_final: 0.6379 (ttm) REVERT: C 212 VAL cc_start: 0.8385 (p) cc_final: 0.8012 (t) REVERT: C 314 PHE cc_start: 0.6704 (m-80) cc_final: 0.6440 (m-80) REVERT: C 401 MET cc_start: 0.7284 (tmm) cc_final: 0.7056 (ptm) REVERT: C 441 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6818 (mpp80) REVERT: C 467 TRP cc_start: 0.7803 (t60) cc_final: 0.7394 (t60) REVERT: C 531 ASN cc_start: 0.6816 (m-40) cc_final: 0.6362 (m-40) REVERT: C 632 ILE cc_start: 0.7277 (tp) cc_final: 0.6974 (tp) REVERT: C 656 ILE cc_start: 0.8500 (pt) cc_final: 0.8203 (mt) REVERT: C 664 PHE cc_start: 0.7530 (m-80) cc_final: 0.7081 (m-80) REVERT: C 681 LYS cc_start: 0.8628 (mttt) cc_final: 0.8237 (ttmm) REVERT: C 692 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: C 697 MET cc_start: 0.6048 (mtt) cc_final: 0.5568 (mtm) REVERT: D 38 LYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5276 (ptmm) REVERT: D 149 LYS cc_start: 0.8019 (pttm) cc_final: 0.7819 (pttm) REVERT: D 179 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.6043 (tt) REVERT: D 180 VAL cc_start: 0.8010 (t) cc_final: 0.7615 (m) REVERT: D 305 PHE cc_start: 0.7077 (t80) cc_final: 0.6744 (t80) REVERT: D 344 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6954 (pt) REVERT: D 397 ILE cc_start: 0.7829 (tt) cc_final: 0.7125 (tp) REVERT: D 401 MET cc_start: 0.7006 (tpp) cc_final: 0.6397 (mpp) REVERT: D 636 TRP cc_start: 0.7051 (OUTLIER) cc_final: 0.6539 (t-100) REVERT: D 677 ASN cc_start: 0.8275 (t0) cc_final: 0.7988 (t0) REVERT: D 691 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6743 (tm-30) REVERT: D 693 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8214 (ttp-170) outliers start: 40 outliers final: 27 residues processed: 391 average time/residue: 0.1394 time to fit residues: 82.1547 Evaluate side-chains 404 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 628 MET Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 636 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 110 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS D 259 HIS ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135817 restraints weight = 31794.985| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.71 r_work: 0.3621 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18843 Z= 0.145 Angle : 0.684 10.578 25720 Z= 0.350 Chirality : 0.041 0.156 3070 Planarity : 0.004 0.073 3158 Dihedral : 4.908 27.973 2627 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.80 % Favored : 90.16 % Rotamer: Outliers : 2.11 % Allowed : 22.21 % Favored : 75.68 % 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: -1.76 (0.17), residues: 2450 helix: -0.36 (0.13), residues: 1737 sheet: None (None), residues: 0 loop : -3.07 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 251 TYR 0.029 0.001 TYR B 117 PHE 0.044 0.001 PHE C 314 TRP 0.039 0.002 TRP D 324 HIS 0.007 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00315 (18835) covalent geometry : angle 0.68378 (25704) SS BOND : bond 0.00255 ( 8) SS BOND : angle 1.19085 ( 16) hydrogen bonds : bond 0.04459 ( 970) hydrogen bonds : angle 4.55873 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4292.53 seconds wall clock time: 74 minutes 15.45 seconds (4455.45 seconds total)