Starting phenix.real_space_refine on Fri Feb 6 17:26:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvd_49833/02_2026/9nvd_49833_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvd_49833/02_2026/9nvd_49833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nvd_49833/02_2026/9nvd_49833_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvd_49833/02_2026/9nvd_49833_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nvd_49833/02_2026/9nvd_49833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvd_49833/02_2026/9nvd_49833.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 142 5.16 5 C 16472 2.51 5 N 4552 2.21 5 O 4949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s 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: 26147 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4036 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 1 Chain: "B" Number of atoms: 4018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4018 Classifications: {'peptide': 514} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 489} Chain breaks: 3 Chain: "C" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4056 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 497} Chain breaks: 1 Chain: "D" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4141 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 507} Chain breaks: 1 Chain: "E" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4132 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 506} Chain breaks: 1 Chain: "F" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5427 Classifications: {'peptide': 694} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 662} Chain breaks: 6 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.99, per 1000 atoms: 0.23 Number of scatterers: 26147 At special positions: 0 Unit cell: (150.152, 151.248, 162.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 32 15.00 O 4949 8.00 N 4552 7.00 C 16472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 875.1 milliseconds 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6138 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 21 sheets defined 55.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.818A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.944A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 347 through 359 removed outlier: 3.642A pdb=" N VAL A 351 " --> pdb=" O HIS A 347 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.500A pdb=" N LEU A 384 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 385 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 417 removed outlier: 4.878A pdb=" N ARG A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 removed outlier: 3.727A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 463 Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.515A pdb=" N ALA A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.244A pdb=" N PHE A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 removed outlier: 4.033A pdb=" N ALA A 500 " --> pdb=" O GLN A 496 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 530 removed outlier: 4.461A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 4.244A pdb=" N ASN A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.690A pdb=" N LYS A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 619 through 630 removed outlier: 4.068A pdb=" N LEU A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 672 through 684 Processing helix chain 'A' and resid 687 through 698 Processing helix chain 'A' and resid 706 through 718 Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'B' and resid 214 through 219 removed outlier: 3.956A pdb=" N GLY B 219 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 235 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.548A pdb=" N VAL B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.613A pdb=" N VAL B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 277 removed outlier: 3.862A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 removed outlier: 3.607A pdb=" N ALA B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.538A pdb=" N LEU B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 379' Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.531A pdb=" N LEU B 383 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 411 Processing helix chain 'B' and resid 412 through 417 removed outlier: 3.533A pdb=" N HIS B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 removed outlier: 3.601A pdb=" N LEU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 455 removed outlier: 3.650A pdb=" N VAL B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.566A pdb=" N PHE B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.914A pdb=" N TYR B 499 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 4.100A pdb=" N THR B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.672A pdb=" N LEU B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.684A pdb=" N LYS B 572 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 619 through 630 removed outlier: 3.820A pdb=" N LEU B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.518A pdb=" N LEU B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 672 through 684 Processing helix chain 'B' and resid 687 through 699 removed outlier: 3.564A pdb=" N GLN B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 718 Processing helix chain 'B' and resid 724 through 737 Processing helix chain 'C' and resid 214 through 219 removed outlier: 3.607A pdb=" N MET C 218 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 219' Processing helix chain 'C' and resid 223 through 240 removed outlier: 4.161A pdb=" N ALA C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARG C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 265 through 276 removed outlier: 3.575A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.843A pdb=" N ALA C 300 " --> pdb=" O GLY C 296 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 348 through 359 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.982A pdb=" N ARG C 385 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 417 removed outlier: 5.021A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 Processing helix chain 'C' and resid 437 through 455 removed outlier: 3.808A pdb=" N ARG C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 removed outlier: 3.619A pdb=" N ALA C 470 " --> pdb=" O MET C 467 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 471 " --> pdb=" O GLU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.699A pdb=" N PHE C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 530 removed outlier: 4.535A pdb=" N THR C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.955A pdb=" N LEU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 573 removed outlier: 3.719A pdb=" N LYS C 572 " --> pdb=" O SER C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 592 removed outlier: 3.697A pdb=" N ALA C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 619 through 630 removed outlier: 3.871A pdb=" N LEU C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 655 removed outlier: 3.800A pdb=" N LEU C 652 " --> pdb=" O ARG C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 684 Processing helix chain 'C' and resid 687 through 699 removed outlier: 3.713A pdb=" N THR C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 697 " --> pdb=" O THR C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 719 removed outlier: 3.888A pdb=" N GLN C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 737 removed outlier: 4.153A pdb=" N GLY C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 removed outlier: 3.697A pdb=" N MET D 218 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 219 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 240 removed outlier: 3.925A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.894A pdb=" N VAL D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 296 through 317 removed outlier: 3.810A pdb=" N PHE D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 343 through 359 removed outlier: 4.119A pdb=" N HIS D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.727A pdb=" N ILE D 379 " --> pdb=" O PRO D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.966A pdb=" N ARG D 385 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 417 removed outlier: 5.328A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 433 removed outlier: 3.584A pdb=" N LEU D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 455 removed outlier: 3.875A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 484 removed outlier: 3.741A pdb=" N PHE D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 removed outlier: 3.629A pdb=" N SER D 501 " --> pdb=" O GLU D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 531 removed outlier: 4.442A