Starting phenix.real_space_refine on Mon Jul 6 15:19:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kak_62209/07_2026/9kak_62209_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kak_62209/07_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_62209/07_2026/9kak_62209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kak_62209/07_2026/9kak_62209.map" model { file = "/net/cci-nas-00/data/ceres_data/9kak_62209/07_2026/9kak_62209_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kak_62209/07_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-dev-6108/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: 5.81, 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: 3.26 Conformation dependent library (CDL) restraints added in 773.3 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: 6.33 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: 9.31 Time building geometry restraints manager: 4.42 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=" 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 angle pdb=" N3 DT T -1 " pdb=" C4 DT T -1 " pdb=" O4 DT T -1 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 38.460 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.950 ------------------------------------------------------------------------------- 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 : 1.012 17.383 25364 Z= 0.606 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 1.01192 / 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 : 1.003 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: 0.8515 (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: 0.8319 (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: 0.4106 time to fit residues: 203.5647 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 : 0.688 ------------------------------------------------------------------------------- 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 E 513 HIS F 267 GLN F 467 GLN ** F 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.064290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.050242 restraints weight = 123724.790| |-----------------------------------------------------------------------------| r_work (start): 0.2453 rms_B_bonded: 1.76 r_work: 0.2351 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2234 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18712 Z= 0.206 Angle : 0.717 7.237 25364 Z= 0.397 Chirality : 0.041 0.280 2800 Planarity : 0.006 0.117 3079 Dihedral : 14.767 172.214 2822 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -0.27 (0.16), residues: 2160 helix: 0.19 (0.13), residues: 1296 sheet: -0.03 (0.42), residues: 157 loop : -0.69 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 548 TYR 0.028 0.002 TYR D 552 PHE 0.017 0.002 PHE E 468 TRP 0.013 0.001 TRP E 599 HIS 0.007 0.002 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (18712) covalent geometry : angle 0.71666 / 0.40 (25364) hydrogen bonds : bond 0.07057 / 4.73 ( 1008) hydrogen bonds : angle 5.25864 / 3.78 ( 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 294 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 289 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8606 (p90) cc_final: 0.8323 (p90) REVERT: A 548 ARG cc_start: 0.8841 (ttm-80) cc_final: 0.8437 (mtm-85) REVERT: B 401 MET cc_start: 0.8993 (tpt) cc_final: 0.8512 (tpt) REVERT: B 484 ASP cc_start: 0.8884 (t0) cc_final: 0.8620 (t0) REVERT: B 548 ARG cc_start: 0.8659 (ttm110) cc_final: 0.8278 (mtm-85) REVERT: C 278 MET cc_start: 0.9200 (mmm) cc_final: 0.8555 (mmm) REVERT: C 614 LYS cc_start: 0.8773 (tppt) cc_final: 0.8206 (ttpt) REVERT: D 484 ASP cc_start: 0.8738 (t0) cc_final: 0.8326 (t0) REVERT: D 578 MET cc_start: 0.9073 (ttm) cc_final: 0.8844 (ttp) REVERT: E 396 CYS cc_start: 0.8929 (t) cc_final: 0.8543 (t) REVERT: E 474 ASP cc_start: 0.8513 (t0) cc_final: 0.8167 (p0) REVERT: E 553 LEU cc_start: 0.8821 (mt) cc_final: 0.8509 (mm) REVERT: F 454 LEU cc_start: 0.8143 (tp) cc_final: 0.7840 (tt) REVERT: F 511 LYS cc_start: 0.8915 (tttt) cc_final: 0.8607 (ttmm) REVERT: F 538 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7895 (tm-30) REVERT: F 558 GLU cc_start: 0.8737 (tt0) cc_final: 0.8441 (tp30) outliers start: 5 outliers final: 2 residues processed: 290 average time/residue: 0.3797 time to fit residues: 156.1079 Evaluate side-chains 272 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 3.9990 chunk 96 optimal weight: 2.9990 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: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.2827 r_free = 0.2827 target = 0.064142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.050123 restraints weight = 