Starting phenix.real_space_refine on Sun Aug 9 16:56:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fb6_50289/08_2026/9fb6_50289_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fb6_50289/08_2026/9fb6_50289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fb6_50289/08_2026/9fb6_50289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fb6_50289/08_2026/9fb6_50289.map" model { file = "/net/cci-nas-00/data/ceres_data/9fb6_50289/08_2026/9fb6_50289_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fb6_50289/08_2026/9fb6_50289_trim.cif" } resolution = 3.13 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= -0.011 sd= 0.508 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: 6 Type Number sf(0) Gaussians P 46 5.49 5 S 126 5.16 5 C 11668 2.51 5 N 3077 2.21 5 O 3432 1.98 5 H 18237 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36586 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" 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: "B" 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: "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: 5919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5919 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "E" 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: "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: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 352 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 544 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.34, per 1000 atoms: 0.17 Number of scatterers: 36586 At special positions: 0 Unit cell: (125.25, 141.95, 106.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 126 16.00 P 46 15.00 O 3432 8.00 N 3077 7.00 C 11668 6.00 H 18237 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: 3.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 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 69.1% alpha, 6.5% beta 11 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'A' and resid 269 through 281 removed outlier: 3.788A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.963A pdb=" N PHE A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 297 No H-bonds generated for 'chain 'A' and resid 296 through 297' Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.504A pdb=" N MET A 301 " --> pdb=" O SER A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 316 through 330 removed outlier: 5.237A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 355 Processing helix chain 'A' and resid 356 through 376 Processing helix chain 'A' and resid 383 through 398 removed outlier: 3.574A pdb=" N TRP A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 397 " --> pdb=" O TRP A 393 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 456 through 462 removed outlier: 3.700A 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 480 through 484 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 550 through 560 removed outlier: 3.838A pdb=" N LYS A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 567 through 570 Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.731A 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: 3.718A 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: 5.224A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASN B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.825A 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 removed outlier: 3.661A pdb=" N TRP B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) 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 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 456 through 462 removed outlier: 3.624A 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 479 through 484 removed outlier: 3.508A pdb=" N SER B 482 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 497 removed outlier: 3.516A pdb=" N ASN B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 503 removed outlier: 3.655A pdb=" N GLY B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 550 through 560 removed outlier: 3.530A pdb=" N LYS B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.595A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.776A pdb=" N VAL C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' 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 329 removed outlier: 5.338A pdb=" N ALA C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASN C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.699A 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 396 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: 3.815A 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 560 removed outlier: 4.074A pdb=" N LYS C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 566 Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.766A pdb=" N LEU C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) 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 622 Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.748A 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: 3.536A 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 329 removed outlier: 5.528A pdb=" N ALA D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASN D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 