pdb=" N THR D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.723A pdb=" N LEU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 573 removed outlier: 3.667A pdb=" N LYS D 572 " --> pdb=" O SER D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 removed outlier: 4.056A pdb=" N SER D 595 " --> pdb=" O ASP D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 619 through 630 removed outlier: 3.630A pdb=" N LEU D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 656 removed outlier: 3.797A pdb=" N LEU D 652 " --> pdb=" O ARG D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 661 removed outlier: 3.795A pdb=" N PHE D 661 " --> pdb=" O LEU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 684 Processing helix chain 'D' and resid 687 through 699 removed outlier: 3.693A pdb=" N THR D 693 " --> pdb=" O LYS D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 719 removed outlier: 3.520A pdb=" N MET D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN D 719 " --> pdb=" O GLU D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 723 removed outlier: 6.153A pdb=" N GLU D 723 " --> pdb=" O MET D 720 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 720 through 723' Processing helix chain 'D' and resid 724 through 737 removed outlier: 3.920A pdb=" N LYS D 728 " --> pdb=" O TYR D 724 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.812A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 239 " --> pdb=" O PHE E 235 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 249 Processing helix chain 'E' and resid 265 through 277 Processing helix chain 'E' and resid 296 through 317 removed outlier: 3.659A pdb=" N PHE E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 329 through 334 removed outlier: 4.093A pdb=" N ILE E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 359 removed outlier: 4.415A pdb=" N ASP E 348 " --> pdb=" O THR E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 379 Processing helix chain 'E' and resid 380 through 384 removed outlier: 3.642A pdb=" N LEU E 383 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 417 removed outlier: 5.069A pdb=" N ARG E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 437 through 455 removed outlier: 3.888A pdb=" N ARG E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.097A pdb=" N PHE E 480 " --> pdb=" O THR E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 511 through 530 removed outlier: 3.932A pdb=" N THR E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 560 Processing helix chain 'E' and resid 569 through 573 removed outlier: 3.752A pdb=" N LYS E 572 " --> pdb=" O SER E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 594 removed outlier: 4.223A pdb=" N CYS E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 619 through 632 removed outlier: 3.838A pdb=" N LEU E 623 " --> pdb=" O SER E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 655 removed outlier: 3.899A pdb=" N LEU E 652 " --> pdb=" O ARG E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 684 Processing helix chain 'E' and resid 687 through 699 removed outlier: 3.731A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 718 Processing helix chain 'E' and resid 724 through 737 Processing helix chain 'F' and resid 13 through 19 removed outlier: 3.527A pdb=" N SER F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.594A pdb=" N ILE F 107 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 156 through 161 removed outlier: 3.853A pdb=" N LEU F 160 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 236 removed outlier: 3.847A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 241 through 249 removed outlier: 3.553A pdb=" N VAL F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 277 removed outlier: 3.796A pdb=" N LEU F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 306 removed outlier: 3.609A pdb=" N ILE F 302 " --> pdb=" O SER F 298 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 351 through 359 Processing helix chain 'F' and resid 375 through 379 Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 399 through 417 removed outlier: 4.726A pdb=" N ARG F 413 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N MET F 414 " --> pdb=" O HIS F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 Processing helix chain 'F' and resid 437 through 454 Processing helix chain 'F' and resid 455 through 457 No H-bonds generated for 'chain 'F' and resid 455 through 457' Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.532A pdb=" N PHE F 480 " --> pdb=" O THR F 476 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER F 483 " --> pdb=" O ASP F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 503 Processing helix chain 'F' and resid 511 through 530 removed outlier: 4.554A pdb=" N THR F 515 " --> pdb=" O GLY F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 561 removed outlier: 4.272A pdb=" N LEU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 573 removed outlier: 3.567A pdb=" N LYS F 572 " --> pdb=" O SER F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 594 removed outlier: 3.857A pdb=" N LYS F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 619 through 630 removed outlier: 3.931A pdb=" N LEU F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 655 removed outlier: 3.621A pdb=" N LEU F 652 " --> pdb=" O ARG F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 684 Processing helix chain 'F' and resid 687 through 699 removed outlier: 3.744A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 719 removed outlier: 3.802A pdb=" N GLN F 719 " --> pdb=" O GLU F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 736 Processing sheet with id=AA1, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.547A pdb=" N VAL A 285 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 256 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR A 373 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 258 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 391 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 259 " --> pdb=" O MET A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 564 through 568 removed outlier: 4.057A pdb=" N PHE A 564 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 599 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A 566 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 601 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 537 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY A 644 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 539 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE A 665 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 540 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.767A pdb=" N LYS B 283 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 326 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 285 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B 328 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N HIS B 323 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE B 370 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 325 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N MET B 372 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE B 327 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 258 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B 373 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY B 255 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 391 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 536 through 537 removed outlier: 3.989A pdb=" N VAL B 537 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 642 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 536 through 537 removed outlier: 3.989A pdb=" N VAL B 537 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 642 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 564 " --> pdb=" O LEU B 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 283 through 285 removed outlier: 6.916A pdb=" N LYS C 283 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 325 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 370 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 327 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET C 372 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 256 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR C 373 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C 258 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 257 " --> pdb=" O MET C 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 564 through 568 removed outlier: 4.049A pdb=" N PHE C 564 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 566 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 601 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 537 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE