Starting phenix.real_space_refine on Sun Aug 9 16:44:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kak_62209/08_2026/9kak_62209_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kak_62209/08_2026/9kak_62209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kak_62209/08_2026/9kak_62209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kak_62209/08_2026/9kak_62209.map" model { file = "/net/cci-nas-00/data/ceres_data/9kak_62209/08_2026/9kak_62209_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kak_62209/08_2026/9kak_62209_trim.cif" } resolution = 3.1 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= -0.006 sd= 0.563 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: 7 Type Number sf(0) Gaussians P 43 5.49 5 Mg 6 5.21 5 S 126 5.16 5 C 11638 2.51 5 N 3074 2.21 5 O 3407 1.98 5 H 18197 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36491 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "B" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "C" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5917 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "D" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5918 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "E" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "F" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5917 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 321 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 481 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.76, per 1000 atoms: 0.16 Number of scatterers: 36491 At special positions: 0 Unit cell: (101.37, 123.69, 142.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 126 16.00 P 43 15.00 Mg 6 11.99 O 3407 8.00 N 3074 7.00 C 11638 6.00 H 18197 1.00 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: 3.21 Conformation dependent library (CDL) restraints added in 932.2 milliseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 12 sheets defined 69.5% alpha, 6.3% beta 10 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'A' and resid 269 through 281 removed outlier: 3.665A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.774A pdb=" N PHE A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.618A pdb=" N LYS A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 5.291A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASN A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 355 Processing helix chain 'A' and resid 356 through 377 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 400 through 414 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 456 through 462 removed outlier: 4.027A pdb=" N GLU A 460 " --> pdb=" O ARG A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 481 through 485 removed outlier: 4.014A pdb=" N LEU A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 497 through 503 removed outlier: 3.666A pdb=" N LEU A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 567 through 570 removed outlier: 3.600A pdb=" N GLN A 570 " --> pdb=" O ARG A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 570' Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.535A pdb=" N LEU A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 592 through 607 Processing helix chain 'A' and resid 608 through 622 Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.563A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 302 through 308 Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 316 through 330 removed outlier: 5.261A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 355 Processing helix chain 'B' and resid 356 through 376 Processing helix chain 'B' and resid 383 through 396 Processing helix chain 'B' and resid 400 through 415 Processing helix chain 'B' and resid 431 through 444 Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.843A pdb=" N ASN B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 460 " --> pdb=" O ARG B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 480 through 484 Processing helix chain 'B' and resid 489 through 497 Processing helix chain 'B' and resid 497 through 503 Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 567 through 570 Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 589 through 607 removed outlier: 4.493A pdb=" N SER B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ARG B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 621 Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.634A pdb=" N VAL C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 removed outlier: 3.856A pdb=" N PHE C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 308 Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 316 through 330 removed outlier: 5.029A pdb=" N ALA C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 355 Processing helix chain 'C' and resid 356 through 377 Processing helix chain 'C' and resid 383 through 398 removed outlier: 4.262A pdb=" N LEU C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 415 Processing helix chain 'C' and resid 431 through 444 Processing helix chain 'C' and resid 456 through 462 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 480 through 484 Processing helix chain 'C' and resid 489 through 497 Processing helix chain 'C' and resid 497 through 503 removed outlier: 3.578A pdb=" N GLY C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 561 through 566 Processing helix chain 'C' and resid 571 through 583 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 592 through 607 Processing helix chain 