124117.732| |-----------------------------------------------------------------------------| r_work (start): 0.2454 rms_B_bonded: 1.76 r_work: 0.2353 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2237 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18712 Z= 0.177 Angle : 0.618 6.318 25364 Z= 0.344 Chirality : 0.038 0.273 2800 Planarity : 0.005 0.081 3079 Dihedral : 14.408 170.737 2822 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.26 % Allowed : 6.30 % Favored : 93.45 % 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: -0.03 (0.17), residues: 2160 helix: 0.48 (0.14), residues: 1285 sheet: -0.00 (0.43), residues: 141 loop : -0.75 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 559 TYR 0.023 0.002 TYR C 314 PHE 0.026 0.001 PHE C 299 TRP 0.010 0.001 TRP D 387 HIS 0.005 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (18712) covalent geometry : angle 0.61784 / 0.34 (25364) hydrogen bonds : bond 0.06014 / 4.02 ( 1008) hydrogen bonds : angle 4.94395 / 3.56 ( 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 279 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 0.932 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: 0.8464 (p90) cc_final: 0.8182 (p90) REVERT: A 548 ARG cc_start: 0.8827 (ttm-80) cc_final: 0.8446 (mtm-85) REVERT: B 401 MET cc_start: 0.8995 (tpt) cc_final: 0.8574 (tpt) REVERT: B 484 ASP cc_start: 0.8875 (t0) cc_final: 0.8582 (t0) REVERT: C 412 MET cc_start: 0.8816 (mmp) cc_final: 0.8204 (mmp) REVERT: C 614 LYS cc_start: 0.8779 (tppt) cc_final: 0.8211 (ttpt) REVERT: D 484 ASP cc_start: 0.8718 (t0) cc_final: 0.8308 (t0) REVERT: E 396 CYS cc_start: 0.8935 (t) cc_final: 0.8628 (t) REVERT: E 412 MET cc_start: 0.8926 (mmp) cc_final: 0.8427 (mmp) REVERT: E 441 GLU cc_start: 0.8096 (tp30) cc_final: 0.7770 (tp30) REVERT: E 474 ASP cc_start: 0.8529 (t0) cc_final: 0.8275 (p0) REVERT: F 454 LEU cc_start: 0.8157 (tp) cc_final: 0.7861 (tt) REVERT: F 466 ASP cc_start: 0.7608 (m-30) cc_final: 0.7368 (m-30) REVERT: F 538 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7964 (tm-30) REVERT: F 558 GLU cc_start: 0.8723 (tt0) cc_final: 0.8427 (tp30) outliers start: 5 outliers final: 3 residues processed: 275 average time/residue: 0.3744 time to fit residues: 146.4056 Evaluate side-chains 268 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET 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: 4.9990 chunk 91 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 529 ASN F 555 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.063351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.049408 restraints weight = 124407.551| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 1.76 r_work: 0.2324 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2207 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18712 Z= 0.217 Angle : 0.613 7.687 25364 Z= 0.341 Chirality : 0.039 0.268 2800 Planarity : 0.005 0.060 3079 Dihedral : 14.310 171.301 2822 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.62 % Allowed : 6.60 % Favored : 92.78 % 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: 0.10 (0.17), residues: 2160 helix: 0.61 (0.14), residues: 1274 sheet: 0.74 (0.48), residues: 109 loop : -0.82 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 548 TYR 0.022 0.002 TYR D 552 PHE 0.018 0.002 PHE C 299 TRP 0.013 0.002 TRP E 393 HIS 0.005 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (18712) covalent geometry : angle 0.61282 / 0.34 (25364) hydrogen bonds : bond 0.05683 / 3.79 ( 1008) hydrogen bonds : angle 4.80924 / 3.46 ( 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 288 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 276 time to evaluate : 0.973 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 299 PHE cc_start: 0.8473 (p90) cc_final: 0.8256 (p90) REVERT: A 353 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8924 (mp) REVERT: A 548 ARG cc_start: 0.8895 (ttm-80) cc_final: 0.8524 (mtm-85) REVERT: B 401 MET cc_start: 0.8988 (tpt) cc_final: 0.8595 (tpt) REVERT: B 484 ASP cc_start: 0.8938 (t0) cc_final: 0.8621 (t0) REVERT: C 383 ASP cc_start: 0.8471 (t70) cc_final: 0.8271 (t70) REVERT: C 412 MET cc_start: 0.8849 (mmp) cc_final: 0.8234 (mmp) REVERT: C 614 LYS cc_start: 0.8783 (tppt) cc_final: 0.8218 (ttpt) REVERT: D 484 ASP cc_start: 0.8743 (t0) cc_final: 0.8335 (t0) REVERT: E 396 CYS cc_start: 0.8944 (t) cc_final: 0.8631 (t) REVERT: E 412 MET cc_start: 0.8956 (mmp) cc_final: 0.8389 (mmp) REVERT: E 420 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.6964 (ttp80) REVERT: E 474 ASP cc_start: 0.8550 (t0) cc_final: 0.8263 (p0) REVERT: F 454 LEU cc_start: 0.8135 (tp) cc_final: 0.7771 (tt) REVERT: F 538 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7982 (tm-30) REVERT: F 558 GLU cc_start: 0.8753 (tt0) cc_final: 0.8531 (tp30) outliers start: 12 outliers final: 8 residues processed: 282 average time/residue: 0.3735 time to fit residues: 149.2042 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 : 0.721 ------------------------------------------------------------------------------- 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 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 581 TRP 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: 2.9990 chunk 215 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.2796 r_free = 0.2796 target = 0.063040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.049197 restraints weight = 124633.899| |-----------------------------------------------------------------------------| r_work (start): 0.2443 rms_B_bonded: 1.74 r_work: 0.2344 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2236 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2667 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= 0.230 Angle : 0.610 7.040 25364 Z= 0.339 Chirality : 0.039 0.268 2800 Planarity : 0.005 0.058 3079 Dihedral : 14.249 170.436 2822 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.72 % Allowed : 7.07 % Favored : 92.21 % 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: 0.13 (0.17), residues: 2160 helix: 0.66 (0.14), residues: 1274 sheet: 0.75 (0.45), residues: 125 loop : -0.90 (0.19), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 548 TYR 0.020 0.002 TYR D 552 PHE 0.018 0.002 PHE C 617 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 0.00534 / 0.23 (18712) covalent geometry : angle 0.60990 / 0.34 (25364) hydrogen bonds : bond 0.05631 / 3.76 ( 1008) hydrogen bonds : angle 4.76835 / 3.43 ( 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: 14 poor density : 269 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8662 (p90) cc_final: 0.7746 (p90) REVERT: A 353 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8913 (mp) REVERT: A 548 ARG cc_start: 0.8893 (ttm-80) cc_final: 0.8526 (mtm-85) REVERT: B 401 MET cc_start: 0.8982 (tpt) cc_final: 0.8609 (tpt) REVERT: B 484 ASP cc_start: 0.8929 (t0) cc_final: 0.8613 (t0) REVERT: C 383 ASP cc_start: 0.8471 (t70) cc_final: 0.8246 (t70) REVERT: C 412 MET cc_start: 0.8853 (mmp) cc_final: 0.8246 (mmp) REVERT: C 614 LYS cc_start: 0.8776 (tppt) cc_final: 0.8236 (ttpt) REVERT: D 484 ASP cc_start: 0.8765 (t0) cc_final: 0.8354 (t0) REVERT: E 396 CYS cc_start: 0.8895 (t) cc_final: 0.8564 (t) REVERT: E 412 MET cc_start: 0.8939 (mmp) cc_final: 0.8450 (mmp) REVERT: E 420 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.6922 (ttp80) REVERT: E 474 ASP cc_start: 0.8506 (t0) cc_final: 0.8285 (p0) REVERT: F 454 LEU cc_start: 0.8097 (tp) cc_final: 0.7834 (tt) REVERT: F 538 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7964 (tm-30) outliers start: 14 outliers final: 10 residues processed: 275 average time/residue: 0.4068 time to fit residues: 156.7694 Evaluate side-chains 278 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 266 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain E residue 594 SER 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: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 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: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.2806 r_free = 0.2806 target = 0.062649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.048235 restraints weight = 123162.544| |-----------------------------------------------------------------------------| r_work (start): 0.2436 rms_B_bonded: 1.82 r_work: 0.2329 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2206 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18712 Z= 0.188 Angle : 0.581 6.492 25364 Z= 0.321 Chirality : 0.038 0.267 2800 Planarity : 0.004 0.051 3079 Dihedral : 14.111 167.709 2822 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.83 % Allowed : 7.43 % 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: 0.23 (0.17), residues: 2160 helix: 0.80 (0.14), residues: 1294 sheet: 0.73 (0.45), residues: 125 loop : -1.01 (0.19), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 420 TYR 0.022 0.002 TYR E 314 PHE 0.017 0.002 PHE E 468 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 0.00433 / 0.19 (18712) covalent geometry : angle 0.58092 / 0.32 (25364) hydrogen bonds : bond 0.05198 / 3.47 ( 1008) hydrogen bonds : angle 4.66537 / 3.36 ( 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 285 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 269 time to evaluate : 1.119 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 299 PHE cc_start: 0.7902 (p90) cc_final: 0.7667 (p90) REVERT: A 353 