3.764A 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 377 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 456 through 462 removed outlier: 4.349A 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 503 removed outlier: 3.600A pdb=" N GLY D 503 " --> pdb=" O ASP D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 561 through 566 Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.649A pdb=" N LEU D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 588 removed outlier: 3.695A pdb=" N GLU D 587 " --> pdb=" O PRO D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 607 removed outlier: 4.591A pdb=" N SER D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 621 removed outlier: 3.819A pdb=" N MET D 621 " --> pdb=" O PHE D 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 281 Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 295 through 297 No H-bonds generated for 'chain 'E' and resid 295 through 297' Processing helix chain 'E' and resid 302 through 308 Processing helix chain 'E' and resid 310 through 315 removed outlier: 3.748A pdb=" N LYS E 315 " --> pdb=" O PRO E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 330 removed outlier: 5.469A pdb=" N ALA E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASN E 323 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 3.617A 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 376 Processing helix chain 'E' and resid 383 through 398 removed outlier: 3.550A pdb=" N LEU E 397 " --> pdb=" O TRP E 393 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 415 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 456 through 462 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 480 through 484 Processing helix chain 'E' and resid 489 through 497 Processing helix chain 'E' and resid 497 through 503 removed outlier: 3.517A pdb=" N GLY E 503 " --> pdb=" O ASP E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 550 through 560 removed outlier: 3.623A pdb=" N ARG E 559 " --> pdb=" O HIS E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.732A 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 removed outlier: 3.627A pdb=" N GLU E 598 " --> pdb=" O SER E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 622 Processing helix chain 'F' and resid 269 through 281 removed outlier: 3.675A 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 302 through 308 Processing helix chain 'F' and resid 310 through 315 Processing helix chain 'F' and resid 316 through 329 removed outlier: 5.148A pdb=" N ALA F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASN F 323 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP F 329 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 353 Processing helix chain 'F' and resid 356 through 373 removed outlier: 3.649A pdb=" N ASN F 366 " --> pdb=" O THR F 362 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 398 removed outlier: 3.786A pdb=" N TRP F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU F 398 " --> pdb=" O LEU F 394 " (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 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 456 through 462 removed outlier: 3.761A pdb=" N GLU F 460 " --> pdb=" O ARG F 456 " (cutoff:3.500A) 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 480 through 484 Processing helix chain 'F' and resid 489 through 496 removed outlier: 3.646A pdb=" N ASN F 496 " --> pdb=" O ASN F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 503 removed outlier: 3.681A pdb=" N GLY F 503 " --> pdb=" O ASP F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 550 through 560 Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'F' and resid 572 through 583 removed outlier: 3.608A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP F 581 " --> pdb=" O LEU F 577 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 607 removed outlier: 4.710A pdb=" N SER F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ARG F 595 " --> pdb=" O SER F 591 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG F 602 " --> pdb=" O GLU F 598 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU F 603 " --> pdb=" O TRP F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 622 Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 448 removed outlier: 7.022A pdb=" N TYR A 421 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE A 545 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 6.385A 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 509 Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 448 removed outlier: 7.399A pdb=" N TYR B 421 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ILE B 545 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.613A 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: 7.384A pdb=" N TYR C 421 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE C 545 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.652A 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: 7.390A pdb=" N TYR D 421 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ILE D 545 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.615A 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 445 through 448 removed outlier: 7.276A pdb=" N TYR E 421 