'C' and resid 608 through 621 Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.724A pdb=" N VAL D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 298 through 301 removed outlier: 3.833A pdb=" N MET D 301 " --> pdb=" O SER D 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 302 through 308 Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 316 through 330 removed outlier: 5.259A pdb=" N ALA D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASN D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 355 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 383 through 396 Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 456 through 462 removed outlier: 4.099A pdb=" N GLU D 460 " --> pdb=" O ARG D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 480 through 484 Processing helix chain 'D' and resid 489 through 497 Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 561 through 566 Processing helix chain 'D' and resid 567 through 570 removed outlier: 3.543A pdb=" N GLN D 570 " --> pdb=" O ARG D 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 567 through 570' Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.512A pdb=" N LEU D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 588 Processing helix chain 'D' and resid 589 through 607 removed outlier: 4.384A pdb=" N SER D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ARG D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 621 Processing helix chain 'E' and resid 269 through 281 removed outlier: 3.588A pdb=" N VAL E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 295 removed outlier: 3.666A pdb=" N PHE E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 308 Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 316 through 330 removed outlier: 5.252A pdb=" N ALA E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN E 323 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 355 Processing helix chain 'E' and resid 356 through 377 Processing helix chain 'E' and resid 383 through 396 Processing helix chain 'E' and resid 400 through 415 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 453 through 462 removed outlier: 3.727A pdb=" N LEU E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN E 458 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.227A pdb=" N GLU E 481 " --> pdb=" O THR E 478 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER E 482 " --> pdb=" O GLY E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 497 Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 550 through 559 Processing helix chain 'E' and resid 561 through 566 Processing helix chain 'E' and resid 567 through 570 Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.648A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 588 Processing helix chain 'E' and resid 592 through 607 Processing helix chain 'E' and resid 608 through 621 Processing helix chain 'F' and resid 269 through 281 removed outlier: 3.597A pdb=" N VAL F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 294 Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 298 through 301 removed outlier: 3.636A pdb=" N MET F 301 " --> pdb=" O SER F 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 298 through 301' Processing helix chain 'F' and resid 302 through 308 Processing helix chain 'F' and resid 310 through 315 Processing helix chain 'F' and resid 316 through 330 removed outlier: 5.059A pdb=" N ALA F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN F 323 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP F 329 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 355 Processing helix chain 'F' and resid 356 through 376 removed outlier: 3.528A pdb=" N LEU F 361 " --> pdb=" O ARG F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 396 removed outlier: 3.675A pdb=" N CYS F 396 " --> pdb=" O ALA F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 415 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 453 through 456 Processing helix chain 'F' and resid 457 through 462 Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 479 through 484 removed outlier: 4.402A pdb=" N SER F 482 " --> pdb=" O GLY F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 496 Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 550 through 559 Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'F' and resid 571 through 583 Processing helix chain 'F' and resid 584 through 588 Processing helix chain 'F' and resid 592 through 607 removed outlier: 4.204A pdb=" N GLU F 598 " --> pdb=" O SER F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 621 Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 448 removed outlier: 7.238A pdb=" N TYR A 421 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ILE A 545 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 423 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 507 through 511 removed outlier: 5.116A pdb=" N LYS A 511 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASN A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 448 removed outlier: 7.138A pdb=" N TYR B 421 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ILE B 545 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 423 " --> pdb=" O ILE B 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 507 through 509 Processing sheet with id=AA5, first strand: chain 'C' and resid 445 through 448 removed outlier: 3.561A pdb=" N LYS C 446 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR C 421 