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8870 (mp) REVERT: A 548 ARG cc_start: 0.8923 (ttm-80) cc_final: 0.8569 (mtm-85) REVERT: B 484 ASP cc_start: 0.8883 (t0) cc_final: 0.8568 (t0) REVERT: C 412 MET cc_start: 0.8827 (mmp) cc_final: 0.8200 (mmp) REVERT: C 614 LYS cc_start: 0.8752 (tppt) cc_final: 0.8229 (ttpt) REVERT: D 484 ASP cc_start: 0.8836 (t0) cc_final: 0.8426 (t0) REVERT: E 412 MET cc_start: 0.8933 (mmp) cc_final: 0.8486 (mmp) REVERT: E 420 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.6807 (ttp80) REVERT: E 474 ASP cc_start: 0.8661 (t0) cc_final: 0.8282 (p0) REVERT: F 353 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8719 (mp) REVERT: F 454 LEU cc_start: 0.8079 (tp) cc_final: 0.7809 (tt) REVERT: F 466 ASP cc_start: 0.7634 (m-30) cc_final: 0.7420 (m-30) REVERT: F 538 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7886 (tm-30) outliers start: 16 outliers final: 11 residues processed: 273 average time/residue: 0.4240 time to fit residues: 164.0116 Evaluate side-chains 278 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 264 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 530 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 217 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 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: 0.9980 chunk 87 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.2813 r_free = 0.2813 target = 0.063065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.048691 restraints weight = 122755.024| |-----------------------------------------------------------------------------| r_work (start): 0.2445 rms_B_bonded: 1.83 r_work: 0.2338 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2218 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18712 Z= 0.166 Angle : 0.564 6.587 25364 Z= 0.312 Chirality : 0.037 0.267 2800 Planarity : 0.004 0.051 3079 Dihedral : 14.007 167.249 2822 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.77 % Allowed : 7.89 % Favored : 91.33 % 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: 0.35 (0.17), residues: 2160 helix: 0.91 (0.14), residues: 1303 sheet: 0.29 (0.43), residues: 142 loop : -0.94 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 420 TYR 0.020 0.002 TYR C 314 PHE 0.032 0.001 PHE C 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 0.00376 / 0.17 (18712) covalent geometry : angle 0.56406 / 0.31 (25364) hydrogen bonds : bond 0.04963 / 3.30 ( 1008) hydrogen bonds : angle 4.60468 / 3.32 ( 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 278 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 1.050 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 299 PHE cc_start: 0.7846 (p90) cc_final: 0.7641 (p90) REVERT: A 300 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8326 (mm-30) REVERT: A 353 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8862 (mp) REVERT: A 548 ARG cc_start: 0.8895 (ttm-80) cc_final: 0.8545 (mtm-85) REVERT: B 484 ASP cc_start: 0.8882 (t0) cc_final: 0.8567 (t0) REVERT: C 412 MET cc_start: 0.8820 (mmp) cc_final: 0.8190 (mmp) REVERT: C 614 LYS cc_start: 0.8718 (tppt) cc_final: 0.8194 (ttpt) REVERT: D 484 ASP cc_start: 0.8811 (t0) cc_final: 0.8408 (t0) REVERT: E 396 CYS cc_start: 0.8954 (t) cc_final: 0.8679 (t) REVERT: E 412 MET cc_start: 0.8928 (mmp) cc_final: 0.8497 (mmp) REVERT: E 420 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.6787 (ttp80) REVERT: E 441 GLU cc_start: 0.8191 (tp30) cc_final: 0.7811 (tp30) REVERT: E 474 ASP cc_start: 0.8619 (t0) cc_final: 0.8251 (p0) REVERT: F 353 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8701 (mp) REVERT: F 454 LEU cc_start: 0.8077 (tp) cc_final: 0.7840 (tt) REVERT: F 538 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7865 (tm-30) REVERT: F 561 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7815 (tm-30) outliers start: 15 outliers final: 9 residues processed: 266 average time/residue: 0.4264 time to fit residues: 159.7537 Evaluate side-chains 277 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 265 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 530 GLU 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: 1.9990 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 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: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.2801 r_free = 0.2801 target = 0.062394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.048056 restraints weight = 123216.004| |-----------------------------------------------------------------------------| r_work (start): 0.2436 rms_B_bonded: 1.82 r_work: 0.2328 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18712 Z= 0.196 Angle : 0.575 6.919 25364 Z= 0.317 Chirality : 0.037 0.269 2800 Planarity : 