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ILE E 545 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU E 423 " --> pdb=" O ILE E 545 " (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 448 removed outlier: 7.861A pdb=" N TYR F 421 " --> pdb=" O VAL F 542 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN F 544 " --> pdb=" O TYR F 421 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 423 " --> pdb=" O GLN F 544 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP F 546 " --> pdb=" O LEU F 423 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS F 425 " --> pdb=" O ASP F 546 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 507 through 509 974 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 7.63 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18189 1.03 - 1.23: 239 1.23 - 1.42: 7569 1.42 - 1.62: 10816 1.62 - 1.82: 204 Bond restraints: 37017 Sorted by residual: bond pdb=" C3' DT T -1 " pdb=" C2' DT T -1 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.16e+01 bond pdb=" C3' DT T -8 " pdb=" C2' DT T -8 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C1' DT T 1 " pdb=" N1 DT T 1 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.29e+01 bond pdb=" C3' DA P 7 " pdb=" C2' DA P 7 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT T -2 " pdb=" C2' DT T -2 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 ... (remaining 37012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 63743 1.75 - 3.50: 3136 3.50 - 5.24: 176 5.24 - 6.99: 30 6.99 - 8.74: 3 Bond angle restraints: 67088 Sorted by residual: angle pdb=" O4' DT T -2 " pdb=" C1' DT T -2 " pdb=" N1 DT T -2 " ideal model delta sigma weight residual 108.00 104.17 3.83 7.00e-01 2.04e+00 2.99e+01 angle pdb=" C4' DT T -5 " pdb=" O4' DT T -5 " pdb=" C1' DT T -5 " ideal model delta sigma weight residual 110.10 104.82 5.28 1.00e+00 1.00e+00 2.78e+01 angle pdb=" O4' DT T -5 " pdb=" C1' DT T -5 " pdb=" N1 DT T -5 " ideal model delta sigma weight residual 108.00 111.24 -3.24 7.00e-01 2.04e+00 2.15e+01 angle pdb=" O4' DT T 2 " pdb=" C1' DT T 2 " pdb=" N1 DT T 2 " ideal model delta sigma weight residual 108.00 111.20 -3.20 7.00e-01 2.04e+00 2.09e+01 angle pdb=" C4' DA P 5 " pdb=" O4' DA P 5 " pdb=" C1' DA P 5 " ideal model delta sigma weight residual 110.10 105.59 4.51 1.00e+00 1.00e+00 2.03e+01 ... (remaining 67083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 15587 17.83 - 35.66: 884 35.66 - 53.49: 421 53.49 - 71.32: 314 71.32 - 89.15: 30 Dihedral angle restraints: 17236 sinusoidal: 9698 harmonic: 7538 Sorted by residual: dihedral pdb=" CA MET B 528 " pdb=" C MET B 528 " pdb=" N ASN B 529 " pdb=" CA ASN B 529 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ASP A 495 " pdb=" C ASP A 495 " pdb=" N ASN A 496 " pdb=" CA ASN A 496 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA MET F 528 " pdb=" C MET F 528 " pdb=" N ASN F 529 " pdb=" CA ASN F 529 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 17233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1853 0.048 - 0.095: 709 0.095 - 0.143: 194 0.143 - 0.190: 46 0.190 - 0.238: 10 Chirality restraints: 2812 Sorted by residual: chirality pdb=" CA ASN D 366 " pdb=" N ASN D 366 " pdb=" C ASN D 366 " pdb=" CB ASN D 366 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DT T -2 " pdb=" C4' DT T -2 " pdb=" O3' DT T -2 " pdb=" C2' DT T -2 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA HIS E 513 " pdb=" N HIS E 513 " pdb=" C HIS E 513 " pdb=" CB HIS E 513 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2809 not shown) Planarity restraints: 5193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 602 " -0.458 9.50e-02 1.11e+02 1.59e-01 7.04e+01 pdb=" NE ARG F 602 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG F 602 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG F 602 " 0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG F 602 " 0.072 2.00e-02 2.50e+03 pdb="HH11 ARG F 602 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG F 602 " -0.045 2.00e-02 2.50e+03 pdb="HH21 ARG F 602 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 602 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 540 " 0.482 9.50e-02 1.11e+02 1.66e-01 6.40e+01 pdb=" NE ARG D 540 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG D 540 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 540 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 540 " -0.084 2.00e-02 2.50e+03 pdb="HH11 ARG D 540 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG D 540 " -0.017 2.00e-02 2.50e+03 pdb="HH21 ARG D 540 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG D 540 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 517 " -0.361 9.50e-02 1.11e+02 1.26e-01 4.76e+01 pdb=" NE ARG E 517 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG E 517 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG E 517 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG E 517 " 0.074 2.00e-02 2.50e+03 pdb="HH11 ARG E 517 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 517 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG E 517 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 517 " -0.075 2.00e-02 2.50e+03 ... (remaining 5190 