C 642 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 539 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 644 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 670 through 672 removed outlier: 3.532A pdb=" N ILE C 705 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR C 672 " --> pdb=" O VAL C 703 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 703 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 283 through 285 removed outlier: 3.622A pdb=" N VAL D 285 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP D 328 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS D 323 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE D 370 " --> pdb=" O HIS D 323 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE D 325 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N MET D 372 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE D 327 " --> pdb=" O MET D 372 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 256 " --> pdb=" O GLY D 371 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR D 373 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU D 258 " --> pdb=" O THR D 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 457 through 458 removed outlier: 3.878A pdb=" N LYS D 458 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL D 465 " --> pdb=" O LYS D 458 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 564 through 568 removed outlier: 4.169A pdb=" N PHE D 564 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N CYS D 599 " --> pdb=" O PHE D 564 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 566 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 601 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER D 598 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE D 643 " --> pdb=" O SER D 598 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 600 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR D 645 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL D 602 " --> pdb=" O THR D 645 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 537 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N THR D 663 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER D 538 " --> pdb=" O THR D 663 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE D 665 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 540 " --> pdb=" O ILE D 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 283 through 286 removed outlier: 6.063A pdb=" N LYS E 283 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP E 328 " --> pdb=" O LYS E 283 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL E 285 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET E 372 " --> pdb=" O PHE E 327 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N MET E 393 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU E 257 " --> pdb=" O MET E 393 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 457 through 458 Processing sheet with id=AB5, first strand: chain 'E' and resid 564 through 568 removed outlier: 4.527A pdb=" N PHE E 564 " --> pdb=" O LEU E 597 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS E 599 " --> pdb=" O PHE E 564 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS E 566 " --> pdb=" O CYS E 599 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 601 " --> pdb=" O LYS E 566 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP E 603 " --> pdb=" O CYS E 568 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 537 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 642 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 539 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N THR E 663 " --> pdb=" O LEU E 536 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER E 538 " --> pdb=" O THR E 663 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE E 665 " --> pdb=" O SER E 538 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 540 " --> pdb=" O ILE E 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 670 through 672 removed outlier: 3.996A pdb=" N ALA E 671 " --> pdb=" O VAL E 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 23 through 24 removed outlier: 7.697A pdb=" N VAL F 60 " --> pdb=" O SER F 5 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLN F 7 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE F 62 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA F 9 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 12.635A pdb=" N GLU F 77 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER F 40 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU F 79 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 140 removed outlier: 5.827A pdb=" N PHE F 145 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE F 101 " --> pdb=" O PHE F 145 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU F 147 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE F 99 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 149 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE F 97 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP F 151 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N MET F 95 " --> pdb=" O ASP F 151 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLU F 153 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ALA F 184 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET F 95 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLU F 186 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE F 97 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 129 through 131 Processing sheet with id=AC1, first strand: chain 'F' and resid 283 through 286 removed outlier: 4.020A pdb=" N LYS F 283 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS F 323 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE F 370 " --> pdb=" O HIS F 323 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE F 325 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N MET F 372 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE F 327 " --> pdb=" O MET F 372 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 564 through 568 removed outlier: 4.301A pdb=" N PHE F 564 " --> pdb=" O LEU F 597 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS F 599 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS F 566 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL F 601 " --> pdb=" O LYS F 566 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 537 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR F 663 " --> pdb=" O SER F 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 611 through 612 removed outlier: 3.583A pdb=" N ARG F 617 " --> pdb=" O VAL F 612 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3360 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: 3.73 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8478 1.34 - 1.46: 3330 1.46 - 1.57: 14459 1.57 - 1.69: 41 1.69 - 1.81: 245 Bond restraints: 26553 Sorted by residual: bond pdb=" CA ILE F 46 " pdb=" CB ILE F 46 " ideal model delta sigma weight residual 1.539 1.583 -0.045 1.19e-02 7.06e+03 1.40e+01 bond pdb=" CA VAL F 60 " pdb=" CB VAL F 60 " ideal model delta sigma weight residual 1.537 1.580 -0.043 1.26e-02 6.30e+03 1.16e+01 bond pdb=" CB MET A 453 " pdb=" CG MET A 453 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" C VAL F 60 " pdb=" N ALA F 61 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.41e-02 5.03e+03 5.15e+00 bond pdb=" C TYR F 29 " pdb=" O TYR F 29 " ideal model delta sigma weight residual 1.234 1.262 -0.028 1.25e-02 6.40e+03 5.08e+00 ... (remaining 26548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 34545 2.23 - 4.46: 1161 4.46 - 6.69: 115 6.69 - 8.91: 17 8.91 - 11.14: 4 Bond angle restraints: 35842 Sorted by residual: angle pdb=" N PHE F 240 " pdb=" CA PHE F 240 " pdb=" C PHE F 240 " ideal model delta sigma weight residual 110.20 117.61 -7.41 1.44e+00 4.82e-01 2.65e+01 angle pdb=" CA ASN F 106 " pdb=" CB ASN F 106 " pdb=" CG ASN F 106 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.00e+00 1.00e+00 1.90e+01 angle pdb=" O1A ATP D 802 " pdb=" PA ATP D 802 " pdb=" O3A ATP D 802 " ideal model delta sigma weight residual 111.24 100.64 10.60 2.72e+00 1.35e-01 1.52e+01 angle pdb=" O2A ATP D 802 " pdb=" PA ATP D 802 " pdb=" O3A ATP D 802 " ideal model delta sigma weight residual 106.94 99.72 7.22 1.88e+00 2.83e-01 1.48e+01 angle pdb=" C GLY F 197 " pdb=" N LYS F 198 " pdb=" CA LYS F 198 " ideal model delta sigma weight residual 121.54 128.73 -7.19 1.91e+00 2.74e-01 1.42e+01 ... (remaining 35837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.34: 15365 20.34 - 40.68: 956 40.68 - 61.02: 216 61.02 - 81.36: 55 81.36 - 101.70: 18 Dihedral angle restraints: 16610 sinusoidal: 7133 harmonic: 9477 Sorted by residual: dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 41.71 -101.70 1 2.00e+01 