0.004 0.057 3079 Dihedral : 13.991 166.708 2822 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.67 % Allowed : 8.10 % Favored : 91.23 % 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: 0.35 (0.17), residues: 2160 helix: 0.92 (0.14), residues: 1303 sheet: 0.31 (0.43), residues: 142 loop : -0.97 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.019 0.002 TYR C 314 PHE 0.022 0.002 PHE D 299 TRP 0.011 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (18712) covalent geometry : angle 0.57518 / 0.32 (25364) hydrogen bonds : bond 0.05076 / 3.39 ( 1008) hydrogen bonds : angle 4.59519 / 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 284 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 1.042 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 299 PHE cc_start: 0.8041 (p90) cc_final: 0.7703 (p90) REVERT: A 353 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8866 (mp) REVERT: A 548 ARG cc_start: 0.8939 (ttm-80) cc_final: 0.8581 (mtm-85) REVERT: B 484 ASP cc_start: 0.8894 (t0) cc_final: 0.8582 (t0) REVERT: C 412 MET cc_start: 0.8829 (mmp) cc_final: 0.8200 (mmp) REVERT: C 614 LYS cc_start: 0.8726 (tppt) cc_final: 0.8204 (ttpt) REVERT: D 484 ASP cc_start: 0.8807 (t0) cc_final: 0.8397 (t0) REVERT: E 412 MET cc_start: 0.8931 (mmp) cc_final: 0.8485 (mmp) REVERT: E 420 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.6827 (ttp80) REVERT: E 441 GLU cc_start: 0.8200 (tp30) cc_final: 0.7807 (tp30) REVERT: E 474 ASP cc_start: 0.8640 (t0) cc_final: 0.8225 (p0) REVERT: E 530 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: F 353 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8733 (mp) REVERT: F 412 MET cc_start: 0.8026 (mmt) cc_final: 0.7614 (mmt) REVERT: F 454 LEU cc_start: 0.8068 (tp) cc_final: 0.7852 (tt) REVERT: F 538 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7910 (tm-30) REVERT: F 561 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7831 (tm-30) outliers start: 13 outliers final: 9 residues processed: 275 average time/residue: 0.3950 time to fit residues: 154.5960 Evaluate side-chains 276 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 263 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 530 GLU 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: 0.9990 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: 1.9990 chunk 126 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 332 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 = 0.061811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.047516 restraints weight = 124340.155| |-----------------------------------------------------------------------------| r_work (start): 0.2421 rms_B_bonded: 1.83 r_work: 0.2312 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2192 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3090 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= 0.220 Angle : 0.587 6.911 25364 Z= 0.324 Chirality : 0.038 0.269 2800 Planarity : 0.005 0.057 3079 Dihedral : 14.003 166.849 2822 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 0.31 (0.17), residues: 2160 helix: 0.87 (0.14), residues: 1288 sheet: 0.30 (0.43), residues: 142 loop : -0.91 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.019 0.002 TYR D 552 PHE 0.021 0.002 PHE C 299 TRP 0.011 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (18712) covalent geometry : angle 0.58749 / 0.32 (25364) hydrogen bonds : bond 0.05188 / 3.47 ( 1008) hydrogen bonds : angle 4.61474 / 3.33 ( 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 276 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 263 time to evaluate : 1.053 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 353 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8863 (mp) REVERT: A 548 ARG cc_start: 0.8952 (ttm-80) cc_final: 0.8578 (mtm-85) REVERT: B 484 ASP cc_start: 0.8896 (t0) cc_final: 0.8575 (t0) REVERT: C 412 MET cc_start: 0.8835 (mmp) cc_final: 0.8215 (mmp) REVERT: C 614 LYS cc_start: 0.8747 (tppt) cc_final: 0.8215 (ttpt) REVERT: D 484 ASP cc_start: 0.8776 (t0) cc_final: 0.8330 (t0) REVERT: E 412 MET cc_start: 0.8929 (mmp) cc_final: 0.8471 (mmp) REVERT: E 420 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.6795 (ttp80) REVERT: E 441 GLU cc_start: 0.8212 (tp30) cc_final: 0.7804 (tp30) REVERT: E 474 ASP cc_start: 0.8615 (t0) cc_final: 0.8235 (p0) REVERT: E 530 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: F 353 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8727 (mp) REVERT: F 412 MET cc_start: 0.8067 (mmt) cc_final: 0.7671 (mmt) REVERT: F 454 LEU cc_start: 0.8081 (tp) cc_final: 0.7847 (tt) REVERT: F 538 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7951 (tm-30) REVERT: F 561 