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 692 2.11 - 2.73: 62213 2.73 - 3.36: 101264 3.36 - 3.98: 127166 3.98 - 4.60: 205947 Nonbonded interactions: 497282 Sorted by model distance: nonbonded pdb=" HG1 THR D 335 " pdb=" OP2 DT T -3 " model vdw 1.491 2.450 nonbonded pdb=" HG1 THR F 433 " pdb=" O1B ATP F 800 " model vdw 1.552 2.450 nonbonded pdb=" OD1 ASP C 495 " pdb=" HG1 THR C 536 " model vdw 1.644 2.450 nonbonded pdb=" OD1 ASP B 370 " pdb="HH22 ARG B 595 " model vdw 1.648 2.450 nonbonded pdb=" O PRO F 427 " pdb=" HG SER F 430 " model vdw 1.657 2.450 ... (remaining 497277 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' selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 266 through 312 or (resid 313 and (name N or name CA or na \ me 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 HD1 or name HD2 or nam \ e HE1)) or resid 314 through 316 or (resid 317 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 318 through 800)) selection = chain 'E' selection = chain 'F' } 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.750 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18780 Z= 0.318 Angle : 0.976 8.738 25469 Z= 0.623 Chirality : 0.056 0.238 2812 Planarity : 0.010 0.167 3082 Dihedral : 15.199 89.150 7320 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2160 helix: -0.39 (0.13), residues: 1252 sheet: 1.21 (0.41), residues: 169 loop : -0.49 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG C 498 TYR 0.042 0.006 TYR D 406 PHE 0.025 0.004 PHE C 327 TRP 0.026 0.005 TRP E 599 HIS 0.021 0.005 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.32 (18780) covalent geometry : angle 0.97584 / 0.62 (25469) hydrogen bonds : bond 0.20049 / 13.73 ( 996) hydrogen bonds : angle 6.59261 / 4.66 ( 2864) *********************** 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 361 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.991 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 578 MET cc_start: 0.9177 (ttm) cc_final: 0.8925 (ttm) REVERT: B 291 MET cc_start: 0.8731 (mmm) cc_final: 0.8402 (mmp) REVERT: B 388 MET cc_start: 0.9031 (mmm) cc_final: 0.8740 (mmt) REVERT: B 412 MET cc_start: 0.9178 (mmp) cc_final: 0.8111 (mmt) REVERT: B 495 ASP cc_start: 0.8685 (m-30) cc_final: 0.8435 (m-30) REVERT: C 484 ASP cc_start: 0.8579 (t0) cc_final: 0.8196 (t0) REVERT: D 474 ASP cc_start: 0.8479 (t0) cc_final: 0.8121 (t0) REVERT: D 614 LYS cc_start: 0.8641 (tptt) cc_final: 0.8357 (ttpt) REVERT: E 388 MET cc_start: 0.9232 (mmm) cc_final: 0.8837 (mmt) REVERT: E 412 MET cc_start: 0.9188 (mmp) cc_final: 0.8385 (mmt) REVERT: F 299 PHE cc_start: 0.8759 (p90) cc_final: 0.8539 (p90) REVERT: F 395 HIS cc_start: 0.8693 (t-90) cc_final: 0.8481 (t-90) REVERT: F 412 MET cc_start: 0.8674 (mmp) cc_final: 0.8254 (mmt) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.5001 time to fit residues: 242.2856 Evaluate side-chains 285 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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: 9.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 458 ASN C 555 HIS D 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.060472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.048392 restraints weight = 132269.426| |-----------------------------------------------------------------------------| r_work (start): 0.2360 rms_B_bonded: 1.70 r_work: 0.2258 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2154 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18780 Z= 0.216 Angle : 0.715 7.719 25469 Z= 0.403 Chirality : 0.040 0.160 2812 Planarity : 0.006 0.088 3082 Dihedral : 15.342 88.958 2868 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.41 % Allowed : 4.80 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2160 helix: 0.36 (0.14), residues: 1279 sheet: 1.26 (0.42), residues: 142 loop : -0.61 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 559 TYR 0.023 0.002 TYR E 552 PHE 0.023 0.002 PHE E 299 TRP 0.015 0.002 TRP E 387 HIS 0.007 0.002 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (18780) covalent geometry : angle 0.71547 / 0.40 (25469) hydrogen bonds : bond 0.07724 / 5.22 ( 996) hydrogen bonds : angle 5.29097 / 3.73 ( 2864) *********************** 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 303 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 295 time to evaluate : 1.000 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 412 MET cc_start: 0.9222 (mmp) cc_final: 0.8498 (mmt) REVERT: A 502 ASP cc_start: 0.8338 (m-30) cc_final: 0.8107 (m-30) REVERT: A 540 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7818 (mtt-85) REVERT: A 609 LEU cc_start: 0.9080 (tt) cc_final: 0.8776 (tt) REVERT: B 388 MET cc_start: 0.8894 (mmm) cc_final: 0.8563 (mmt) REVERT: B 412 MET cc_start: 0.9113 (mmp) cc_final: 0.8181 (mmt) REVERT: C 484 ASP cc_start: 0.8792 (t0) cc_final: 0.8412 (t0) REVERT: D 474 ASP cc_start: 0.8576 (t0) cc_final: 0.8264 (t0) REVERT: D 614 LYS cc_start: 0.8597 (tptt) cc_final: 0.8253 (ttpt) REVERT: E 412 MET cc_start: 0.9136 (mmp) cc_final: 0.8434 (mmt) REVERT: F 412 MET cc_start: 0.8618 (mmp) cc_final: 0.8223 (mmt) outliers start: 8 outliers final: 5 residues processed: 299 average time/residue: 0.4363 time to fit residues: 178.2987 