2.50e-03 2.89e+01 dihedral pdb=" CA ASP F 113 " pdb=" C ASP F 113 " pdb=" N THR F 114 " pdb=" CA THR F 114 " ideal model delta harmonic sigma weight residual -180.00 -155.24 -24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ALA F 154 " pdb=" C ALA F 154 " pdb=" N MET F 155 " pdb=" CA MET F 155 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 16607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3161 0.057 - 0.115: 778 0.115 - 0.172: 147 0.172 - 0.230: 11 0.230 - 0.287: 3 Chirality restraints: 4100 Sorted by residual: chirality pdb=" CA HIS F 252 " pdb=" N HIS F 252 " pdb=" C HIS F 252 " pdb=" CB HIS F 252 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C4' ATP F 801 " pdb=" C3' ATP F 801 " pdb=" C5' ATP F 801 " pdb=" O4' ATP F 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C4' ATP D 801 " pdb=" C3' ATP D 801 " pdb=" C5' ATP D 801 " pdb=" O4' ATP D 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.74 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 4097 not shown) Planarity restraints: 4572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 240 " -0.024 2.00e-02 2.50e+03 2.88e-02 1.45e+01 pdb=" CG PHE F 240 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE F 240 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE F 240 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 240 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE F 240 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE F 240 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 313 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C GLN C 313 " 0.063 2.00e-02 2.50e+03 pdb=" O GLN C 313 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG C 314 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 298 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C SER C 298 " -0.054 2.00e-02 2.50e+03 pdb=" O SER C 298 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU C 299 " 0.018 2.00e-02 2.50e+03 ... (remaining 4569 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 10881 2.92 - 3.42: 25826 3.42 - 3.91: 38151 3.91 - 4.41: 43078 4.41 - 4.90: 71654 Nonbonded interactions: 189590 Sorted by model distance: nonbonded pdb=" O GLU D 471 " pdb=" OG SER D 472 " model vdw 2.430 3.040 nonbonded pdb=" O LEU D 407 " pdb=" OG1 THR D 411 " model vdw 2.444 3.040 nonbonded pdb=" O PRO D 242 " pdb=" OE1 GLU D 246 " model vdw 2.445 3.040 nonbonded pdb=" O ALA F 447 " pdb=" OG SER F 450 " model vdw 2.458 3.040 nonbonded pdb=" O ASP A 603 " pdb=" OG1 THR A 645 " model vdw 2.459 3.040 ... (remaining 189585 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 218 through 338 or resid 345 through 457 or resid 471 thro \ ugh 484 or resid 499 through 801)) selection = (chain 'B' and (resid 218 through 484 or resid 499 through 801)) selection = (chain 'C' and (resid 218 through 338 or resid 345 through 457 or resid 471 thro \ ugh 801)) selection = (chain 'D' and (resid 218 through 338 or resid 345 through 457 or resid 471 thro \ ugh 484 or resid 499 through 801)) selection = (chain 'E' and (resid 218 through 338 or resid 345 through 457 or resid 471 thro \ ugh 484 or resid 499 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.580 Find NCS groups from input model: 0.650 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.006 0.096 26553 Z= 0.276 Angle : 0.931 11.142 35842 Z= 0.519 Chirality : 0.051 0.287 4100 Planarity : 0.005 0.051 4572 Dihedral : 14.714 101.703 10472 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.14 % Favored : 97.34 % Rotamer: Outliers : 1.20 % Allowed : 0.92 % Favored : 97.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.05 % 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: 1.19 (0.15), residues: 3274 helix: 1.75 (0.14), residues: 1553 sheet: 1.16 (0.24), residues: 457 loop : -0.55 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG D 388 TYR 0.021 0.003 TYR F 83 PHE 0.057 0.002 PHE F 240 TRP 0.016 0.003 TRP E 213 HIS 0.017 0.003 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00561 (26553) covalent geometry : angle 0.93097 (35842) hydrogen bonds : bond 0.15790 ( 1171) hydrogen bonds : angle 5.88803 ( 3360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 405 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 SER cc_start: 0.8515 (t) cc_final: 0.8026 (m) REVERT: A 547 SER cc_start: 0.8614 (t) cc_final: 0.8310 (m) REVERT: A 582 CYS cc_start: 0.9404 (m) cc_final: 0.9108 (m) REVERT: A 720 MET cc_start: 0.8978 (tpp) cc_final: 0.8299 (tmm) REVERT: A 724 TYR cc_start: 0.8808 (m-80) cc_final: 0.8181 (m-80) REVERT: B 286 ASN cc_start: 0.9213 (m-40) cc_final: 0.8863 (t0) REVERT: B 328 ASP cc_start: 0.9219 (t0) cc_final: 0.8852 (t0) REVERT: B 372 MET cc_start: 0.8652 (mtm) cc_final: 0.8077 (mmm) REVERT: B 453 MET cc_start: 0.9373 (mtp) cc_final: 0.9130 (mtp) REVERT: B 539 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7696 (p) REVERT: B 542 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: B 630 LEU cc_start: 0.9362 (mt) cc_final: 0.9052 (tt) REVERT: B 713 LEU cc_start: 0.9695 (mt) cc_final: 0.9246 (pp) REVERT: B 716 MET cc_start: 0.9147 (mtm) cc_final: 0.8868 (mmp) REVERT: C 245 VAL cc_start: 0.9437 (t) cc_final: 0.9194 (m) REVERT: C 657 MET cc_start: 0.9329 (ttt) cc_final: 0.9116 (ttm) REVERT: D 206 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: D 226 GLU cc_start: 0.8773 (mp0) cc_final: 0.8319 (mt-10) REVERT: D 286 ASN cc_start: 0.8502 (m110) cc_final: 0.7949 (p0) REVERT: D 444 LEU cc_start: 0.9335 (tp) cc_final: 0.9065 (mt) REVERT: D 573 MET cc_start: 0.9326 (ptp) cc_final: 0.8832 (ptp) REVERT: D 623 LEU cc_start: 0.9759 (tp) cc_final: 0.9553 (tt) REVERT: D 712 MET cc_start: 0.8931 (tpt) cc_final: 0.8637 (tpp) REVERT: D 720 MET cc_start: 0.8955 (mmm) cc_final: 0.8654 (mtt) REVERT: E 329 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8068 (mt-10) REVERT: E 367 ILE cc_start: 0.9293 (pt) cc_final: 0.9044 (mm) REVERT: E 428 GLU cc_start: 0.9039 (tt0) cc_final: 0.8797 (pp20) REVERT: E 503 ILE cc_start: 0.9361 (mt) cc_final: 0.9018 (mp) REVERT: E 712 MET cc_start: 0.9464 (tpp) cc_final: 0.8927 (tpp) REVERT: E 716 MET cc_start: 0.9324 (mtp) cc_final: 0.8766 (mtm) REVERT: E 720 MET cc_start: 0.8621 (mmm) cc_final: 0.8038 (tpp) REVERT: E 724 TYR cc_start: 0.8851 (m-80) cc_final: 0.8044 (m-80) REVERT: F 87 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8478 (mmtm) REVERT: F 229 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6711 (t0) REVERT: F 233 ARG cc_start: 0.9347 (ttt180) cc_final: 0.9029 (ptp90) REVERT: F 354 LEU cc_start: 0.9181 (tp) cc_final: 0.8846 (pp) REVERT: F 573 MET cc_start: 0.9429 (ptp) cc_final: 0.9116 (ptp) REVERT: F 582 CYS cc_start: 0.9312 (m) cc_final: 0.8859 (p) REVERT: F 642 ILE cc_start: 0.9582 (mt) cc_final: 0.9259 (tp) REVERT: F 712 MET cc_start: 0.9591 (tpp) cc_final: 0.9385 (tpp) outliers start: 34 outliers final: 8 residues processed: 434 average time/residue: 0.1725 time to fit residues: 117.3968 Evaluate side-chains 225 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.0770 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 546 HIS ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 HIS F 675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.032194 restraints weight = 219657.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.033322 restraints weight = 138103.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.034129 restraints weight = 98093.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.034703 restraints weight = 75523.