Starting phenix.real_space_refine on Mon Jul 6 15:29:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fb6_50289/07_2026/9fb6_50289_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fb6_50289/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fb6_50289/07_2026/9fb6_50289_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fb6_50289/07_2026/9fb6_50289_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fb6_50289/07_2026/9fb6_50289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fb6_50289/07_2026/9fb6_50289.map" } 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-dev-6108/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: 6.52, per 1000 atoms: 0.18 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 1.1 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: 6.35 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: 9.43 Time building geometry restraints manager: 4.28 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: 63749 1.75 - 3.50: 3132 3.50 - 5.24: 174 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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.230 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 40.170 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- 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= 0.317 Angle : 0.975 8.738 25469 Z= 0.620 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 0.97456 / 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 : 1.106 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: 0.8739 (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: 0.8436 (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: 0.8384 (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: 0.8482 (t-90) REVERT: F 412 MET cc_start: 0.8674 (mmp) cc_final: 0.8253 (mmt) REVERT: F 458 ASN cc_start: 0.9020 (m-40) cc_final: 0.8820 (m-40) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.4568 time to fit residues: 220.9066 Evaluate side-chains 284 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.2708 r_free = 0.2708 target = 0.059691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.047353 restraints weight = 131645.234| |-----------------------------------------------------------------------------| r_work (start): 0.2362 rms_B_bonded: 1.75 r_work: 0.2259 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2157 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1974 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= 0.214 Angle : 0.718 7.826 25469 Z= 0.404 Chirality : 0.040 0.172 2812 Planarity : 0.006 0.085 3082 Dihedral : 15.347 89.092 2868 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.46 % Allowed : 4.75 % 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: 0.04 (0.17), residues: 2160 helix: 0.36 (0.14), residues: 1279 sheet: 1.25 (0.42), residues: 142 loop : -0.62 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 548 TYR 0.023 0.002 TYR E 552 PHE 0.021 0.002 PHE E 299 TRP 0.014 0.002 TRP E 387 HIS 0.007 0.002 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (18780) covalent geometry : angle 0.71830 / 0.40 (25469) hydrogen bonds : bond 0.07520 / 5.07 ( 996) hydrogen bonds : angle 5.29308 / 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 304 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 295 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.9223 (mmp) cc_final: 0.8503 (mmt) REVERT: A 502 ASP cc_start: 0.8335 (m-30) cc_final: 0.8102 (m-30) REVERT: A 540 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7824 (mtt-85) REVERT: A 609 LEU cc_start: 0.9084 (tt) cc_final: 0.8782 (tt) REVERT: B 388 MET cc_start: 0.8894 (mmm) cc_final: 0.8570 (mmt) REVERT: B 412 MET cc_start: 0.9107 (mmp) cc_final: 0.8175 (mmt) REVERT: B 495 ASP cc_start: 0.8599 (m-30) cc_final: 0.8399 (m-30) REVERT: C 484 ASP cc_start: 0.8786 (t0) cc_final: 0.8409 (t0) REVERT: D 474 ASP cc_start: 0.8572 (t0) cc_final: 0.8268 (t0) REVERT: D 614 LYS cc_start: 0.8599 (tptt) cc_final: 0.8256 (ttpt) REVERT: E 412 MET cc_start: 0.9135 (mmp) cc_final: 0.8435 (mmt) REVERT: F 412 MET cc_start: 0.8619 (mmp) cc_final: 0.8225 (mmt) outliers start: 9 outliers final: 6 residues processed: 299 average time/residue: 0.4205 time to fit residues: 172.3905 