Evaluate side-chains 291 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 286 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 374 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 143 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 593 GLN F 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.058622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.046291 restraints weight = 131791.699| |-----------------------------------------------------------------------------| r_work (start): 0.2331 rms_B_bonded: 1.73 r_work: 0.2229 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2124 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 18780 Z= 0.255 Angle : 0.667 7.784 25469 Z= 0.378 Chirality : 0.040 0.141 2812 Planarity : 0.005 0.064 3082 Dihedral : 15.115 89.792 2868 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.57 % Allowed : 6.04 % Favored : 93.40 % 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: 0.56 (0.14), residues: 1287 sheet: 0.90 (0.39), residues: 148 loop : -0.82 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 420 TYR 0.025 0.002 TYR E 552 PHE 0.027 0.002 PHE F 617 TRP 0.016 0.002 TRP E 387 HIS 0.011 0.002 HIS F 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (18780) covalent geometry : angle 0.66703 / 0.38 (25469) hydrogen bonds : bond 0.07186 / 4.86 ( 996) hydrogen bonds : angle 4.97666 / 3.51 ( 2864) *********************** 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 294 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 283 time to evaluate : 1.020 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 406 TYR cc_start: 0.8678 (t80) cc_final: 0.8372 (t80) REVERT: A 412 MET cc_start: 0.9228 (mmp) cc_final: 0.8495 (mmt) REVERT: A 561 GLU cc_start: 0.8237 (pm20) cc_final: 0.7979 (pm20) REVERT: B 388 MET cc_start: 0.8880 (mmm) cc_final: 0.8516 (mmt) REVERT: B 412 MET cc_start: 0.9135 (mmp) cc_final: 0.8184 (mmt) REVERT: B 614 LYS cc_start: 0.7378 (tttt) cc_final: 0.7173 (tttt) REVERT: C 484 ASP cc_start: 0.8826 (t0) cc_final: 0.8464 (t0) REVERT: D 578 MET cc_start: 0.9004 (ttm) cc_final: 0.8756 (ttm) REVERT: D 614 LYS cc_start: 0.8650 (tptt) cc_final: 0.8275 (ttpt) REVERT: E 388 MET cc_start: 0.9147 (mmm) cc_final: 0.8725 (mmt) REVERT: E 412 MET cc_start: 0.9163 (mmp) cc_final: 0.8420 (mmt) REVERT: E 474 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8440 (m-30) REVERT: F 412 MET cc_start: 0.8631 (mmp) cc_final: 0.8225 (mmt) REVERT: F 548 ARG cc_start: 0.8499 (mtm110) cc_final: 0.8285 (mtm110) REVERT: F 550 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8520 (mmtm) outliers start: 11 outliers final: 9 residues processed: 286 average time/residue: 0.4467 time to fit residues: 175.6769 Evaluate side-chains 283 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 273 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.058794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.046400 restraints weight = 132892.441| |-----------------------------------------------------------------------------| r_work (start): 0.2351 rms_B_bonded: 1.74 r_work: 0.2250 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2145 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18780 Z= 0.177 Angle : 0.605 9.000 25469 Z= 0.339 Chirality : 0.037 0.138 2812 Planarity : 0.004 0.042 3082 Dihedral : 14.969 89.962 2868 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.72 % Allowed : 6.24 % Favored : 93.03 % 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: 0.32 (0.17), residues: 2160 helix: 0.78 (0.14), residues: 1284 sheet: 0.78 (0.39), residues: 148 loop : -0.82 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 420 TYR 0.021 0.002 TYR A 314 PHE 0.015 0.002 PHE B 617 TRP 0.013 0.001 TRP E 387 HIS 0.007 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (18780) covalent geometry : angle 0.60457 / 0.34 (25469) hydrogen bonds : bond 0.06091 / 4.11 ( 996) hydrogen bonds : angle 4.77861 / 3.37 ( 2864) *********************** 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 293 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 279 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.9219 (mmp) cc_final: 0.8513 (mmt) REVERT: B 412 MET cc_start: 0.9101 (mmp) cc_final: 0.8218 (mmt) REVERT: C 484 ASP cc_start: 0.8821 (t0) cc_final: 0.8453 (t0) REVERT: C 558 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8361 (mt-10) REVERT: D 578 MET cc_start: 0.8993 (ttm) cc_final: 0.8749 (ttm) REVERT: E 388 MET cc_start: 0.9153 (mmm) cc_final: 0.8686 (mmt) REVERT: E 517 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8232 (mtp85) REVERT: F 412 MET cc_start: 0.8613 (mmp) cc_final: 0.8219 (mmt) outliers start: 14 outliers final: 11 residues processed: 284 average time/residue: 0.4446 time to fit residues: 173.5619 Evaluate side-chains 280 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 268 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 489 GLN Chi-restraints excluded: chain E residue 517 ARG Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 360 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 77 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.2674 r_free = 0.2674 target = 0.057798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.045510 