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.035144 restraints weight = 61961.231| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26553 Z= 0.141 Angle : 0.603 15.029 35842 Z= 0.318 Chirality : 0.044 0.183 4100 Planarity : 0.004 0.051 4572 Dihedral : 10.494 87.985 3864 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.17 % Favored : 97.62 % Rotamer: Outliers : 0.14 % Allowed : 2.05 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.44 (0.15), residues: 3274 helix: 1.92 (0.13), residues: 1590 sheet: 1.03 (0.23), residues: 461 loop : -0.34 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 403 TYR 0.013 0.001 TYR E 502 PHE 0.015 0.001 PHE F 240 TRP 0.011 0.001 TRP C 704 HIS 0.004 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00293 (26553) covalent geometry : angle 0.60323 (35842) hydrogen bonds : bond 0.04268 ( 1171) hydrogen bonds : angle 4.49174 ( 3360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.8489 (ptp) cc_final: 0.8236 (pmm) REVERT: A 343 SER cc_start: 0.8108 (t) cc_final: 0.7839 (m) REVERT: A 520 ASP cc_start: 0.9352 (t0) cc_final: 0.9006 (t0) REVERT: A 547 SER cc_start: 0.9033 (t) cc_final: 0.8778 (p) REVERT: A 582 CYS cc_start: 0.9374 (m) cc_final: 0.9122 (m) REVERT: A 585 MET cc_start: 0.9213 (mmm) cc_final: 0.8940 (mmt) REVERT: A 712 MET cc_start: 0.9294 (tpp) cc_final: 0.8712 (tpp) REVERT: A 720 MET cc_start: 0.8967 (tpp) cc_final: 0.8249 (tpp) REVERT: A 724 TYR cc_start: 0.8850 (m-80) cc_final: 0.8458 (m-80) REVERT: B 286 ASN cc_start: 0.9298 (m-40) cc_final: 0.8975 (t0) REVERT: B 328 ASP cc_start: 0.9433 (t0) cc_final: 0.9008 (t0) REVERT: B 372 MET cc_start: 0.8488 (mtm) cc_final: 0.7986 (mmm) REVERT: B 414 MET cc_start: 0.9563 (ptp) cc_final: 0.9314 (ttt) REVERT: B 585 MET cc_start: 0.9372 (tpp) cc_final: 0.9104 (tpp) REVERT: B 645 THR cc_start: 0.9248 (m) cc_final: 0.8683 (p) REVERT: B 657 MET cc_start: 0.7927 (mmp) cc_final: 0.7377 (tpp) REVERT: B 715 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8868 (tp30) REVERT: C 248 MET cc_start: 0.9524 (mtm) cc_final: 0.9307 (mtp) REVERT: C 467 MET cc_start: 0.6975 (mpp) cc_final: 0.5320 (mpp) REVERT: C 712 MET cc_start: 0.9203 (tpp) cc_final: 0.8768 (tpp) REVERT: C 716 MET cc_start: 0.9227 (tpp) cc_final: 0.8929 (mtt) REVERT: D 286 ASN cc_start: 0.8587 (m110) cc_final: 0.8008 (p0) REVERT: D 393 MET cc_start: 0.8445 (tpp) cc_final: 0.7580 (tpp) REVERT: D 720 MET cc_start: 0.8916 (mmm) cc_final: 0.8553 (mtt) REVERT: E 248 MET cc_start: 0.7153 (tpt) cc_final: 0.6938 (mmm) REVERT: E 329 GLU cc_start: 0.8859 (mm-30) cc_final: 0.7882 (mt-10) REVERT: E 367 ILE cc_start: 0.9479 (pt) cc_final: 0.9181 (mm) REVERT: E 573 MET cc_start: 0.9244 (mpp) cc_final: 0.8847 (mpp) REVERT: E 604 ASP cc_start: 0.9240 (m-30) cc_final: 0.8942 (m-30) REVERT: E 655 MET cc_start: 0.9372 (mmp) cc_final: 0.8976 (mmm) REVERT: E 657 MET cc_start: 0.9374 (tmm) cc_final: 0.9071 (tmm) REVERT: E 712 MET cc_start: 0.9533 (tpp) cc_final: 0.9288 (tmm) REVERT: E 720 MET cc_start: 0.8643 (mmm) cc_final: 0.7861 (tpp) REVERT: E 724 TYR cc_start: 0.8857 (m-80) cc_final: 0.7981 (m-80) REVERT: F 354 LEU cc_start: 0.9378 (tp) cc_final: 0.9009 (pp) REVERT: F 573 MET cc_start: 0.9385 (ptp) cc_final: 0.9096 (ptp) REVERT: F 712 MET cc_start: 0.9678 (tpp) cc_final: 0.9043 (tpp) REVERT: F 720 MET cc_start: 0.9348 (tpt) cc_final: 0.8881 (tpp) outliers start: 4 outliers final: 0 residues processed: 230 average time/residue: 0.1520 time to fit residues: 57.1867 Evaluate side-chains 162 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 71 optimal weight: 8.9990 chunk 318 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 297 optimal weight: 30.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 GLN C 353 GLN C 408 HIS C 527 GLN C 696 GLN D 624 GLN ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 410 HIS ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.041560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.030164 restraints weight = 233485.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.031168 restraints weight = 148952.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.031873 restraints weight = 107083.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.032418 restraints weight = 83487.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.032801 restraints weight = 69029.598| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 26553 Z= 0.239 Angle : 0.704 9.113 35842 Z= 0.364 Chirality : 0.045 0.343 4100 Planarity : 0.005 0.057 4572 Dihedral : 9.991 87.762 3864 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.57 % Favored : 97.25 % Rotamer: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3274 helix: 1.46 (0.13), residues: 1589 sheet: 0.66 (0.23), residues: 458 loop : -0.48 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 233 TYR 0.017 0.002 TYR D 611 PHE 0.025 0.002 PHE D 240 TRP 0.012 0.001 TRP C 213 HIS 0.012 0.002 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00510 (26553) covalent geometry : angle 0.70438 (35842) hydrogen bonds : bond 0.04282 ( 1171) hydrogen bonds : angle 4.68817 ( 3360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 SER cc_start: 0.8105 (t) cc_final: 0.7887 (m) REVERT: A 520 ASP cc_start: 0.9448 (t0) cc_final: 0.9132 (t0) REVERT: A 720 MET cc_start: 0.9097 (tpp) cc_final: 0.8386 (tmm) REVERT: A 724 TYR cc_start: 0.8946 (m-80) cc_final: 0.8351 (m-80) REVERT: B 286 ASN cc_start: 0.9386 (m-40) cc_final: 0.8871 (t0) REVERT: B 328 ASP cc_start: 0.9410 (t0) cc_final: 0.9175 (t0) REVERT: B 372 MET cc_start: 0.8638 (mtm) cc_final: 0.7959 (mmm) REVERT: B 414 MET cc_start: 0.9566 (ptp) cc_final: 0.9298 (ttt) REVERT: B 504 MET cc_start: 0.9206 (ttm) cc_final: 0.8975 (mmm) REVERT: B 655 MET cc_start: 0.9234 (tpt) cc_final: 0.8548 (tpp) REVERT: B 657 MET cc_start: 0.8643 (mmp) cc_final: 0.7273 (mmp) REVERT: B 712 MET cc_start: 0.9232 (tmm) cc_final: 0.8328 (tmm) REVERT: B 715 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8864 (mm-30) REVERT: B 716 MET cc_start: 0.9049 (mmp) cc_final: 0.8675 (mmp) REVERT: C 248 MET cc_start: 0.9392 (mtm) cc_final: 0.9152 (mtp) REVERT: C 393 MET cc_start: 0.8885 (mmm) cc_final: 0.8584 (mmm) REVERT: C 657 MET cc_start: 0.9149 (ttp) cc_final: 0.8678 (ptp) REVERT: D 393 MET cc_start: 0.8433 (tpp) cc_final: 0.7751 (tpp) REVERT: D 712 MET cc_start: 0.8933 (tpt) cc_final: 0.8007 (tpt) REVERT: D 716 MET cc_start: 0.8857 (ptp) cc_final: 0.7873 (ptp) REVERT: D 720 MET cc_start: 0.8926 (mmm) cc_final: 0.8548 (mtt) REVERT: E 248 MET cc_start: 0.7531 (tpt) cc_final: 0.7210 (mmm) REVERT: E 329 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8697 (mm-30) REVERT: E 367 ILE cc_start: 0.9502 (pt) cc_final: 0.9219 (mm) REVERT: E 655 MET cc_start: 0.9341 (mmp) cc_final: 0.8780 (mmm) REVERT: E 657 MET cc_start: 0.9457 (tmm) cc_final: 0.8999 (tmm) REVERT: E 712 MET cc_start: 0.9506 (tpp) cc_final: 0.9040 (tpp) REVERT: E 716 MET cc_start: 0.9352 (mtp) cc_final: 0.8995 (mtm) REVERT: E 720 MET cc_start: 0.8749 (mmm) cc_final: 0.7961 (tpp) REVERT: E 724 TYR cc_start: 0.8928 (m-80) cc_final: 0.8070 (m-80) REVERT: F 1 MET cc_start: 0.5237 (mtm) cc_final: 0.4624 (pmm) REVERT: F 354 LEU cc_start: 0.9409 (tp) cc_final: 0.9021 (pp) REVERT: F 453 MET cc_start: 0.8700 (mtm) cc_final: 0.8463 (ptp) REVERT: F 467 MET cc_start: 0.3540 (ptp) cc_final: 0.3217 (ptp) REVERT: F 712 MET cc_start: 0.9622 (tpp) cc_final: 0.9143 (tpp) REVERT: F 720 MET cc_start: 0.9498 (tpt) cc_final: 0.8983 (tpp) outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 0.1477 time to fit residues: 42.3830 Evaluate side-chains 138 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 32 optimal weight: 0.7980 chunk 197 optimal weight: 0.0870 chunk 164 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 HIS C 214 ASN C 410 HIS E 323 HIS ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN F 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.031330 restraints weight = 224544.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.032385 restraints weight = 142397.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.033142 restraints weight = 101931.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.033687 restraints weight = 79077.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.034088 restraints weight = 65207.960| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26553 Z= 0.100 Angle : 0.525 9.807 35842 Z= 0.275 Chirality : 0.042 0.142 4100 Planarity : 0.004 0.055 4572 Dihedral : 9.479 86.390 3864 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.68 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.39 (0.15), residues: 3274 helix: 1.95 (0.13), residues: 1582 sheet: 0.83 (0.23), residues: 462 loop : -0.37 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 648 TYR 0.010 0.001 TYR C 724 PHE 0.013 0.001 PHE F 240 TRP 0.012 0.001 TRP F 510 HIS 0.005 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00211 (26553) covalent geometry : angle 0.52450 (35842) hydrogen bonds : bond 0.03185 ( 1171) hydrogen bonds : angle 4.06511 ( 3360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ASP cc_start: 0.9453 (t0) cc_final: 0.9101 (t0) REVERT: A 720 MET cc_start: 0.9024 (tpp) cc_final: 0.8282 (tpp) REVERT: A 724 TYR cc_start: 0.8906 (m-80) cc_final: 0.8482 (m-80) REVERT: B 286 ASN cc_start: 0.9336 (m-40) cc_final: 0.8845 (t0) REVERT: B 328 ASP cc_start: 0.9427 (t0) cc_final: 0.9186 (t0) REVERT: B 372 MET cc_start: 0.8343 (mtm) cc_final: 0.7817 (mmm) REVERT: B 397 LEU cc_start: 0.8970 (tp) cc_final: 0.8762 (tp) REVERT: B 414 MET cc_start: 0.9582 (ptp) cc_final: 0.9338 (ttp) REVERT: B 504 MET cc_start: 0.9171 (ttm) cc_final: 0.8908 (mmm) REVERT: B 655 MET cc_start: 0.9111 (tpt) cc_final: 0.8799 (tpp) REVERT: B 657 MET cc_start: 0.8556 (mmp) cc_final: 0.7782 (mmm) REVERT: B 712 MET cc_start: 0.9307 (tmm) cc_final: 0.8535 (tmm) REVERT: B 715 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8820 (mm-30) REVERT: B 716 MET cc_start: 0.9074 (mmp) cc_final: 0.8700 (mmp) REVERT: C 248 MET cc_start: 0.9382 (mtm) cc_final: 0.9087 (mtp) REVERT: C 393 MET cc_start: 0.8920 (mmm) cc_final: 