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE C 545 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 423 " --> pdb=" O ILE C 545 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 507 through 509 Processing sheet with id=AA7, first strand: chain 'D' and resid 445 through 448 removed outlier: 7.434A pdb=" N TYR D 421 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE D 545 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU D 423 " --> pdb=" O ILE D 545 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 507 through 509 Processing sheet with id=AA9, first strand: chain 'E' and resid 446 through 448 removed outlier: 6.570A pdb=" N TYR E 421 " --> pdb=" O PHE E 541 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS E 543 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 507 through 509 Processing sheet with id=AB2, first strand: chain 'F' and resid 446 through 447 removed outlier: 6.698A pdb=" N LYS F 446 " --> pdb=" O VAL F 471 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR F 421 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N ILE F 545 " --> pdb=" O TYR F 421 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU F 423 " --> pdb=" O ILE F 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 507 through 509 988 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18155 1.03 - 1.23: 209 1.23 - 1.42: 7547 1.42 - 1.62: 10792 1.62 - 1.81: 206 Bond restraints: 36909 Sorted by residual: bond pdb=" N3B ANP F 800 " pdb=" PG ANP F 800 " ideal model delta sigma weight residual 1.795 1.611 0.184 2.00e-02 2.50e+03 8.45e+01 bond pdb=" N3B ANP C 802 " pdb=" PG ANP C 802 " ideal model delta sigma weight residual 1.795 1.614 0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" N3B ANP A 800 " pdb=" PG ANP A 800 " ideal model delta sigma weight residual 1.795 1.614 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" N3B ANP E 800 " pdb=" PG ANP E 800 " ideal model delta sigma weight residual 1.795 1.616 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" N3B ANP D 802 " pdb=" PG ANP D 802 " ideal model delta sigma weight residual 1.795 1.617 0.178 2.00e-02 2.50e+03 7.89e+01 ... (remaining 36904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 66603 3.48 - 6.95: 272 6.95 - 10.43: 10 10.43 - 13.91: 7 13.91 - 17.38: 1 Bond angle restraints: 66893 Sorted by residual: angle pdb=" PB ANP F 800 " pdb=" N3B ANP F 800 " pdb=" PG ANP F 800 " ideal model delta sigma weight residual 126.95 109.57 17.38 3.00e+00 1.11e-01 3.36e+01 angle pdb=" O4' DA P 9 " pdb=" C1' DA P 9 " pdb=" N9 DA P 9 " ideal model delta sigma weight residual 108.00 104.58 3.42 7.00e-01 2.04e+00 2.38e+01 angle pdb=" C3' DA P 1 " pdb=" O3' DA P 1 " pdb=" P DA P 2 " ideal model delta sigma weight residual 119.70 125.13 -5.43 1.20e+00 6.94e-01 2.04e+01 angle pdb=" N GLY C 490 " pdb=" CA GLY C 490 " pdb=" C GLY C 490 " ideal model delta sigma weight residual 112.64 117.76 -5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" C4' DT T -8 " pdb=" O4' DT T -8 " pdb=" C1' DT T -8 " ideal model delta sigma weight residual 110.10 105.89 4.21 1.00e+00 1.00e+00 1.77e+01 ... (remaining 66888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 16372 33.50 - 67.00: 756 67.00 - 100.50: 50 100.50 - 134.00: 0 134.00 - 167.50: 2 Dihedral angle restraints: 17180 sinusoidal: 9643 harmonic: 7537 Sorted by residual: dihedral pdb=" CA LEU C 469 " pdb=" C LEU C 469 " pdb=" N VAL C 470 " pdb=" CA VAL C 470 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LYS E 419 " pdb=" C LYS E 419 " pdb=" N ARG E 420 " pdb=" CA ARG E 420 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA LEU F 469 " pdb=" C LEU F 469 " pdb=" N VAL F 470 " pdb=" CA VAL F 470 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 17177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2354 0.073 - 0.146: 393 0.146 - 0.220: 42 0.220 - 0.293: 5 0.293 - 0.366: 6 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C3' DA P 1 " pdb=" C4' DA P 1 " pdb=" O3' DA P 1 " pdb=" C2' DA P 1 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C3' ANP F 800 " pdb=" C2' ANP F 800 " pdb=" C4' ANP F 800 " pdb=" O3' ANP F 800 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C3' ANP B 802 " pdb=" C2' ANP B 802 " pdb=" C4' ANP B 802 " pdb=" O3' ANP B 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2797 not shown) Planarity restraints: 5189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP A 800 " 0.200 2.00e-02 2.50e+03 8.42e-02 1.95e+02 pdb=" C2 ANP A 800 " -0.017 2.00e-02 2.50e+03 pdb=" C4 ANP A 800 " -0.079 2.00e-02 2.50e+03 pdb=" C5 ANP A 800 " -0.059 2.00e-02 2.50e+03 pdb=" C6 ANP A 800 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ANP A 800 " -0.039 2.00e-02 2.50e+03 pdb=" N1 ANP A 800 " 0.028 2.00e-02 2.50e+03 pdb=" N3 ANP A 800 " -0.058 2.00e-02 2.50e+03 pdb=" N6 ANP A 800 " 0.129 2.00e-02 2.50e+03 pdb=" N7 ANP A 800 " -0.046 2.00e-02 2.50e+03 pdb=" N9 ANP A 800 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP E 800 " -0.187 2.00e-02 2.50e+03 8.04e-02 1.78e+02 pdb=" C2 ANP E 800 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ANP E 800 " 0.085 2.00e-02 2.50e+03 pdb=" C5 ANP E 800 " 0.068 2.00e-02 2.50e+03 pdb=" C6 ANP E 800 " 0.001 2.00e-02 2.50e+03 pdb=" C8 ANP E 800 " 0.023 2.00e-02 2.50e+03 pdb=" N1 ANP E 800 " -0.033 2.00e-02 2.50e+03 pdb=" N3 ANP E 800 " 0.070 2.00e-02 2.50e+03 pdb=" N6 ANP E 800 " -0.116 2.00e-02 2.50e+03 pdb=" N7 ANP E 800 " 0.037 2.00e-02 2.50e+03 pdb=" N9 ANP E 800 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP F 800 " -0.174 2.00e-02 2.50e+03 7.36e-02 1.49e+02 pdb=" C2 ANP F 800 " 0.006 2.00e-02 2.50e+03 pdb=" C4 ANP F 800 " 0.070 2.00e-02 2.50e+03 pdb=" C5 ANP F 800 " 0.056 2.00e-02 2.50e+03 pdb=" C6 ANP F 800 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ANP F 800 " 0.026 2.00e-02 2.50e+03 pdb=" N1 ANP F 800 " -0.028 2.00e-02 2.50e+03 pdb=" N3 ANP F 800 " 0.061 2.00e-02 2.50e+03 pdb=" N6 ANP F 800 " -0.109 2.00e-02 2.50e+03 pdb=" N7 ANP F 800 " 0.040 2.00e-02 2.50e+03 pdb=" N9 ANP F 800 " 0.053 2.00e-02 2.50e+03 ... (remaining 5186 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1308 2.17 - 2.77: 70200 2.77 - 3.38: 103240 3.38 - 3.99: 132348 3.99 - 4.60: 211408 Nonbonded interactions: 518504 Sorted by model distance: nonbonded pdb="MG MG D 801 " pdb=" O2G ANP D 802 " model vdw 1.557 2.050 nonbonded pdb=" O GLY E 431 " pdb=" HG1 THR E 434 " model vdw 1.612 2.450 nonbonded pdb=" HG1 THR A 433 " pdb=" OE2 GLU A 473 " model vdw 1.616 2.450 nonbonded pdb="HH22 ARG A 420 " pdb=" O PHE A 521 " model vdw 1.650 2.450 nonbonded pdb=" HZ1 LYS F 512 " pdb=" OP1 DT T 1 " model vdw 1.686 2.450 ... (remaining 518499 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 266 through 627) selection = (chain 'B' and resid 266 through 627) selection = (chain 'C' and (resid 266 through 301 or (resid 302 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 303 through 304 or (resid 305 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 306 through 627)) selection = (chain 'D' and (resid 266 through 301 or (resid 302 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 303 through 304 or (resid 305 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 306 through 312 or (resid 313 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 3 \ 14 through 627)) selection = (chain 'E' and resid 266 through 627) selection = (chain 'F' and (resid 266 through 301 or (resid 302 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 303 through 304 or (resid 305 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 306 through 627)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.220 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.210 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.184 18712 Z= 0.387 Angle : 1.013 17.383 25364 Z= 0.608 Chirality : 0.058 0.366 2800 Planarity : 0.012 0.276 3079 Dihedral : 15.296 167.504 7274 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.15), residues: 2160 helix: -0.70 (0.12), residues: 1285 sheet: -0.18 (0.42), residues: 161 loop : -0.58 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG F 498 TYR 0.030 0.006 TYR D 552 PHE 0.025 0.004 PHE F 521 TRP 0.025 0.005 TRP E 599 HIS 0.011 0.004 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.39 (18712) covalent geometry : angle 1.01290 / 0.61 (25364) hydrogen bonds : bond 0.19027 / 12.88 ( 1008) hydrogen bonds : angle 6.64282 / 4.76 ( 2896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8604 (p90) cc_final: 0.8244 (p90) REVERT: B 484 ASP cc_start: 0.8917 (t0) cc_final: 0.8682 (t0) REVERT: B 502 ASP cc_start: 0.8530 (m-30) cc_final: 0.8152 (m-30) REVERT: C 412 MET cc_start: 0.8858 (mmp) cc_final: 0.8516 (mmp) REVERT: C 484 ASP cc_start: 0.8634 (t0) cc_final: 0.8408 (t0) REVERT: C 614 LYS cc_start: 0.8708 (tppt) cc_final: 0.8167 (ttpt) REVERT: D 484 ASP cc_start: 0.8608 (t0) cc_final: 0.8315 (t0) REVERT: E 396 CYS cc_start: 0.8857 (t) cc_final: 0.8477 (t) REVERT: E 474 ASP cc_start: 0.8417 (t0) cc_final: 0.8176 (p0) REVERT: E 540 ARG cc_start: 0.8870 (mtt-85) cc_final: 0.8499 (mtt-85) REVERT: E 615 MET cc_start: 0.7934 (mtm) cc_final: 0.7590 (mtm) REVERT: F 401 MET cc_start: 0.9240 (tpp) cc_final: 0.8889 (tpt) REVERT: F 502 ASP cc_start: 0.8520 (m-30) cc_final: 0.8320 (m-30) REVERT: F 511 LYS cc_start: 0.9020 (tttt) cc_final: 0.8647 (ttmm) REVERT: F 558 GLU cc_start: 0.8736 (tt0) cc_final: 0.8417 (tp30) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.4208 time to fit residues: 210.1187 Evaluate side-chains 273 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 593 GLN E 323 ASN F 267 GLN F 467 GLN ** F 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.064355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.050291 restraints weight = 123866.977| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 1.77 r_work: 0.2356 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2239 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18712 Z= 0.209 Angle : 0.717 7.187 25364 Z= 0.396 Chirality : 0.040 0.289 2800 Planarity : 0.006 0.109 3079 Dihedral : 14.765 172.404 2822 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.26 % Allowed : 5.06 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2160 helix: 0.19 (0.14), residues: 1292 sheet: -0.04 (0.42), residues: 157 loop : -0.71 (0.20), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 548 TYR 0.029 0.002 TYR D 552 PHE 0.018 0.002 PHE C 299 TRP 0.012 0.001 TRP D 270 HIS 0.009 0.002 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (18712) covalent geometry : angle 0.71653 / 0.40 (25364) hydrogen bonds : bond 0.06814 / 4.56 ( 1008) hydrogen bonds : angle 5.22776 / 3.75 ( 2896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 292 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 ARG cc_start: 0.8834 (ttm-80) cc_final: 0.8434 (mtm-85) REVERT: B 401 MET cc_start: 0.8990 (tpt) cc_final: 0.8514 (tpt) REVERT: B 484 ASP cc_start: 0.8876 (t0) cc_final: 0.8614 (t0) REVERT: B 548 ARG cc_start: 0.8649 (ttm110) cc_final: 