Evaluate side-chains 293 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 287 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 MET 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: 1.9990 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: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.2686 r_free = 0.2686 target = 0.058840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.046525 restraints weight = 131732.822| |-----------------------------------------------------------------------------| r_work (start): 0.2336 rms_B_bonded: 1.73 r_work: 0.2236 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2132 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 18780 Z= 0.238 Angle : 0.659 7.860 25469 Z= 0.372 Chirality : 0.039 0.165 2812 Planarity : 0.005 0.063 3082 Dihedral : 15.121 89.390 2868 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.72 % Allowed : 5.68 % Favored : 93.60 % 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: 0.17 (0.17), residues: 2160 helix: 0.59 (0.14), residues: 1287 sheet: 0.95 (0.39), residues: 147 loop : -0.80 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 420 TYR 0.024 0.002 TYR E 552 PHE 0.031 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 0.00553 / 0.24 (18780) covalent geometry : angle 0.65873 / 0.37 (25469) hydrogen bonds : bond 0.07098 / 4.80 ( 996) hydrogen bonds : angle 4.96516 / 3.50 ( 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 298 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 284 time to evaluate : 0.840 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 412 MET cc_start: 0.9228 (mmp) cc_final: 0.8496 (mmt) REVERT: A 561 GLU cc_start: 0.8213 (pm20) cc_final: 0.7968 (pm20) REVERT: B 388 MET cc_start: 0.8883 (mmm) cc_final: 0.8530 (mmt) REVERT: B 412 MET cc_start: 0.9136 (mmp) cc_final: 0.8192 (mmt) REVERT: B 495 ASP cc_start: 0.8577 (m-30) cc_final: 0.8348 (m-30) REVERT: C 484 ASP cc_start: 0.8815 (t0) cc_final: 0.8447 (t0) REVERT: D 614 LYS cc_start: 0.8637 (tptt) cc_final: 0.8252 (ttpt) REVERT: E 388 MET cc_start: 0.9143 (mmm) cc_final: 0.8679 (mmt) REVERT: E 412 MET cc_start: 0.9159 (mmp) cc_final: 0.8426 (mmt) REVERT: F 412 MET cc_start: 0.8631 (mmp) cc_final: 0.8231 (mmt) REVERT: F 550 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8495 (mmtm) outliers start: 14 outliers final: 12 residues processed: 288 average time/residue: 0.4016 time to fit residues: 159.2202 Evaluate side-chains 286 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 274 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 MET 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 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 374 ILE 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: 0.9980 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.058761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.046391 restraints weight = 133193.211| |-----------------------------------------------------------------------------| r_work (start): 0.2351 rms_B_bonded: 1.74 r_work: 0.2252 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2148 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18780 Z= 0.182 Angle : 0.601 6.158 25469 Z= 0.338 Chirality : 0.038 0.139 2812 Planarity : 0.005 0.061 3082 Dihedral : 14.969 89.971 2868 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.72 % Allowed : 6.14 % Favored : 93.14 % 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: 0.34 (0.17), residues: 2160 helix: 0.80 (0.14), residues: 1288 sheet: 0.77 (0.39), residues: 148 loop : -0.80 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 548 TYR 0.021 0.002 TYR D 314 PHE 0.015 0.002 PHE C 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 0.00409 / 0.18 (18780) covalent geometry : angle 0.60050 / 0.34 (25469) hydrogen bonds : bond 0.06075 / 4.10 ( 996) hydrogen bonds : angle 4.77136 / 3.36 ( 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 294 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 280 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.9222 (mmp) cc_final: 0.8529 (mmt) REVERT: A 561 GLU cc_start: 0.8232 (pm20) cc_final: 0.7977 (pm20) REVERT: A 587 GLU cc_start: 0.7873 (tt0) cc_final: 0.7671 (tt0) REVERT: A 621 