0.8578 (mmm) REVERT: C 657 MET cc_start: 0.9126 (ttp) cc_final: 0.8644 (ptp) REVERT: D 334 CYS cc_start: 0.8710 (m) cc_final: 0.8509 (m) REVERT: D 393 MET cc_start: 0.8437 (tpp) cc_final: 0.7962 (tpp) REVERT: D 712 MET cc_start: 0.8882 (tpt) cc_final: 0.8223 (tpt) REVERT: D 720 MET cc_start: 0.8864 (mmm) cc_final: 0.8529 (mtt) REVERT: E 367 ILE cc_start: 0.9474 (pt) cc_final: 0.9191 (mm) REVERT: E 573 MET cc_start: 0.9132 (mpp) cc_final: 0.8891 (mpp) REVERT: E 655 MET cc_start: 0.9389 (mmp) cc_final: 0.9088 (mmm) REVERT: E 657 MET cc_start: 0.9386 (tmm) cc_final: 0.9039 (tmm) REVERT: E 712 MET cc_start: 0.9490 (tpp) cc_final: 0.8798 (tpp) REVERT: E 716 MET cc_start: 0.9315 (mtp) cc_final: 0.8700 (mtm) REVERT: E 720 MET cc_start: 0.8732 (mmm) cc_final: 0.7937 (tpp) REVERT: E 724 TYR cc_start: 0.8927 (m-80) cc_final: 0.7994 (m-80) REVERT: F 354 LEU cc_start: 0.9390 (tp) cc_final: 0.9014 (pp) REVERT: F 453 MET cc_start: 0.8548 (mtm) cc_final: 0.8344 (ptp) REVERT: F 712 MET cc_start: 0.9647 (tpp) cc_final: 0.9078 (tmm) REVERT: F 716 MET cc_start: 0.9041 (ptm) cc_final: 0.8246 (ptm) REVERT: F 720 MET cc_start: 0.9550 (tpt) cc_final: 0.9007 (tpp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1442 time to fit residues: 43.3846 Evaluate side-chains 144 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 10 optimal weight: 20.0000 chunk 290 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 293 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 128 optimal weight: 0.4980 chunk 204 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN D 454 ASN ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.031782 restraints weight = 225773.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032809 restraints weight = 144227.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.033532 restraints weight = 103772.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.034089 restraints weight = 80734.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.034458 restraints weight = 66455.316| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 26553 Z= 0.089 Angle : 0.488 8.794 35842 Z= 0.256 Chirality : 0.041 0.146 4100 Planarity : 0.004 0.053 4572 Dihedral : 8.875 84.684 3864 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.95 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.59 (0.15), residues: 3274 helix: 2.10 (0.13), residues: 1580 sheet: 0.94 (0.23), residues: 464 loop : -0.24 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 375 TYR 0.011 0.001 TYR C 724 PHE 0.012 0.001 PHE F 240 TRP 0.014 0.001 TRP F 510 HIS 0.005 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00185 (26553) covalent geometry : angle 0.48812 (35842) hydrogen bonds : bond 0.02778 ( 1171) hydrogen bonds : angle 3.78361 ( 3360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ASP cc_start: 0.9380 (t0) cc_final: 0.9028 (t0) REVERT: A 720 MET cc_start: 0.8988 (tpp) cc_final: 0.8291 (tpp) REVERT: A 724 TYR cc_start: 0.8847 (m-80) cc_final: 0.8485 (m-80) REVERT: B 286 ASN cc_start: 0.9377 (m-40) cc_final: 0.8971 (t0) REVERT: B 328 ASP cc_start: 0.9357 (t0) cc_final: 0.9154 (t0) REVERT: B 372 MET cc_start: 0.8321 (mtm) cc_final: 0.7905 (mmm) REVERT: B 397 LEU cc_start: 0.9010 (tp) cc_final: 0.8753 (tp) REVERT: B 414 MET cc_start: 0.9496 (ptp) cc_final: 0.9261 (ttp) REVERT: B 453 MET cc_start: 0.9586 (mpp) cc_final: 0.9382 (mpp) REVERT: B 645 THR cc_start: 0.9272 (m) cc_final: 0.8721 (p) REVERT: B 655 MET cc_start: 0.8970 (tpt) cc_final: 0.8414 (tpp) REVERT: B 657 MET cc_start: 0.8666 (mmp) cc_final: 0.7247 (mmp) REVERT: B 712 MET cc_start: 0.9231 (tmm) cc_final: 0.8424 (tmm) REVERT: B 715 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8810 (tp30) REVERT: B 716 MET cc_start: 0.8955 (mmp) cc_final: 0.8608 (mmp) REVERT: C 248 MET cc_start: 0.9302 (mtm) cc_final: 0.9019 (mtp) REVERT: C 393 MET cc_start: 0.8783 (mmm) cc_final: 0.8402 (mmm) REVERT: C 504 MET cc_start: 0.8806 (ptm) cc_final: 0.8058 (tmm) REVERT: D 393 MET cc_start: 0.8617 (tpp) cc_final: 0.8158 (tpp) REVERT: D 716 MET cc_start: 0.8548 (ptp) cc_final: 0.8338 (ptp) REVERT: D 720 MET cc_start: 0.8880 (mmm) cc_final: 0.8562 (mtt) REVERT: E 367 ILE cc_start: 0.9367 (pt) cc_final: 0.9093 (mm) REVERT: E 573 MET cc_start: 0.9063 (mpp) cc_final: 0.8827 (mpp) REVERT: E 655 MET cc_start: 0.9364 (mmp) cc_final: 0.9105 (mmp) REVERT: E 657 MET cc_start: 0.9424 (tmm) cc_final: 0.9078 (tmm) REVERT: E 712 MET cc_start: 0.9420 (tpp) cc_final: 0.8644 (tpp) REVERT: E 716 MET cc_start: 0.9251 (mtp) cc_final: 0.8609 (mtm) REVERT: E 720 MET cc_start: 0.8710 (mmm) cc_final: 0.7920 (tpp) REVERT: E 724 TYR cc_start: 0.8996 (m-80) cc_final: 0.8193 (m-80) REVERT: F 1 MET cc_start: 0.5029 (pmm) cc_final: 0.3358 (tpp) REVERT: F 354 LEU cc_start: 0.9368 (tp) cc_final: 0.8990 (pp) REVERT: F 453 MET cc_start: 0.8455 (mtm) cc_final: 0.8204 (ptp) REVERT: F 712 MET cc_start: 0.9636 (tpp) cc_final: 0.9061 (tmm) REVERT: F 716 MET cc_start: 0.8945 (ptm) cc_final: 0.8157 (ptm) REVERT: F 720 MET cc_start: 0.9505 (tpt) cc_final: 0.9039 (tpp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1555 time to fit residues: 46.1285 Evaluate side-chains 141 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 276 optimal weight: 30.0000 chunk 117 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 183 optimal weight: 0.0770 chunk 221 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 292 optimal weight: 1.9990 chunk 262 optimal weight: 20.0000 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 ASN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.031221 restraints weight = 225752.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.032262 restraints weight = 143824.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.033014 restraints weight = 103068.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.033559 restraints weight = 79912.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.033944 restraints weight = 65794.402| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 26553 Z= 0.099 Angle : 0.488 8.698 35842 Z= 0.256 Chirality : 0.041 0.165 4100 Planarity : 0.004 0.054 4572 Dihedral : 8.517 87.780 3864 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.17 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.68 (0.15), residues: 3274 helix: 2.18 (0.13), residues: 1583 sheet: 0.93 (0.23), residues: 470 loop : -0.21 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 385 TYR 0.009 0.001 TYR C 724 PHE 0.017 0.001 PHE F 492 TRP 0.011 0.001 TRP F 510 HIS 0.004 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00210 (26553) covalent geometry : angle 0.48788 (35842) hydrogen bonds : bond 0.02735 ( 1171) hydrogen bonds : angle 3.80137 ( 3360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ASP cc_start: 0.9469 (t0) cc_final: 0.9131 (t0) REVERT: A 720 MET cc_start: 0.9025 (tpp) cc_final: 0.8346 (tpp) REVERT: A 724 TYR cc_start: 0.8916 (m-80) cc_final: 0.8517 (m-80) REVERT: B 286 ASN cc_start: 0.9325 (m-40) cc_final: 0.8832 (t0) REVERT: B 328 ASP cc_start: 0.9430 (t0) cc_final: 0.9202 (t0) REVERT: B 372 MET cc_start: 0.8454 (mtm) cc_final: 0.7884 (mmm) REVERT: B 397 LEU cc_start: 0.8971 (tp) cc_final: 0.8734 (tp) REVERT: B 414 MET cc_start: 0.9552 (ptp) cc_final: 0.9313 (ttp) REVERT: B 655 MET cc_start: 0.9164 (tpt) cc_final: 0.8947 (tpp) REVERT: B 657 MET cc_start: 0.8792 (mmp) cc_final: 0.8069 (mmp) REVERT: B 712 MET cc_start: 0.9295 (tmm) cc_final: 0.8517 (tmm) REVERT: B 715 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8825 (tp30) REVERT: B 716 MET cc_start: 0.9103 (mmp) cc_final: 0.8669 (mmp) REVERT: C 248 MET cc_start: 0.9344 (mtm) cc_final: 0.9064 (mtp) REVERT: C 393 MET cc_start: 0.8883 (mmm) cc_final: 0.8482 (mmm) REVERT: C 504 MET cc_start: 0.8958 (ptm) cc_final: 0.8150 (tmm) REVERT: C 655 MET cc_start: 0.9360 (ttm) cc_final: 0.9117 (ttm) REVERT: C 657 MET cc_start: 0.8878 (ptp) cc_final: 0.8550 (ptp) REVERT: D 248 MET cc_start: 0.8363 (tpp) cc_final: 0.8135 (tpp) REVERT: D 393 MET cc_start: 0.8869 (tpp) cc_final: 0.8460 (tpp) REVERT: D 720 MET cc_start: 0.8836 (mmm) cc_final: 0.8372 (mtt) REVERT: E 367 ILE cc_start: 0.9396 (pt) cc_final: 0.9113 (mm) REVERT: E 573 MET cc_start: 0.9152 (mpp) cc_final: 0.8928 (mpp) REVERT: E 655 MET cc_start: 0.9367 (mmp) cc_final: 0.9105 (mmp) REVERT: E 657 MET cc_start: 0.9406 (tmm) cc_final: 0.9134 (tmm) REVERT: E 712 MET cc_start: 0.9454 (tpp) cc_final: 0.8722 (tpp) REVERT: E 716 MET cc_start: 0.9298 (mtp) cc_final: 0.8714 (mtm) REVERT: E 720 MET cc_start: 0.8715 (mmm) cc_final: 0.7921 (tpp) REVERT: E 724 TYR cc_start: 0.9021 (m-80) cc_final: 0.8245 (m-80) REVERT: F 1 MET cc_start: 0.4896 (pmm) cc_final: 0.3349 (tpp) REVERT: F 95 MET cc_start: 0.8619 (tpp) cc_final: 0.8419 (tpp) REVERT: F 354 LEU cc_start: 0.9403 (tp) cc_final: 0.9015 (pp) REVERT: F 712 MET cc_start: 0.9643 (tpp) cc_final: 0.9335 (tmm) REVERT: F 720 MET cc_start: 0.9613 (tpt) cc_final: 0.9147 (tpp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1480 time to fit residues: 41.9859 Evaluate side-chains 140 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 93 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 201 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 264 optimal weight: 30.0000 chunk 272 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN E 323 HIS ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.029943 restraints weight = 234271.