restraints weight = 133038.357| |-----------------------------------------------------------------------------| r_work (start): 0.2326 rms_B_bonded: 1.72 r_work: 0.2221 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2114 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 18780 Z= 0.228 Angle : 0.615 6.511 25469 Z= 0.346 Chirality : 0.038 0.137 2812 Planarity : 0.005 0.081 3082 Dihedral : 14.911 88.505 2868 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.77 % Allowed : 6.97 % Favored : 92.26 % 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: 0.33 (0.17), residues: 2160 helix: 0.84 (0.14), residues: 1279 sheet: 0.80 (0.40), residues: 148 loop : -0.91 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 548 TYR 0.022 0.002 TYR E 552 PHE 0.024 0.002 PHE F 617 TRP 0.015 0.002 TRP E 387 HIS 0.004 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (18780) covalent geometry : angle 0.61462 / 0.35 (25469) hydrogen bonds : bond 0.06318 / 4.27 ( 996) hydrogen bonds : angle 4.74247 / 3.35 ( 2864) *********************** 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 287 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 272 time to evaluate : 0.905 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 412 MET cc_start: 0.9236 (mmp) cc_final: 0.8539 (mmt) REVERT: B 412 MET cc_start: 0.9098 (mmp) cc_final: 0.8207 (mmt) REVERT: C 484 ASP cc_start: 0.8822 (t0) cc_final: 0.8449 (t0) REVERT: C 602 ARG cc_start: 0.8723 (ttt180) cc_final: 0.8488 (ttt180) REVERT: D 578 MET cc_start: 0.8996 (ttm) cc_final: 0.8747 (ttm) REVERT: E 388 MET cc_start: 0.9159 (mmm) cc_final: 0.8737 (mmt) REVERT: E 517 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8188 (mtp85) REVERT: F 412 MET cc_start: 0.8617 (mmp) cc_final: 0.8202 (mmt) outliers start: 15 outliers final: 13 residues processed: 278 average time/residue: 0.4541 time to fit residues: 173.6232 Evaluate side-chains 281 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 267 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 489 GLN Chi-restraints excluded: chain E residue 517 ARG Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 403 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 145 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 267 GLN F 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.058519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.046196 restraints weight = 132815.781| |-----------------------------------------------------------------------------| r_work (start): 0.2340 rms_B_bonded: 1.73 r_work: 0.2235 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2130 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18780 Z= 0.177 Angle : 0.581 7.120 25469 Z= 0.326 Chirality : 0.037 0.137 2812 Planarity : 0.004 0.040 3082 Dihedral : 14.804 88.208 2868 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.83 % Allowed : 7.33 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2160 helix: 0.98 (0.14), residues: 1278 sheet: 0.66 (0.39), residues: 153 loop : -0.89 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 420 TYR 0.020 0.002 TYR A 314 PHE 0.016 0.002 PHE F 327 TRP 0.014 0.001 TRP E 387 HIS 0.007 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (18780) covalent geometry : angle 0.58080 / 0.33 (25469) hydrogen bonds : bond 0.05810 / 3.93 ( 996) hydrogen bonds : angle 4.64369 / 3.27 ( 2864) *********************** 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 296 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.9232 (mmp) cc_final: 0.8536 (mmt) REVERT: A 540 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8139 (mtt-85) REVERT: A 607 PHE cc_start: 0.8887 (m-80) cc_final: 0.8678 (m-80) REVERT: A 621 MET cc_start: 0.8718 (mmm) cc_final: 0.8501 (mmm) REVERT: B 412 MET cc_start: 0.9082 (mmp) cc_final: 0.8210 (mmt) REVERT: C 484 ASP cc_start: 0.8747 (t0) cc_final: 0.8399 (t0) REVERT: C 602 ARG cc_start: 0.8728 (ttt180) cc_final: 0.8502 (ttt180) REVERT: D 578 MET cc_start: 0.8986 (ttm) cc_final: 0.8733 (ttm) REVERT: E 388 MET cc_start: 0.9164 (mmm) cc_final: 0.8701 (mmt) REVERT: E 517 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8184 (mtp85) REVERT: F 412 MET cc_start: 0.8594 (mmp) cc_final: 0.8195 (mmt) outliers start: 16 outliers final: 12 residues processed: 287 average time/residue: 0.3895 time to fit residues: 154.3871 Evaluate side-chains 280 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 267 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 489 GLN Chi-restraints excluded: chain E residue 517 ARG Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 360 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 106 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 210 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.2691 r_free = 0.2691 target = 0.059191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.046792 restraints weight = 132220.245| |-----------------------------------------------------------------------------| r_work (start): 0.2341 rms_B_bonded: 1.73 r_work: 0.2236 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2129 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18780 Z= 0.175 Angle : 0.571 7.575 25469 Z= 0.321 