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7852 (tm-30) outliers start: 13 outliers final: 7 residues processed: 267 average time/residue: 0.4047 time to fit residues: 152.6280 Evaluate side-chains 275 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 264 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 530 GLU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 605 LYS 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: 1.9990 chunk 169 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 211 optimal weight: 0.0770 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.062816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.048371 restraints weight = 123729.322| |-----------------------------------------------------------------------------| r_work (start): 0.2441 rms_B_bonded: 1.84 r_work: 0.2335 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2217 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18712 Z= 0.159 Angle : 0.565 7.427 25364 Z= 0.312 Chirality : 0.036 0.269 2800 Planarity : 0.004 0.059 3079 Dihedral : 13.893 166.330 2822 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.57 % Allowed : 8.46 % Favored : 90.97 % 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: 0.44 (0.17), residues: 2160 helix: 1.00 (0.14), residues: 1303 sheet: 0.26 (0.43), residues: 142 loop : -0.93 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 559 TYR 0.020 0.002 TYR C 314 PHE 0.018 0.001 PHE C 299 TRP 0.011 0.001 TRP D 387 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (18712) covalent geometry : angle 0.56549 / 0.31 (25364) hydrogen bonds : bond 0.04830 / 3.22 ( 1008) hydrogen bonds : angle 4.56001 / 3.29 ( 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 275 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 264 time to evaluate : 0.721 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: A 353 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 548 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8520 (mtm-85) REVERT: B 484 ASP cc_start: 0.8887 (t0) cc_final: 0.8580 (t0) REVERT: C 412 MET cc_start: 0.8796 (mmp) cc_final: 0.8173 (mmp) REVERT: C 614 LYS cc_start: 0.8715 (tppt) cc_final: 0.8186 (ttpt) REVERT: D 484 ASP cc_start: 0.8803 (t0) cc_final: 0.8375 (t0) REVERT: E 412 MET cc_start: 0.8913 (mmp) cc_final: 0.8480 (mmp) REVERT: E 420 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.6780 (ttp80) REVERT: E 441 GLU cc_start: 0.8259 (tp30) cc_final: 0.7882 (tp30) REVERT: E 474 ASP cc_start: 0.8590 (t0) cc_final: 0.8205 (p0) REVERT: E 530 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: F 353 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8699 (mp) REVERT: F 412 MET cc_start: 0.8091 (mmt) cc_final: 0.7704 (mmt) REVERT: F 454 LEU cc_start: 0.8057 (tp) cc_final: 0.7701 (tt) REVERT: F 538 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7928 (tm-30) REVERT: F 561 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7838 (tm-30) outliers start: 11 outliers final: 5 residues processed: 266 average time/residue: 0.3887 time to fit residues: 146.2333 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 : 1.004 ------------------------------------------------------------------------------- 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 383 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 530 GLU 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: 2.9990 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 332 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 = 0.2818 r_free = 0.2818 target = 0.062867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.048424 restraints weight = 123069.436| |-----------------------------------------------------------------------------| r_work (start): 0.2450 rms_B_bonded: 1.83 r_work: 0.2349 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2233 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18712 Z= 0.152 Angle : 0.548 7.575 25364 Z= 0.301 Chirality : 0.036 0.269 2800 Planarity : 0.004 0.053 3079 Dihedral : 13.763 166.124 2822 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.41 % Allowed : 8.72 % 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: 0.55 (0.17), residues: 2160 helix: 1.10 (0.14), residues: 1302 sheet: 0.25 (0.43), residues: 142 loop : -0.90 (0.20), residues: 716 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 0.016 0.001 PHE C 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 0.00343 / 0.15 (18712) covalent geometry : angle 0.54789 / 0.30 (25364) hydrogen bonds : bond 0.04636 / 3.09 ( 1008) hydrogen bonds : angle 4.48887 / 3.24 ( 2896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7942.54 seconds wall clock time: 135 minutes 47.06 seconds (8147.06 seconds total)