MET cc_start: 0.8662 (mmm) cc_final: 0.8393 (mmm) REVERT: B 412 MET cc_start: 0.9101 (mmp) cc_final: 0.8214 (mmt) REVERT: B 495 ASP cc_start: 0.8555 (m-30) cc_final: 0.8353 (m-30) REVERT: C 484 ASP cc_start: 0.8808 (t0) cc_final: 0.8441 (t0) REVERT: C 602 ARG cc_start: 0.8670 (ttt180) cc_final: 0.8398 (ttt180) REVERT: D 578 MET cc_start: 0.9000 (ttm) cc_final: 0.8760 (ttm) REVERT: E 388 MET cc_start: 0.9146 (mmm) cc_final: 0.8680 (mmt) REVERT: E 517 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8242 (mtp85) REVERT: F 412 MET cc_start: 0.8607 (mmp) cc_final: 0.8214 (mmt) outliers start: 14 outliers final: 11 residues processed: 285 average time/residue: 0.4100 time to fit residues: 160.7535 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 : 0.993 ------------------------------------------------------------------------------- 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: 8.9990 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... ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 HIS F 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.057982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.045630 restraints weight = 133947.363| |-----------------------------------------------------------------------------| r_work (start): 0.2330 rms_B_bonded: 1.74 r_work: 0.2231 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2126 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 18780 Z= 0.224 Angle : 0.608 6.023 25469 Z= 0.343 Chirality : 0.038 0.138 2812 Planarity : 0.005 0.070 3082 Dihedral : 14.910 88.551 2868 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 0.35 (0.17), residues: 2160 helix: 0.85 (0.14), residues: 1279 sheet: 0.79 (0.40), residues: 148 loop : -0.89 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 420 TYR 0.022 0.002 TYR E 552 PHE 0.022 0.002 PHE F 617 TRP 0.014 0.002 TRP E 387 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (18780) covalent geometry : angle 0.60827 / 0.34 (25469) hydrogen bonds : bond 0.06293 / 4.26 ( 996) hydrogen bonds : angle 4.73327 / 3.34 ( 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 290 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 275 time to evaluate : 0.691 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: 0.9230 (mmp) cc_final: 0.8529 (mmt) REVERT: A 621 MET cc_start: 0.8686 (mmm) cc_final: 0.8421 (mmm) REVERT: B 412 MET cc_start: 0.9096 (mmp) cc_final: 0.8196 (mmt) REVERT: B 495 ASP cc_start: 0.8569 (m-30) cc_final: 0.8336 (m-30) REVERT: C 484 ASP cc_start: 0.8751 (t0) cc_final: 0.8396 (t0) REVERT: C 602 ARG cc_start: 0.8720 (ttt180) cc_final: 0.8490 (ttt180) REVERT: D 578 MET cc_start: 0.9010 (ttm) cc_final: 0.8763 (ttm) REVERT: E 388 MET cc_start: 0.9151 (mmm) cc_final: 0.8711 (mmt) REVERT: E 517 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8181 (mtp85) REVERT: F 412 MET cc_start: 0.8621 (mmp) cc_final: 0.8208 (mmt) outliers start: 15 outliers final: 13 residues processed: 281 average time/residue: 0.4032 time to fit residues: 156.5895 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 : 0.943 ------------------------------------------------------------------------------- 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: 0.9990 chunk 67 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.2705 r_free = 0.2705 target = 0.060026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.047666 restraints weight = 132387.327| |-----------------------------------------------------------------------------| r_work (start): 0.2356 rms_B_bonded: 1.72 r_work: 0.2253 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2146 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18780 Z= 0.143 Angle : 0.564 7.377 25469 Z= 0.316 Chirality : 0.036 0.139 2812 Planarity : 0.004 0.061 3082 Dihedral : 14.773 89.060 2868 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.83 % Allowed : 7.12 % Favored : 92.05 % 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: 0.57 (0.18), residues: 2160 helix: 1.08 (0.14), residues: 1266 sheet: 0.60 (0.39), residues: 153 loop : -0.82 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 548 TYR 0.020 0.002 TYR A 314 PHE 0.014 0.001 PHE F 327 TRP 0.012 0.001 TRP E 387 HIS 0.007 