Chirality : 0.037 0.137 2812 Planarity : 0.004 0.064 3082 Dihedral : 14.742 88.313 2868 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.77 % Allowed : 7.43 % Favored : 91.80 % 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: 1.09 (0.14), residues: 1262 sheet: 0.64 (0.39), residues: 153 loop : -0.87 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 420 TYR 0.020 0.002 TYR D 314 PHE 0.037 0.002 PHE C 299 TRP 0.014 0.001 TRP E 387 HIS 0.005 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (18780) covalent geometry : angle 0.57063 / 0.32 (25469) hydrogen bonds : bond 0.05644 / 3.82 ( 996) hydrogen bonds : angle 4.58418 / 3.23 ( 2864) *********************** 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 289 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 274 time to evaluate : 0.952 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: A 412 MET cc_start: 0.9237 (mmp) cc_final: 0.8546 (mmt) REVERT: A 540 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.8154 (mtt-85) REVERT: A 607 PHE cc_start: 0.8866 (m-80) cc_final: 0.8647 (m-80) REVERT: A 621 MET cc_start: 0.8761 (mmm) cc_final: 0.8517 (mmm) REVERT: B 412 MET cc_start: 0.9078 (mmp) cc_final: 0.8216 (mmt) REVERT: C 484 ASP cc_start: 0.8798 (t0) cc_final: 0.8427 (t0) REVERT: D 578 MET cc_start: 0.8991 (ttm) cc_final: 0.8738 (ttm) REVERT: E 388 MET cc_start: 0.9150 (mmm) cc_final: 0.8724 (mmt) REVERT: E 474 ASP cc_start: 0.8591 (t0) cc_final: 0.8390 (m-30) REVERT: E 517 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8145 (mtp85) REVERT: F 412 MET cc_start: 0.8598 (mmp) cc_final: 0.8196 (mmt) outliers start: 15 outliers final: 13 residues processed: 281 average time/residue: 0.4053 time to fit residues: 158.2130 Evaluate side-chains 286 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 272 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 489 GLN Chi-restraints excluded: chain E residue 517 ARG Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 403 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 58 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.2701 r_free = 0.2701 target = 0.059506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.047129 restraints weight = 132122.559| |-----------------------------------------------------------------------------| r_work (start): 0.2351 rms_B_bonded: 1.71 r_work: 0.2248 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2141 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18780 Z= 0.154 Angle : 0.561 6.039 25469 Z= 0.314 Chirality : 0.036 0.137 2812 Planarity : 0.004 0.063 3082 Dihedral : 14.659 88.622 2868 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.77 % Allowed : 7.74 % Favored : 91.49 % 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: 0.66 (0.18), residues: 2160 helix: 1.19 (0.15), residues: 1262 sheet: 0.62 (0.39), residues: 153 loop : -0.85 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 548 TYR 0.020 0.002 TYR D 314 PHE 0.040 0.001 PHE C 299 TRP 0.012 0.001 TRP E 387 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18780) covalent geometry : angle 0.56112 / 0.31 (25469) hydrogen bonds : bond 0.05350 / 3.62 ( 996) hydrogen bonds : angle 4.51589 / 3.18 ( 2864) *********************** 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 289 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 274 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.9240 (mmp) cc_final: 0.8558 (mmt) REVERT: A 609 LEU cc_start: 0.9035 (tt) cc_final: 0.8830 (tt) REVERT: B 412 MET cc_start: 0.9069 (mmp) cc_final: 0.8211 (mmt) REVERT: C 484 ASP cc_start: 0.8782 (t0) cc_final: 0.8384 (t0) REVERT: D 491 ILE cc_start: 0.8787 (pt) cc_final: 0.8444 (mm) REVERT: D 498 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8468 (ttt90) REVERT: D 578 MET cc_start: 0.8993 (ttm) cc_final: 0.8743 (ttm) REVERT: E 299 PHE cc_start: 0.8157 (t80) cc_final: 0.7896 (t80) REVERT: E 388 MET cc_start: 0.9148 (mmm) cc_final: 0.8721 (mmt) REVERT: F 412 MET cc_start: 0.8589 (mmp) cc_final: 0.8186 (mmt) outliers start: 15 outliers final: 12 residues processed: 279 average time/residue: 0.4058 time to fit residues: 157.5848 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 : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 489 GLN Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 403 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 166 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 395 HIS F 395 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.059173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.046832 restraints weight = 133149.580| |-----------------------------------------------------------------------------| r_work (start): 0.2341 rms_B_bonded: 1.72 r_work: 0.2238 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2131 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18780 Z= 0.183 Angle : 0.575 9.325 25469 Z= 0.321 Chirality : 0.037 0.135 2812 Planarity : 0.004 0.069 3082 Dihedral : 14.641 87.945 2868 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.83 % Allowed : 8.10 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2160 helix: 1.20 (0.15), residues: 1258 sheet: 0.66 (0.39), residues: 153 loop : -0.88 