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.030900 restraints weight = 152020.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.031602 restraints weight = 110451.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.032110 restraints weight = 86518.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.032468 restraints weight = 71729.318| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26553 Z= 0.183 Angle : 0.599 8.991 35842 Z= 0.310 Chirality : 0.042 0.157 4100 Planarity : 0.004 0.058 4572 Dihedral : 8.607 83.296 3864 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.34 (0.15), residues: 3274 helix: 1.94 (0.13), residues: 1584 sheet: 0.56 (0.23), residues: 462 loop : -0.32 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 385 TYR 0.013 0.001 TYR E 611 PHE 0.020 0.002 PHE A 576 TRP 0.010 0.001 TRP D 213 HIS 0.007 0.002 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00386 (26553) covalent geometry : angle 0.59936 (35842) hydrogen bonds : bond 0.03365 ( 1171) hydrogen bonds : angle 4.13969 ( 3360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 TYR cc_start: 0.9059 (m-10) cc_final: 0.8778 (m-80) REVERT: A 520 ASP cc_start: 0.9468 (t0) cc_final: 0.9144 (t0) REVERT: A 576 PHE cc_start: 0.8856 (m-10) cc_final: 0.8597 (m-80) REVERT: A 582 CYS cc_start: 0.9394 (m) cc_final: 0.9186 (m) REVERT: A 720 MET cc_start: 0.9070 (tpp) cc_final: 0.8346 (tmm) REVERT: A 724 TYR cc_start: 0.8958 (m-80) cc_final: 0.8433 (m-80) REVERT: B 286 ASN cc_start: 0.9452 (m-40) cc_final: 0.9070 (t0) REVERT: B 328 ASP cc_start: 0.9393 (t0) cc_final: 0.8691 (p0) REVERT: B 372 MET cc_start: 0.8460 (mtm) cc_final: 0.7800 (mmm) REVERT: B 397 LEU cc_start: 0.9094 (tp) cc_final: 0.8795 (tp) REVERT: B 655 MET cc_start: 0.9158 (tpt) cc_final: 0.8753 (tpp) REVERT: B 657 MET cc_start: 0.8879 (mmp) cc_final: 0.7863 (mmp) REVERT: B 712 MET cc_start: 0.9329 (tmm) cc_final: 0.8552 (tmm) REVERT: B 715 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8882 (tp30) REVERT: B 716 MET cc_start: 0.9087 (mmp) cc_final: 0.8841 (mmm) REVERT: B 720 MET cc_start: 0.7012 (ppp) cc_final: 0.6699 (ppp) REVERT: C 248 MET cc_start: 0.9316 (mtm) cc_final: 0.8986 (mtp) REVERT: C 372 MET cc_start: 0.9113 (ptt) cc_final: 0.8632 (pmm) REVERT: C 393 MET cc_start: 0.8935 (mmm) cc_final: 0.8541 (mmm) REVERT: C 655 MET cc_start: 0.9341 (ttm) cc_final: 0.9127 (ttm) REVERT: D 248 MET cc_start: 0.8441 (tpp) cc_final: 0.8217 (tpp) REVERT: D 393 MET cc_start: 0.8658 (tpp) cc_final: 0.8027 (tpp) REVERT: D 712 MET cc_start: 0.8747 (tpt) cc_final: 0.8338 (tpp) REVERT: D 716 MET cc_start: 0.8640 (ptp) cc_final: 0.8165 (ptm) REVERT: D 720 MET cc_start: 0.8851 (mmm) cc_final: 0.8454 (mtt) REVERT: E 367 ILE cc_start: 0.9350 (pt) cc_final: 0.9015 (mm) REVERT: E 655 MET cc_start: 0.9370 (mmp) cc_final: 0.9126 (mmp) REVERT: E 657 MET cc_start: 0.9465 (tmm) cc_final: 0.9078 (tmm) REVERT: E 712 MET cc_start: 0.9442 (tpp) cc_final: 0.9167 (tpp) REVERT: E 716 MET cc_start: 0.9269 (mtp) cc_final: 0.9029 (mtm) REVERT: E 720 MET cc_start: 0.8789 (mmm) cc_final: 0.8004 (tpp) REVERT: E 724 TYR cc_start: 0.8969 (m-80) cc_final: 0.8297 (m-80) REVERT: F 1 MET cc_start: 0.4652 (pmm) cc_final: 0.3021 (tpp) REVERT: F 354 LEU cc_start: 0.9441 (tp) cc_final: 0.9027 (pp) REVERT: F 712 MET cc_start: 0.9632 (tpp) cc_final: 0.9358 (tpp) REVERT: F 720 MET cc_start: 0.9615 (tpt) cc_final: 0.9155 (tpp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1605 time to fit residues: 42.4904 Evaluate side-chains 140 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 248 optimal weight: 3.9990 chunk 176 optimal weight: 0.0170 chunk 240 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 291 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.041677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.030358 restraints weight = 230740.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.031358 restraints weight = 147367.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.032084 restraints weight = 106333.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.032610 restraints weight = 82845.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.032999 restraints weight = 68540.237| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 26553 Z= 0.108 Angle : 0.509 8.776 35842 Z= 0.265 Chirality : 0.042 0.200 4100 Planarity : 0.004 0.057 4572 Dihedral : 8.390 86.708 3864 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.26 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.58 (0.15), residues: 3274 helix: 2.15 (0.13), residues: 1585 sheet: 0.66 (0.23), residues: 461 loop : -0.22 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 727 TYR 0.012 0.001 TYR D 502 PHE 0.018 0.001 PHE A 327 TRP 0.011 0.001 TRP C 704 HIS 0.004 0.001 HIS F 456 Details of bonding type rmsd covalent geometry : bond 0.00233 (26553) covalent geometry : angle 0.50851 (35842) hydrogen bonds : bond 0.02856 ( 1171) hydrogen bonds : angle 3.86772 ( 3360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ASP cc_start: 0.9486 (t0) cc_final: 0.9155 (t0) REVERT: A 576 PHE cc_start: 0.8893 (m-10) cc_final: 0.8586 (m-80) REVERT: A 720 MET cc_start: 0.9029 (tpp) cc_final: 0.8366 (tmm) REVERT: A 724 TYR cc_start: 0.8881 (m-80) cc_final: 0.8345 (m-80) REVERT: B 286 ASN cc_start: 0.9399 (m-40) cc_final: 0.9016 (t0) REVERT: B 328 ASP cc_start: 0.9442 (t0) cc_final: 0.8641 (p0) REVERT: B 372 MET cc_start: 0.8417 (mtm) cc_final: 0.7739 (mmm) REVERT: B 397 LEU cc_start: 0.9089 (tp) cc_final: 0.8844 (tp) REVERT: B 414 MET cc_start: 0.9548 (ptp) cc_final: 0.9171 (ttp) REVERT: B 655 MET cc_start: 0.9160 (tpt) cc_final: 0.8673 (tpp) REVERT: B 657 MET cc_start: 0.8868 (mmp) cc_final: 0.7618 (mmp) REVERT: B 712 MET cc_start: 0.9332 (tmm) cc_final: 0.8549 (tmm) REVERT: B 715 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8853 (tp30) REVERT: B 716 MET cc_start: 0.9148 (mmp) cc_final: 0.8878 (mmm) REVERT: B 720 MET cc_start: 0.6869 (ppp) cc_final: 0.6619 (ppp) REVERT: C 248 MET cc_start: 0.9336 (mtm) cc_final: 0.9003 (mtp) REVERT: C 372 MET cc_start: 0.9048 (ptt) cc_final: 0.8593 (pmm) REVERT: C 393 MET cc_start: 0.8915 (mmm) cc_final: 0.8418 (mmm) REVERT: C 504 MET cc_start: 0.9026 (ptm) cc_final: 0.8213 (tmm) REVERT: C 724 TYR cc_start: 0.9396 (m-80) cc_final: 0.8706 (m-80) REVERT: D 393 MET cc_start: 0.8803 (tpp) cc_final: 0.8171 (tpp) REVERT: D 712 MET cc_start: 0.8708 (tpt) cc_final: 0.8507 (tpt) REVERT: D 716 MET cc_start: 0.8598 (ptp) cc_final: 0.8276 (ptp) REVERT: D 720 MET cc_start: 0.8800 (mmm) cc_final: 0.8385 (mtt) REVERT: E 312 GLU cc_start: 0.9409 (tp30) cc_final: 0.8943 (mt-10) REVERT: E 329 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8440 (mp0) REVERT: E 367 ILE cc_start: 0.9295 (pt) cc_final: 0.8970 (mm) REVERT: E 573 MET cc_start: 0.9141 (mpp) cc_final: 0.8904 (mpp) REVERT: E 657 MET cc_start: 0.9430 (tmm) cc_final: 0.8954 (tmm) REVERT: E 712 MET cc_start: 0.9479 (tpp) cc_final: 0.8666 (tpp) REVERT: E 716 MET cc_start: 0.9308 (mtp) cc_final: 0.8708 (mtm) REVERT: E 720 MET cc_start: 0.8757 (mmm) cc_final: 0.7970 (tpp) REVERT: E 724 TYR cc_start: 0.9025 (m-80) cc_final: 0.8297 (m-80) REVERT: F 1 MET cc_start: 0.4540 (pmm) cc_final: 0.2755 (tpp) REVERT: F 354 LEU cc_start: 0.9445 (tp) cc_final: 0.9019 (pp) REVERT: F 712 MET cc_start: 0.9626 (tpp) cc_final: 0.9387 (tpp) REVERT: F 720 MET cc_start: 0.9626 (tpt) cc_final: 0.9164 (tpp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1424 time to fit residues: 38.8314 Evaluate side-chains 143 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 183 optimal weight: 0.0010 chunk 127 optimal weight: 3.9990 chunk 197 optimal weight: 0.0470 chunk 317 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.042062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.030730 restraints weight = 229136.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.031751 restraints weight = 146343.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.032462 restraints weight = 105015.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.033004 restraints weight = 82124.