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (18780) covalent geometry : angle 0.56356 / 0.32 (25469) hydrogen bonds : bond 0.05445 / 3.68 ( 996) hydrogen bonds : angle 4.60321 / 3.24 ( 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 297 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 281 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.9230 (mmp) cc_final: 0.8558 (mmt) REVERT: A 621 MET cc_start: 0.8660 (mmm) cc_final: 0.8408 (mmm) REVERT: B 412 MET cc_start: 0.9070 (mmp) cc_final: 0.8208 (mmt) REVERT: B 495 ASP cc_start: 0.8552 (m-30) cc_final: 0.8333 (m-30) REVERT: C 484 ASP cc_start: 0.8767 (t0) cc_final: 0.8381 (t0) REVERT: C 602 ARG cc_start: 0.8704 (ttt180) cc_final: 0.8457 (ttt180) REVERT: D 338 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8474 (mm-40) REVERT: D 578 MET cc_start: 0.8980 (ttm) cc_final: 0.8732 (ttm) REVERT: E 388 MET cc_start: 0.9152 (mmm) cc_final: 0.8682 (mmt) REVERT: F 412 MET cc_start: 0.8574 (mmp) cc_final: 0.8180 (mmt) outliers start: 16 outliers final: 14 residues processed: 287 average time/residue: 0.3890 time to fit residues: 155.3068 Evaluate side-chains 284 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 270 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 106 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 210 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.2694 r_free = 0.2694 target = 0.059345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.047064 restraints weight = 132602.598| |-----------------------------------------------------------------------------| r_work (start): 0.2347 rms_B_bonded: 1.72 r_work: 0.2243 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2137 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3007 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= 0.172 Angle : 0.572 7.712 25469 Z= 0.319 Chirality : 0.037 0.157 2812 Planarity : 0.004 0.065 3082 Dihedral : 14.720 88.586 2868 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.88 % Allowed : 7.43 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2160 helix: 1.13 (0.14), residues: 1271 sheet: 0.63 (0.39), residues: 153 loop : -0.84 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 548 TYR 0.020 0.002 TYR D 314 PHE 0.026 0.002 PHE F 617 TRP 0.012 0.001 TRP E 387 HIS 0.005 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (18780) covalent geometry : angle 0.57161 / 0.32 (25469) hydrogen bonds : bond 0.05551 / 3.76 ( 996) hydrogen bonds : angle 4.56320 / 3.22 ( 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 292 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.9239 (mmp) cc_final: 0.8563 (mmt) REVERT: A 621 MET cc_start: 0.8700 (mmm) cc_final: 0.8454 (mmm) REVERT: B 412 MET cc_start: 0.9080 (mmp) cc_final: 0.8222 (mmt) REVERT: B 495 ASP cc_start: 0.8553 (m-30) cc_final: 0.8334 (m-30) REVERT: C 484 ASP cc_start: 0.8778 (t0) cc_final: 0.8406 (t0) REVERT: C 602 ARG cc_start: 0.8747 (ttt180) cc_final: 0.8530 (ttt180) REVERT: D 578 MET cc_start: 0.9000 (ttm) cc_final: 0.8752 (ttm) REVERT: E 388 MET cc_start: 0.9151 (mmm) cc_final: 0.8722 (mmt) REVERT: E 517 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8153 (mtp85) REVERT: F 412 MET cc_start: 0.8588 (mmp) cc_final: 0.8192 (mmt) outliers start: 17 outliers final: 15 residues processed: 283 average time/residue: 0.4106 time to fit residues: 160.2857 Evaluate side-chains 288 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 613 GLN 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: 0.6980 chunk 217 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.2705 r_free = 0.2705 target = 0.059692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.047373 restraints weight = 132269.986| |-----------------------------------------------------------------------------| r_work (start): 0.2357 rms_B_bonded: 1.74 r_work: 0.2253 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2146 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.3108 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= 0.150 Angle : 0.556 6.281 25469 Z= 0.310 Chirality : 0.036 0.136 2812 Planarity : 0.004 0.072 3082 Dihedral : 14.638 88.933 2868 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.83 % Allowed : 7.59 % Favored : 91.59 % 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: 0.71 (0.18), residues: 2160 helix: 1.25 (0.15), residues: 1253 sheet: 0.59 (0.39), residues: 153 loop : -0.81 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 548 TYR 0.019 0.002 TYR D 314 PHE 0.021 0.001 PHE C 299 TRP 0.012 0.001 TRP E 387 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (18780) covalent geometry : angle 0.55590 / 0.31 (25469) hydrogen bonds : bond 0.05262 / 3.56 ( 996) hydrogen bonds : angle 4.49042 / 3.16 ( 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 295 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 0.984 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: 0.9247 (mmp) cc_final: 0.8567 (mmt) REVERT: A 621 MET cc_start: 0.8688 (mmm) cc_final: 0.8455 (mmm) REVERT: B 412 MET cc_start: 0.9070 (mmp) cc_final: 0.8216 (mmt) REVERT: B 495 ASP cc_start: 0.8556 (m-30) cc_final: 0.8336 (m-30) REVERT: C 484 ASP cc_start: 0.8760 (t0) cc_final: 0.8350 (t0) REVERT: C 602 ARG cc_start: 0.8760 (ttt180) cc_final: 0.8529 (ttt180) REVERT: D 491 ILE cc_start: 0.8785 (pt) cc_final: 0.8442 (mm) REVERT: D 578 MET cc_start: 0.8997 (ttm) cc_final: 0.8754 (ttm) REVERT: E 388 MET cc_start: 0.9150 (mmm) cc_final: 0.8718 (mmt) REVERT: E 517 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8134 (mtp85) REVERT: F 412 MET cc_start: 0.8586 (mmp) cc_final: 0.8188 (mmt) outliers start: 16 outliers final: 15 residues processed: 286 average time/residue: 0.4360 time to fit residues: 171.6100 Evaluate side-chains 294 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 278 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 613 GLN 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: 0.8980 chunk 127 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.060116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.047774 restraints weight = 132679.179| |-----------------------------------------------------------------------------| r_work (start): 0.2371 rms_B_bonded: 1.74 r_work: 0.2267 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2161 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18780 Z= 0.135 Angle : 0.551 10.273 25469 Z= 0.305 Chirality : 0.036 0.136 2812 Planarity : 0.004 0.075 3082 Dihedral : 14.538 89.449 2868 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.03 % Allowed : 7.74 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2160 helix: 1.37 (0.15), residues: 1255 sheet: 0.60 (0.40), residues: 153 loop : -0.78 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 548 TYR 0.019 0.002 TYR D 314 PHE 0.040 0.001 PHE F 617 TRP 0.012 0.001 TRP E 387 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (18780) covalent geometry : angle 0.55145 / 0.31 (25469) hydrogen bonds : bond 0.04958 / 3.35 ( 996) hydrogen bonds : angle 4.41907 / 3.11 ( 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 301 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 281 time to evaluate : 0.967 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: 0.9248 (mmp) cc_final: 0.8579 (mmt) REVERT: A 621 MET cc_start: 0.8674 (mmm) cc_final: 0.8453 (mmm) REVERT: B 412 MET cc_start: 0.9063 (mmp) cc_final: 0.8220 (mmt) REVERT: B 495 ASP cc_start: 0.8547 (m-30) cc_final: 0.8330 (m-30) REVERT: C 484 ASP cc_start: 0.8777 (t0) cc_final: 0.8381 (t0) REVERT: C 602 ARG cc_start: 0.8749 (ttt180) cc_final: 0.8493 (ttt180) REVERT: D 491 ILE cc_start: 0.8762 (pt) cc_final: 0.8455 (mm) REVERT: D 498 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8440 (ttt90) REVERT: D 578 MET cc_start: 0.9002 (ttm) cc_final: 0.8762 (ttm) REVERT: E 517 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8019 (mtp85) REVERT: F 412 MET cc_start: 0.8584 (mmp) cc_final: 0.8193 (mmt) outliers start: 20 outliers final: 13 residues processed: 289 average time/residue: 0.3972 time to fit residues: 158.2972 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 : 0.956 ------------------------------------------------------------------------------- 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 498 ARG 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 E residue 517 ARG Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 613 