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 548 TYR 0.019 0.002 TYR D 314 PHE 0.034 0.002 PHE F 617 TRP 0.013 0.001 TRP E 387 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (18780) covalent geometry : angle 0.57507 / 0.32 (25469) hydrogen bonds : bond 0.05536 / 3.75 ( 996) hydrogen bonds : angle 4.52708 / 3.20 ( 2864) *********************** 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 287 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 271 time to evaluate : 1.044 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: A 412 MET cc_start: 0.9243 (mmp) cc_final: 0.8560 (mmt) REVERT: B 412 MET cc_start: 0.9075 (mmp) cc_final: 0.8218 (mmt) REVERT: C 484 ASP cc_start: 0.8788 (t0) cc_final: 0.8389 (t0) REVERT: D 491 ILE cc_start: 0.8772 (pt) cc_final: 0.8467 (mm) REVERT: D 578 MET cc_start: 0.9000 (ttm) cc_final: 0.8745 (ttm) REVERT: E 299 PHE cc_start: 0.8065 (t80) cc_final: 0.7863 (t80) REVERT: E 388 MET cc_start: 0.9159 (mmm) cc_final: 0.8732 (mmt) REVERT: E 517 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8087 (mtp85) REVERT: F 412 MET cc_start: 0.8595 (mmp) cc_final: 0.8187 (mmt) REVERT: F 550 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8461 (mmtm) outliers start: 16 outliers final: 13 residues processed: 278 average time/residue: 0.4606 time to fit residues: 176.4888 Evaluate side-chains 285 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 271 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 621 MET Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 489 GLN Chi-restraints excluded: chain E residue 517 ARG Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 403 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 117 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 142 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.060113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.047736 restraints weight = 132612.743| |-----------------------------------------------------------------------------| r_work (start): 0.2371 rms_B_bonded: 1.75 r_work: 0.2266 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2160 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18780 Z= 0.130 Angle : 0.549 7.057 25469 Z= 0.304 Chirality : 0.036 0.138 2812 Planarity : 0.004 0.072 3082 Dihedral : 14.522 89.244 2868 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.67 % Allowed : 8.20 % Favored : 91.12 % 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: 0.84 (0.18), residues: 2160 helix: 1.38 (0.15), residues: 1252 sheet: 0.57 (0.39), residues: 153 loop : -0.82 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 548 TYR 0.020 0.002 TYR C 314 PHE 0.046 0.001 PHE E 299 TRP 0.013 0.001 TRP E 387 HIS 0.004 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (18780) covalent geometry : angle 0.54869 / 0.30 (25469) hydrogen bonds : bond 0.04869 / 3.29 ( 996) hydrogen bonds : angle 4.41071 / 3.11 ( 2864) ********************** 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 286 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 273 time to evaluate : 1.021 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: A 412 MET cc_start: 0.9244 (mmp) cc_final: 0.8566 (mmt) REVERT: B 412 MET cc_start: 0.9053 (mmp) cc_final: 0.8162 (mmt) REVERT: C 484 ASP cc_start: 0.8794 (t0) cc_final: 0.8394 (t0) REVERT: D 578 MET cc_start: 0.8991 (ttm) cc_final: 0.8747 (ttm) REVERT: F 412 MET cc_start: 0.8583 (mmp) cc_final: 0.8189 (mmt) REVERT: F 550 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8479 (mmtm) REVERT: F 561 GLU cc_start: 0.8356 (pm20) cc_final: 0.7958 (pm20) outliers start: 13 outliers final: 12 residues processed: 277 average time/residue: 0.4521 time to fit residues: 173.7863 Evaluate side-chains 282 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 621 MET Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 403 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 136 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 210 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.060029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.047748 restraints weight = 132136.615| |-----------------------------------------------------------------------------| r_work (start): 0.2369 rms_B_bonded: 1.71 r_work: 0.2269 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2161 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18780 Z= 0.140 Angle : 0.552 9.571 25469 Z= 0.306 Chirality : 0.035 0.134 2812 Planarity : 0.004 0.070 3082 Dihedral : 14.440 88.979 2868 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.62 % Allowed : 8.41 % 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: 0.86 (0.18), residues: 2160 helix: 1.42 (0.15), residues: 1253 sheet: 0.62 (0.39), residues: 153 loop : -0.85 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 548 TYR 0.019 0.001 TYR D 314 PHE 0.026 0.001 PHE E 299 TRP 0.012 0.001 TRP E 387 HIS 0.003 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (18780) covalent geometry : angle 0.55158 / 0.31 (25469) hydrogen bonds : bond 0.04894 / 3.31 ( 996) hydrogen bonds : angle 4.38161 / 3.09 ( 2864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7896.77 seconds wall clock time: 134 minutes 44.22 seconds (8084.22 seconds total)