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.033385 restraints weight = 67732.641| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26553 Z= 0.090 Angle : 0.494 8.892 35842 Z= 0.256 Chirality : 0.041 0.189 4100 Planarity : 0.004 0.056 4572 Dihedral : 8.094 89.220 3864 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.70 (0.15), residues: 3274 helix: 2.21 (0.13), residues: 1587 sheet: 0.84 (0.23), residues: 468 loop : -0.19 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 303 TYR 0.007 0.001 TYR D 502 PHE 0.010 0.001 PHE F 101 TRP 0.011 0.001 TRP C 704 HIS 0.003 0.001 HIS F 456 Details of bonding type rmsd covalent geometry : bond 0.00189 (26553) covalent geometry : angle 0.49387 (35842) hydrogen bonds : bond 0.02662 ( 1171) hydrogen bonds : angle 3.78107 ( 3360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ASP cc_start: 0.9461 (t0) cc_final: 0.9118 (t0) REVERT: A 576 PHE cc_start: 0.8834 (m-10) cc_final: 0.8571 (m-80) REVERT: A 720 MET cc_start: 0.9020 (tpp) cc_final: 0.8373 (tpp) REVERT: A 724 TYR cc_start: 0.8863 (m-80) cc_final: 0.8436 (m-80) REVERT: B 286 ASN cc_start: 0.9394 (m-40) cc_final: 0.9001 (t0) REVERT: B 328 ASP cc_start: 0.9436 (t0) cc_final: 0.8656 (p0) REVERT: B 372 MET cc_start: 0.8274 (mtm) cc_final: 0.7664 (mmm) REVERT: B 397 LEU cc_start: 0.9086 (tp) cc_final: 0.8831 (tp) REVERT: B 414 MET cc_start: 0.9542 (ptp) cc_final: 0.9195 (ttp) REVERT: B 655 MET cc_start: 0.9112 (tpt) cc_final: 0.8655 (tpp) REVERT: B 657 MET cc_start: 0.8908 (mmp) cc_final: 0.7684 (mmp) REVERT: B 712 MET cc_start: 0.9330 (tmm) cc_final: 0.8542 (tmm) REVERT: B 715 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8848 (tp30) REVERT: B 716 MET cc_start: 0.9136 (mmp) cc_final: 0.8884 (mmm) REVERT: C 248 MET cc_start: 0.9309 (mtm) cc_final: 0.8989 (mtp) REVERT: C 393 MET cc_start: 0.8842 (mmm) cc_final: 0.8355 (mmm) REVERT: C 504 MET cc_start: 0.8996 (ptm) cc_final: 0.8152 (tmm) REVERT: C 657 MET cc_start: 0.9077 (ptp) cc_final: 0.8286 (pmm) REVERT: C 724 TYR cc_start: 0.9377 (m-80) cc_final: 0.8646 (m-80) REVERT: D 393 MET cc_start: 0.8748 (tpp) cc_final: 0.8262 (tpp) REVERT: D 712 MET cc_start: 0.8723 (tpt) cc_final: 0.8495 (tpp) REVERT: D 716 MET cc_start: 0.8591 (ptp) cc_final: 0.8389 (ptm) REVERT: D 720 MET cc_start: 0.8774 (mmm) cc_final: 0.8361 (mtt) REVERT: E 312 GLU cc_start: 0.9410 (tp30) cc_final: 0.8955 (mt-10) REVERT: E 367 ILE cc_start: 0.9347 (pt) cc_final: 0.9016 (mm) REVERT: E 573 MET cc_start: 0.9176 (mpp) cc_final: 0.8944 (mpp) REVERT: E 657 MET cc_start: 0.9450 (tmm) cc_final: 0.9191 (tmm) REVERT: E 712 MET cc_start: 0.9464 (tpp) cc_final: 0.8846 (tpp) REVERT: E 716 MET cc_start: 0.9290 (mtp) cc_final: 0.8878 (mtm) REVERT: E 720 MET cc_start: 0.8721 (mmm) cc_final: 0.7967 (tpp) REVERT: E 724 TYR cc_start: 0.9021 (m-80) cc_final: 0.8293 (m-80) REVERT: F 1 MET cc_start: 0.4654 (pmm) cc_final: 0.2836 (tpp) REVERT: F 95 MET cc_start: 0.8616 (tpp) cc_final: 0.8383 (tpp) REVERT: F 354 LEU cc_start: 0.9444 (tp) cc_final: 0.9022 (pp) REVERT: F 712 MET cc_start: 0.9623 (tpp) cc_final: 0.9412 (tpp) REVERT: F 720 MET cc_start: 0.9644 (tpt) cc_final: 0.9179 (tpp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1640 time to fit residues: 46.3058 Evaluate side-chains 140 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 69 optimal weight: 5.9990 chunk 280 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 262 optimal weight: 40.0000 chunk 329 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 530 ASN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.030741 restraints weight = 232583.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.031751 restraints weight = 148174.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.032485 restraints weight = 106625.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.033019 restraints weight = 82799.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.033407 restraints weight = 68183.696| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26553 Z= 0.095 Angle : 0.494 10.646 35842 Z= 0.257 Chirality : 0.041 0.181 4100 Planarity : 0.004 0.055 4572 Dihedral : 7.952 87.620 3864 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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 (0.15), residues: 3274 helix: 2.26 (0.13), residues: 1587 sheet: 0.89 (0.23), residues: 468 loop : -0.15 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 375 TYR 0.009 0.001 TYR B 502 PHE 0.014 0.001 PHE B 215 TRP 0.009 0.001 TRP C 704 HIS 0.003 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00202 (26553) covalent geometry : angle 0.49377 (35842) hydrogen bonds : bond 0.02587 ( 1171) hydrogen bonds : angle 3.75435 ( 3360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ASP cc_start: 0.9457 (t0) cc_final: 0.9124 (t0) REVERT: A 576 PHE cc_start: 0.8828 (m-10) cc_final: 0.8533 (m-80) REVERT: A 657 MET cc_start: 0.9764 (tpp) cc_final: 0.9199 (tmm) REVERT: A 720 MET cc_start: 0.9033 (tpp) cc_final: 0.8350 (tpp) REVERT: A 724 TYR cc_start: 0.8860 (m-80) cc_final: 0.8437 (m-80) REVERT: B 286 ASN cc_start: 0.9398 (m-40) cc_final: 0.9011 (t0) REVERT: B 328 ASP cc_start: 0.9428 (t0) cc_final: 0.8660 (p0) REVERT: B 372 MET cc_start: 0.8300 (mtm) cc_final: 0.7604 (mmm) REVERT: B 397 LEU cc_start: 0.9088 (tp) cc_final: 0.8829 (tp) REVERT: B 414 MET cc_start: 0.9524 (ptp) cc_final: 0.9182 (ttp) REVERT: B 655 MET cc_start: 0.9127 (tpt) cc_final: 0.8882 (tpp) REVERT: B 657 MET cc_start: 0.8958 (mmp) cc_final: 0.8401 (mmm) REVERT: B 712 MET cc_start: 0.9324 (tmm) cc_final: 0.8533 (tmm) REVERT: B 715 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8860 (tp30) REVERT: B 716 MET cc_start: 0.9130 (mmp) cc_final: 0.8877 (mmm) REVERT: C 248 MET cc_start: 0.9277 (mtm) cc_final: 0.8935 (mtp) REVERT: C 372 MET cc_start: 0.9265 (pmm) cc_final: 0.8690 (pmm) REVERT: C 393 MET cc_start: 0.8841 (mmm) cc_final: 0.8349 (mmm) REVERT: C 504 MET cc_start: 0.8967 (ptm) cc_final: 0.8084 (tmm) REVERT: C 657 MET cc_start: 0.8864 (ptp) cc_final: 0.7193 (pmm) REVERT: C 724 TYR cc_start: 0.9404 (m-80) cc_final: 0.8660 (m-80) REVERT: D 393 MET cc_start: 0.8754 (tpp) cc_final: 0.8108 (tpp) REVERT: D 712 MET cc_start: 0.8711 (tpt) cc_final: 0.8493 (tpp) REVERT: E 312 GLU cc_start: 0.9411 (tp30) cc_final: 0.8959 (mt-10) REVERT: E 367 ILE cc_start: 0.9347 (pt) cc_final: 0.8987 (mm) REVERT: E 573 MET cc_start: 0.9197 (mpp) cc_final: 0.8928 (mpp) REVERT: E 657 MET cc_start: 0.9448 (tmm) cc_final: 0.9241 (tmm) REVERT: E 712 MET cc_start: 0.9460 (tpp) cc_final: 0.8647 (tpp) REVERT: E 716 MET cc_start: 0.9286 (mtp) cc_final: 0.8647 (mtm) REVERT: E 720 MET cc_start: 0.8741 (mmm) cc_final: 0.8004 (tpp) REVERT: E 724 TYR cc_start: 0.9051 (m-80) cc_final: 0.8342 (m-80) REVERT: F 1 MET cc_start: 0.4396 (pmm) cc_final: 0.2554 (tpp) REVERT: F 95 MET cc_start: 0.8562 (tpp) cc_final: 0.8349 (tpp) REVERT: F 354 LEU cc_start: 0.9450 (tp) cc_final: 0.9024 (pp) REVERT: F 712 MET cc_start: 0.9618 (tpp) cc_final: 0.9410 (tpp) REVERT: F 720 MET cc_start: 0.9649 (tpt) cc_final: 0.9186 (tpp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1592 time to fit residues: 44.2049 Evaluate side-chains 137 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 91 optimal weight: 4.9990 chunk 320 optimal weight: 0.0170 chunk 303 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 291 optimal weight: 0.0570 chunk 186 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 329 optimal weight: 0.2980 chunk 185 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 ASN D 624 GLN E 363 GLN ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.042711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.031360 restraints weight = 226122.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.032397 restraints weight = 144374.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.033140 restraints weight = 103456.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.033699 restraints weight = 80399.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.034076 restraints weight = 65946.364| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26553 Z= 0.085 Angle : 0.488 8.616 35842 Z= 0.251 Chirality : 0.041 0.170 4100 Planarity : 0.004 0.054 4572 Dihedral : 7.726 82.547 3864 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % 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: 1.83 (0.15), residues: 3274 helix: 2.29 (0.13), residues: 1587 sheet: 1.01 (0.23), residues: 473 loop : -0.12 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 415 TYR 0.010 0.001 TYR D 502 PHE 0.010 0.001 PHE C 240 TRP 0.010 0.001 TRP C 704 HIS 0.003 0.000 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00173 (26553) covalent geometry : angle 0.48758 (35842) hydrogen bonds : bond 0.02372 ( 1171) hydrogen bonds : angle 3.59818 ( 3360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3485.06 seconds wall clock time: 61 minutes 26.42 seconds (3686.42 seconds total)