0.8273 (mtm-85) REVERT: C 278 MET cc_start: 0.9199 (mmm) cc_final: 0.8552 (mmm) REVERT: C 614 LYS cc_start: 0.8772 (tppt) cc_final: 0.8204 (ttpt) REVERT: D 483 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8112 (mtm110) REVERT: D 484 ASP cc_start: 0.8741 (t0) cc_final: 0.8328 (t0) REVERT: D 578 MET cc_start: 0.9069 (ttm) cc_final: 0.8839 (ttp) REVERT: E 396 CYS cc_start: 0.8920 (t) cc_final: 0.8536 (t) REVERT: E 474 ASP cc_start: 0.8512 (t0) cc_final: 0.8169 (p0) REVERT: E 553 LEU cc_start: 0.8822 (mt) cc_final: 0.8510 (mm) REVERT: F 454 LEU cc_start: 0.8160 (tp) cc_final: 0.7860 (tt) REVERT: F 511 LYS cc_start: 0.8915 (tttt) cc_final: 0.8602 (ttmm) REVERT: F 538 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7907 (tm-30) REVERT: F 558 GLU cc_start: 0.8731 (tt0) cc_final: 0.8440 (tp30) outliers start: 5 outliers final: 2 residues processed: 293 average time/residue: 0.3744 time to fit residues: 155.1592 Evaluate side-chains 274 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain E residue 594 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 168 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.064566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.050537 restraints weight = 124031.166| |-----------------------------------------------------------------------------| r_work (start): 0.2464 rms_B_bonded: 1.76 r_work: 0.2363 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2248 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18712 Z= 0.155 Angle : 0.603 6.398 25364 Z= 0.335 Chirality : 0.038 0.288 2800 Planarity : 0.005 0.077 3079 Dihedral : 14.322 169.190 2822 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.31 % Allowed : 6.50 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2160 helix: 0.56 (0.14), residues: 1281 sheet: 0.01 (0.44), residues: 141 loop : -0.72 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 559 TYR 0.023 0.002 TYR C 314 PHE 0.028 0.001 PHE C 617 TRP 0.010 0.001 TRP F 599 HIS 0.005 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (18712) covalent geometry : angle 0.60350 / 0.34 (25364) hydrogen bonds : bond 0.05853 / 3.92 ( 1008) hydrogen bonds : angle 4.90358 / 3.53 ( 2896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 280 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8364 (p90) cc_final: 0.7287 (p90) REVERT: A 548 ARG cc_start: 0.8848 (ttm-80) cc_final: 0.8497 (mtm-85) REVERT: B 401 MET cc_start: 0.8984 (tpt) cc_final: 0.8581 (tpt) REVERT: B 484 ASP cc_start: 0.8869 (t0) cc_final: 0.8581 (t0) REVERT: C 412 MET cc_start: 0.8800 (mmp) cc_final: 0.8188 (mmp) REVERT: C 614 LYS cc_start: 0.8781 (tppt) cc_final: 0.8207 (ttpt) REVERT: D 484 ASP cc_start: 0.8704 (t0) cc_final: 0.8295 (t0) REVERT: E 396 CYS cc_start: 0.8938 (t) cc_final: 0.8633 (t) REVERT: E 412 MET cc_start: 0.8923 (mmp) cc_final: 0.8440 (mmp) REVERT: E 441 GLU cc_start: 0.8060 (tp30) cc_final: 0.7405 (mp0) REVERT: E 474 ASP cc_start: 0.8518 (t0) cc_final: 0.8262 (p0) REVERT: E 599 TRP cc_start: 0.8968 (m100) cc_final: 0.8664 (m100) REVERT: F 371 ARG cc_start: 0.8832 (mtp85) cc_final: 0.8580 (mtp180) REVERT: F 454 LEU cc_start: 0.8139 (tp) cc_final: 0.7852 (tt) REVERT: F 538 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7966 (tm-30) REVERT: F 558 GLU cc_start: 0.8725 (tt0) cc_final: 0.8402 (tp30) outliers start: 6 outliers final: 3 residues processed: 283 average time/residue: 0.4069 time to fit residues: 162.9459 Evaluate side-chains 270 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain C residue 551 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 613 GLN F 555 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.062981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.049054 restraints weight = 124711.412| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 1.75 r_work: 0.2322 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2202 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18712 Z= 0.274 Angle : 0.649 7.823 25364 Z= 0.360 Chirality : 0.040 0.278 2800 Planarity : 0.005 0.065 3079 Dihedral : 14.391 172.886 2822 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.67 % Allowed : 6.76 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2160 helix: 0.55 (0.14), residues: 1274 sheet: 0.79 (0.45), residues: 125 loop : -0.87 (0.19), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 548 TYR 0.022 0.002 TYR D 552 PHE 0.022 0.002 PHE C 617 TRP 0.011 0.002 TRP D 387 HIS 0.005 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (18712) covalent geometry : angle 0.64926 / 0.36 (25364) hydrogen bonds : bond 0.05982 / 3.99 ( 1008) hydrogen bonds : angle 4.84428 / 3.48 ( 2896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8903 (mp) REVERT: A 548 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8534 (mtm-85) REVERT: A 559 ARG cc_start: 0.9100 (mtt90) cc_final: 0.8692 (mtt90) REVERT: B 401 MET cc_start: 0.9017 (tpt) cc_final: 0.8602 (tpt) REVERT: B 484 ASP cc_start: 0.8952 (t0) cc_final: 0.8634 (t0) REVERT: C 412 MET cc_start: 0.8844 (mmp) cc_final: 0.8235 (mmp) REVERT: C 614 LYS cc_start: 0.8751 (tppt) cc_final: 0.8183 (ttpt) REVERT: D 484 ASP cc_start: 0.8757 (t0) cc_final: 0.8346 (t0) REVERT: E 396 CYS cc_start: 0.9030 (t) cc_final: 0.8724 (t) REVERT: E 412 MET cc_start: 0.8965 (mmp) cc_final: 0.8385 (mmp) REVERT: E 420 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.6952 (ttp80) REVERT: E 474 ASP cc_start: 0.8628 (t0) cc_final: 0.8283 (p0) REVERT: E 558 GLU cc_start: 0.7346 (pt0) cc_final: 0.7139 (pt0) REVERT: F 454 LEU cc_start: 0.8133 (tp) cc_final: 0.7775 (tt) REVERT: F 506 LYS cc_start: 0.9247 (mttt) cc_final: 0.9004 (mtpp) REVERT: F 538 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7962 (tm-30) REVERT: F 558 GLU cc_start: 0.8767 (tt0) cc_final: 0.8537 (tp30) outliers start: 13 outliers final: 7 residues processed: 278 average time/residue: 0.3773 time to fit residues: 147.9461 Evaluate side-chains 274 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 265 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 594 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 75 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 613 GLN F 555 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.063560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.049611 restraints weight = 123689.431| |-----------------------------------------------------------------------------| r_work (start): 0.2439 rms_B_bonded: 1.73 r_work: 0.2338 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2220 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18712 Z= 0.175 Angle : 0.585 6.899 25364 Z= 0.324 Chirality : 0.037 0.281 2800 Planarity : 0.004 0.056 3079 Dihedral : 14.125 167.361 2822 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.62 % Allowed : 7.53 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2160 helix: 0.72 (0.14), residues: 1288 sheet: 0.72 (0.45), residues: 125 loop : -0.90 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 548 TYR 0.021 0.002 TYR B 314 PHE 0.029 0.002 PHE C 299 TRP 0.010 0.001 TRP D 387 HIS 0.004 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (18712) covalent geometry : angle 0.58523 / 0.32 (25364) hydrogen bonds : bond 0.05297 / 3.53 ( 1008) hydrogen bonds : angle 4.71550 / 3.39 ( 2896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8894 (mp) REVERT: A 548 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8530 (mtm-85) REVERT: B 484 ASP cc_start: 0.8879 (t0) cc_final: 0.8564 (t0) REVERT: C 412 MET cc_start: 0.8848 (mmp) cc_final: 0.8237 (mmp) REVERT: C 614 LYS cc_start: 0.8761 (tppt) cc_final: 0.8234 (ttpt) REVERT: D 484 ASP cc_start: 0.8793 (t0) cc_final: 0.8389 (t0) REVERT: E 396 CYS cc_start: 0.8953 (t) cc_final: 0.8628 (t) REVERT: E 412 MET cc_start: 0.8936 (mmp) cc_final: 0.8381 (mmp) REVERT: E 420 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.6832 (ttp80) REVERT: E 474 ASP cc_start: 0.8529 (t0) cc_final: 0.8245 (p0) REVERT: F 454 LEU cc_start: 0.8108 (tp) cc_final: 0.7831 (tt) REVERT: F 538 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7956 (tm-30) REVERT: F 558 GLU cc_start: 0.8748 (tt0) cc_final: 0.8526 (tp30) outliers start: 12 outliers final: 8 residues processed: 276 average time/residue: 0.3867 time to fit residues: 150.7857 Evaluate side-chains 276 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 266 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 530 GLU Chi-restraints excluded: chain E residue 557 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 79 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 555 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.061480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.047196 restraints weight = 123763.273| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 1.79 r_work: 0.2325 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18712 Z= 0.247 Angle : 0.615 6.931 25364 Z= 0.339 Chirality : 0.039 0.282 2800 Planarity : 0.005 0.054 3079 Dihedral : 14.212 170.073 2822 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.67 % Allowed : 7.59 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2160 helix: 0.70 (0.14), residues: 1282 sheet: 0.80 (0.45), residues: 125 loop : -0.98 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 420 TYR 0.021 0.002 TYR D 552 PHE 0.024 0.002 PHE A 299 TRP 0.011 0.001 TRP D 387 HIS 0.004 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (18712) covalent geometry : angle 0.61502 / 0.34 (25364) hydrogen bonds : bond 0.05580 / 3.73 ( 1008) hydrogen bonds : angle 4.71696 / 3.40 ( 2896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 265 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8907 (mp) REVERT: A 548 ARG cc_start: 0.8895 (ttm-80) cc_final: 0.8520 (mtm-85) REVERT: B 401 MET cc_start: 0.8941 (tpt) cc_final: 0.8583 (tpt) REVERT: B 484 ASP cc_start: 0.8927 (t0) cc_final: 0.8606 (t0) REVERT: C 412 MET cc_start: 0.8851 (mmp) cc_final: 0.8241 (mmp) REVERT: C 614 LYS cc_start: 0.8747 (tppt) cc_final: 0.8247 (ttpt) REVERT: D 484 ASP cc_start: 0.8789 (t0) cc_final: 0.8368 (t0) REVERT: E 412 MET cc_start: 0.8943 (mmp) cc_final: 0.8445 (mmp) REVERT: E 420 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.6830 (ttp80) REVERT: E 474 ASP cc_start: 0.8543 (t0) cc_final: 0.8257 (p0) REVERT: F 454 LEU cc_start: 0.8069 (tp) cc_final: 0.7847 (tt) REVERT: F 538 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7981 (tm-30) outliers start: 13 outliers final: 9 residues processed: 269 average time/residue: 0.3951 time to fit residues: 149.7907 Evaluate side-chains 274 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 263 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 217 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 ASN E 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.062719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.048824 restraints weight = 124258.640| |-----------------------------------------------------------------------------| r_work (start): 0.2436 rms_B_bonded: 