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 117 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 96 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN B 395 HIS F 395 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.059258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.046927 restraints weight = 133047.823| |-----------------------------------------------------------------------------| r_work (start): 0.2353 rms_B_bonded: 1.73 r_work: 0.2250 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2143 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18780 Z= 0.175 Angle : 0.565 5.861 25469 Z= 0.316 Chirality : 0.036 0.135 2812 Planarity : 0.004 0.077 3082 Dihedral : 14.533 88.802 2868 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.88 % Allowed : 8.00 % 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: 0.78 (0.18), residues: 2160 helix: 1.31 (0.15), residues: 1265 sheet: 0.65 (0.39), residues: 153 loop : -0.84 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 548 TYR 0.019 0.002 TYR D 314 PHE 0.047 0.002 PHE C 299 TRP 0.012 0.001 TRP E 387 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (18780) covalent geometry : angle 0.56501 / 0.32 (25469) hydrogen bonds : bond 0.05309 / 3.59 ( 996) hydrogen bonds : angle 4.45375 / 3.14 ( 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 292 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 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: A 412 MET cc_start: 0.9253 (mmp) cc_final: 0.8574 (mmt) REVERT: A 621 MET cc_start: 0.8659 (mmm) cc_final: 0.8454 (mmm) REVERT: B 412 MET cc_start: 0.9072 (mmp) cc_final: 0.8164 (mmt) REVERT: B 495 ASP cc_start: 0.8553 (m-30) cc_final: 0.8337 (m-30) REVERT: C 484 ASP cc_start: 0.8786 (t0) cc_final: 0.8379 (t0) REVERT: C 602 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8549 (ttt180) REVERT: D 491 ILE cc_start: 0.8748 (pt) cc_final: 0.8501 (mm) REVERT: D 498 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8441 (ttt90) REVERT: D 578 MET cc_start: 0.9010 (ttm) cc_final: 0.8768 (ttm) REVERT: E 388 MET cc_start: 0.9161 (mmm) cc_final: 0.8738 (mmt) REVERT: E 517 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8036 (mtp85) REVERT: F 412 MET cc_start: 0.8592 (mmp) cc_final: 0.8184 (mmt) REVERT: F 561 GLU cc_start: 0.8333 (pm20) cc_final: 0.7956 (pm20) outliers start: 17 outliers final: 13 residues processed: 282 average time/residue: 0.4420 time to fit residues: 172.2623 Evaluate side-chains 286 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 271 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 GLN 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 307 LYS Chi-restraints excluded: chain E residue 332 ASN 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 Chi-restraints excluded: chain F residue 613 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 136 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 = 0.2700 r_free = 0.2700 target = 0.059309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.047039 restraints weight = 132293.040| |-----------------------------------------------------------------------------| r_work (start): 0.2354 rms_B_bonded: 1.72 r_work: 0.2251 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2144 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.306 18780 Z= 0.233 Angle : 0.737 59.189 25469 Z= 0.440 Chirality : 0.036 0.239 2812 Planarity : 0.004 0.075 3082 Dihedral : 14.531 88.828 2868 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.72 % Allowed : 8.46 % Favored : 90.82 % Cbeta Deviations : 0.05 % 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: 0.78 (0.18), residues: 2160 helix: 1.32 (0.15), residues: 1265 sheet: 0.67 (0.41), residues: 143 loop : -0.85 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 548 TYR 0.019 0.002 TYR D 314 PHE 0.037 0.002 PHE C 299 TRP 0.011 0.001 TRP E 387 HIS 0.003 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (18780) covalent geometry : angle 0.73719 / 0.44 (25469) hydrogen bonds : bond 0.05279 / 3.57 ( 996) hydrogen bonds : angle 4.45339 / 3.14 ( 2864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7776.13 seconds wall clock time: 132 minutes 44.11 seconds (7964.11 seconds total)