1.73 r_work: 0.2336 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2219 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18712 Z= 0.209 Angle : 0.592 6.481 25364 Z= 0.327 Chirality : 0.038 0.283 2800 Planarity : 0.005 0.055 3079 Dihedral : 14.098 166.436 2822 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.72 % Allowed : 8.20 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2160 helix: 0.80 (0.14), residues: 1282 sheet: 0.83 (0.45), residues: 125 loop : -1.00 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 420 TYR 0.021 0.002 TYR C 314 PHE 0.025 0.002 PHE A 299 TRP 0.010 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (18712) covalent geometry : angle 0.59224 / 0.33 (25364) hydrogen bonds : bond 0.05311 / 3.54 ( 1008) hydrogen bonds : angle 4.67355 / 3.36 ( 2896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8909 (mp) REVERT: A 548 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8538 (mtm-85) REVERT: B 484 ASP cc_start: 0.8910 (t0) cc_final: 0.8594 (t0) REVERT: C 412 MET cc_start: 0.8840 (mmp) cc_final: 0.8216 (mmp) REVERT: C 614 LYS cc_start: 0.8739 (tppt) cc_final: 0.8235 (ttpt) REVERT: D 484 ASP cc_start: 0.8787 (t0) cc_final: 0.8366 (t0) REVERT: E 412 MET cc_start: 0.8925 (mmp) cc_final: 0.8476 (mmp) REVERT: E 420 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.6803 (ttp80) REVERT: E 441 GLU cc_start: 0.8222 (tp30) cc_final: 0.7837 (tp30) REVERT: E 474 ASP cc_start: 0.8497 (t0) cc_final: 0.8223 (p0) REVERT: F 353 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8751 (mp) REVERT: F 454 LEU cc_start: 0.8080 (tp) cc_final: 0.7857 (tt) REVERT: F 538 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8047 (tm-30) REVERT: F 561 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7881 (tm-30) outliers start: 14 outliers final: 10 residues processed: 270 average time/residue: 0.4093 time to fit residues: 155.8770 Evaluate side-chains 274 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 261 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 410 LYS Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 183 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.062685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.048365 restraints weight = 122932.261| |-----------------------------------------------------------------------------| r_work (start): 0.2436 rms_B_bonded: 1.82 r_work: 0.2329 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2209 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18712 Z= 0.173 Angle : 0.568 7.033 25364 Z= 0.313 Chirality : 0.037 0.284 2800 Planarity : 0.004 0.056 3079 Dihedral : 13.964 166.166 2822 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.67 % Allowed : 8.46 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2160 helix: 0.93 (0.14), residues: 1303 sheet: 0.37 (0.43), residues: 142 loop : -0.98 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.021 0.002 TYR C 314 PHE 0.026 0.002 PHE A 299 TRP 0.010 0.001 TRP D 387 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (18712) covalent geometry : angle 0.56754 / 0.31 (25364) hydrogen bonds : bond 0.04961 / 3.31 ( 1008) hydrogen bonds : angle 4.59196 / 3.31 ( 2896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8866 (mp) REVERT: A 548 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8535 (mtm-85) REVERT: B 484 ASP cc_start: 0.8897 (t0) cc_final: 0.8583 (t0) REVERT: C 412 MET cc_start: 0.8815 (mmp) cc_final: 0.8183 (mmp) REVERT: C 614 LYS cc_start: 0.8725 (tppt) cc_final: 0.8201 (ttpt) REVERT: D 484 ASP cc_start: 0.8834 (t0) cc_final: 0.8402 (t0) REVERT: E 412 MET cc_start: 0.8924 (mmp) cc_final: 0.8483 (mmp) REVERT: E 420 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.6802 (ttp80) REVERT: E 474 ASP cc_start: 0.8641 (t0) cc_final: 0.8224 (p0) REVERT: F 353 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8716 (mp) REVERT: F 412 MET cc_start: 0.8062 (mmt) cc_final: 0.7645 (mmt) REVERT: F 454 LEU cc_start: 0.8094 (tp) cc_final: 0.7858 (tt) REVERT: F 538 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8062 (tm-30) REVERT: F 561 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7854 (tm-30) outliers start: 13 outliers final: 8 residues processed: 273 average time/residue: 0.4118 time to fit residues: 159.4785 Evaluate side-chains 277 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 266 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 410 LYS Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 144 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.062327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.047968 restraints weight = 123640.396| |-----------------------------------------------------------------------------| r_work (start): 0.2440 rms_B_bonded: 1.82 r_work: 0.2334 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2217 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18712 Z= 0.173 Angle : 0.564 7.548 25364 Z= 0.311 Chirality : 0.037 0.285 2800 Planarity : 0.004 0.057 3079 Dihedral : 13.894 165.907 2822 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.57 % Allowed : 8.82 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2160 helix: 0.98 (0.14), residues: 1303 sheet: 0.33 (0.43), residues: 142 loop : -0.95 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 420 TYR 0.020 0.002 TYR C 314 PHE 0.024 0.001 PHE A 299 TRP 0.010 0.001 TRP D 387 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (18712) covalent geometry : angle 0.56444 / 0.31 (25364) hydrogen bonds : bond 0.04871 / 3.25 ( 1008) hydrogen bonds : angle 4.55693 / 3.28 ( 2896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 267 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8217 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 353 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8864 (mp) REVERT: A 548 ARG cc_start: 0.8885 (ttm-80) cc_final: 0.8528 (mtm-85) REVERT: B 484 ASP cc_start: 0.8883 (t0) cc_final: 0.8567 (t0) REVERT: C 412 MET cc_start: 0.8818 (mmp) cc_final: 0.8190 (mmp) REVERT: C 614 LYS cc_start: 0.8746 (tppt) cc_final: 0.8227 (ttpt) REVERT: D 484 ASP cc_start: 0.8811 (t0) cc_final: 0.8381 (t0) REVERT: E 412 MET cc_start: 0.8914 (mmp) cc_final: 0.8403 (mmp) REVERT: E 420 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.6786 (ttp80) REVERT: E 441 GLU cc_start: 0.8155 (tp30) cc_final: 0.7766 (tp30) REVERT: E 474 ASP cc_start: 0.8611 (t0) cc_final: 0.8218 (p0) REVERT: F 353 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8691 (mp) REVERT: F 412 MET cc_start: 0.8048 (mmt) cc_final: 0.7662 (mmt) REVERT: F 454 LEU cc_start: 0.8081 (tp) cc_final: 0.7716 (tt) REVERT: F 538 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7928 (tm-30) REVERT: F 561 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7825 (tm-30) outliers start: 11 outliers final: 7 residues processed: 270 average time/residue: 0.4203 time to fit residues: 161.2280 Evaluate side-chains 275 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 265 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 87 optimal weight: 0.0870 chunk 169 optimal weight: 0.2980 chunk 205 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN E 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.063196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.048759 restraints weight = 123395.524| |-----------------------------------------------------------------------------| r_work (start): 0.2462 rms_B_bonded: 1.84 r_work: 0.2359 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2242 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18712 Z= 0.127 Angle : 0.546 7.661 25364 Z= 0.299 Chirality : 0.036 0.285 2800 Planarity : 0.004 0.059 3079 Dihedral : 13.712 165.757 2822 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.46 % Allowed : 8.93 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2160 helix: 1.13 (0.14), residues: 1303 sheet: 0.29 (0.44), residues: 142 loop : -0.89 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 559 TYR 0.021 0.001 TYR C 314 PHE 0.022 0.001 PHE A 299 TRP 0.009 0.001 TRP D 387 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (18712) covalent geometry : angle 0.54640 / 0.30 (25364) hydrogen bonds : bond 0.04484 / 2.98 ( 1008) hydrogen bonds : angle 4.47928 / 3.23 ( 2896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 267 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8834 (mp) REVERT: A 548 ARG cc_start: 0.8915 (ttm-80) cc_final: 0.8596 (mtm-85) REVERT: B 484 ASP cc_start: 0.8866 (t0) cc_final: 0.8548 (t0) REVERT: C 412 MET cc_start: 0.8772 (mmp) cc_final: 0.8147 (mmp) REVERT: C 614 LYS cc_start: 0.8711 (tppt) cc_final: 0.8179 (ttpt) REVERT: D 484 ASP cc_start: 0.8764 (t0) cc_final: 0.8330 (t0) REVERT: D 617 PHE cc_start: 0.8128 (t80) cc_final: 0.7883 (t80) REVERT: E 412 MET cc_start: 0.8909 (mmp) cc_final: 0.8427 (mmp) REVERT: E 420 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6641 (ttp80) REVERT: E 474 ASP cc_start: 0.8592 (t0) cc_final: 0.8214 (p0) REVERT: E 599 TRP cc_start: 0.8898 (m100) cc_final: 0.8513 (m100) REVERT: F 353 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8725 (mp) REVERT: F 412 MET cc_start: 0.8027 (mmt) cc_final: 0.7682 (mmt) REVERT: F 454 LEU cc_start: 0.8166 (tp) cc_final: 0.7924 (tt) REVERT: F 538 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8039 (tm-30) REVERT: F 561 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7805 (tm-30) outliers start: 9 outliers final: 6 residues processed: 270 average time/residue: 0.4077 time to fit residues: 155.8091 Evaluate side-chains 273 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 264 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 192 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 177 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN C 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.063422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.048964 restraints weight = 123033.921| |-----------------------------------------------------------------------------| r_work (start): 0.2468 rms_B_bonded: 1.84 r_work: 0.2365 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2238 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18712 Z= 0.123 Angle : 0.542 8.116 25364 Z= 0.296 Chirality : 0.036 0.284 2800 Planarity : 0.004 0.053 3079 Dihedral : 13.627 165.646 2822 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.41 % Allowed : 9.24 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2160 helix: 1.22 (0.14), residues: 1303 sheet: 0.26 (0.43), residues: 142 loop : -0.86 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 420 TYR 0.020 0.001 TYR C 314 PHE 0.025 0.001 PHE A 299 TRP 0.009 0.001 TRP E 599 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (18712) covalent geometry : angle 0.54226 / 0.30 (25364) hydrogen bonds : bond 0.04347 / 2.89 ( 1008) hydrogen bonds : angle 4.41755 / 3.18 ( 2896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7903.39 seconds wall clock time: 135 minutes 1.30 seconds (8101.30 seconds total)