Starting phenix.real_space_refine on Sun Aug 9 17:38:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fb4_50287/08_2026/9fb4_50287_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fb4_50287/08_2026/9fb4_50287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fb4_50287/08_2026/9fb4_50287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fb4_50287/08_2026/9fb4_50287.map" model { file = "/net/cci-nas-00/data/ceres_data/9fb4_50287/08_2026/9fb4_50287_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fb4_50287/08_2026/9fb4_50287_trim.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.095 sd= 0.962 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 18238 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36587 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5918 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "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: 5.57, per 1000 atoms: 0.15 Number of scatterers: 36587 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 18238 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: 3.35 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: 144 helices and 12 sheets defined 69.0% alpha, 5.5% beta 11 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 269 through 281 removed outlier: 3.694A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.713A pdb=" N GLU A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.980A 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: 3.530A 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 307 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 316 through 328 removed outlier: 5.213A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 355 Processing helix chain 'A' and resid 356 through 376 Processing helix chain 'A' and resid 383 through 398 removed outlier: 3.741A pdb=" N TRP A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.547A pdb=" N VAL A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) 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 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 559 removed outlier: 3.722A 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: 3.760A 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: 3.612A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.803A pdb=" N GLU B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) 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 328 removed outlier: 5.128A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASN B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 326 " --> pdb=" O ALA B 322 " (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 398 removed outlier: 3.748A pdb=" N TRP B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 398 " --> pdb=" O LEU B 394 " (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 462 removed outlier: 3.911A pdb=" N ASN B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 460 " --> pdb=" O ARG B 456 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 462 " --> pdb=" O ASN B 458 " (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: 3.928A pdb=" N SER B 482 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 Processing helix chain 'B' and resid 497 through 503 Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 550 through 559 removed outlier: 3.581A pdb=" N GLU B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 559 " --> pdb=" O HIS B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.636A pdb=" N MET B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 589 through 607 removed outlier: 4.590A pdb=" N SER B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 621 Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.729A pdb=" N VAL C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 removed outlier: 3.822A pdb=" N GLU C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 308 Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 316 through 328 removed outlier: 5.055A pdb=" N ALA C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASN C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 355 Processing helix chain 'C' and resid 356 through 376 Processing helix chain 'C' and resid 383 through 398 removed outlier: 3.772A pdb=" N TRP C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 415 Processing helix chain 'C' and resid 431 through 444 removed outlier: 3.623A pdb=" N ALA C 438 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 461 removed outlier: 3.796A pdb=" N ASN C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 removed outlier: 3.626A pdb=" N ILE C 465 " --> pdb=" O GLY C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'C' and resid 480 through 484 Processing helix chain 'C' and resid 489 through 495 Processing helix chain 'C' and resid 497 through 503 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 551 through 560 Processing helix chain 'C' and resid 561 through 566 Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.693A 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 606 Processing helix chain 'C' and resid 608 through 622 Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.615A pdb=" N VAL D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 295 removed outlier: 3.909A pdb=" N PHE D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 297 No H-bonds generated for 'chain 'D' and resid 296 through 297' Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 302 through 307 Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 316 through 328 removed outlier: 5.519A pdb=" N ALA D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 355 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 383 through 398 removed outlier: 4.038A pdb=" N LEU D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 456 through 462 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 496 Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 561 through 566 Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.849A pdb=" N LEU D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 588 Processing helix chain 'D' and resid 589 through 607 removed outlier: 4.773A pdb=" N SER D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 622 Processing helix chain 'E' and resid 269 through 281 Processing helix chain 'E' and resid 284 through 295 removed outlier: 4.019A pdb=" N PHE E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 297 No H-bonds generated for 'chain 'E' and resid 296 through 297' Processing helix chain 'E' and resid 298 through 301 removed outlier: 3.573A pdb=" N MET E 301 " --> pdb=" O SER E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 302 through 308 Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 316 through 330 removed outlier: 5.336A pdb=" N ALA E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN E 323 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.594A pdb=" N CYS E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 4.124A 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 453 through 461 removed outlier: 3.625A pdb=" N LEU E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN E 458 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 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 Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 550 through 559 Processing helix chain 'E' and resid 561 through 566 Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.981A 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: 4.134A pdb=" N LYS E 605 " --> pdb=" O GLU E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 622 Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.654A pdb=" N VAL F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 295 removed outlier: 4.066A pdb=" N PHE F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 297 No H-bonds generated for 'chain 'F' and resid 296 through 297' Processing helix chain 'F' and resid 298 through 301 Processing helix chain 'F' and resid 302 through 307 Processing helix chain 'F' and resid 310 through 315 Processing helix chain 'F' and resid 316 through 328 removed outlier: 5.048A pdb=" N ALA F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN F 323 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 353 Processing helix chain 'F' and resid 356 through 373 Processing helix chain 'F' and resid 383 through 395 removed outlier: 3.649A pdb=" N TRP F 387 " --> pdb=" O ASP F 383 " (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: 3.601A 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 479 through 484 Processing helix chain 'F' and resid 489 through 495 Processing helix chain 'F' and resid 497 through 503 removed outlier: 3.565A 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: 3.548A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP F 581 " --> pdb=" O LEU F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 588 removed outlier: 3.597A pdb=" N GLU F 587 " --> pdb=" O PRO F 584 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE F 588 " --> pdb=" O VAL F 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 584 through 588' Processing helix chain 'F' and resid 589 through 607 removed outlier: 4.357A pdb=" N SER F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG F 595 " --> pdb=" O SER F 591 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 601 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG F 602 " --> pdb=" O GLU F 598 " (cutoff:3.500A) removed outlier: 4.193A 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 446 through 448 removed outlier: 6.875A pdb=" N TYR A 421 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE A 545 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 6.323A 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 446 through 448 removed outlier: 7.186A pdb=" N TYR B 421 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ILE B 545 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.548A 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 446 through 448 removed outlier: 3.994A pdb=" N LYS C 543 " --> pdb=" O TYR C 421 " (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 446 through 448 removed outlier: 7.104A pdb=" N TYR D 421 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ILE D 545 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU D 423 " --> pdb=" O ILE D 545 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 507 through 509 Processing sheet with id=AA9, first strand: chain 'E' and resid 446 through 448 removed outlier: 7.299A pdb=" N TYR E 421 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ILE E 545 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 6.613A 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: 6.601A pdb=" N VAL F 470 " --> pdb=" O ILE F 525 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N THR F 527 " --> pdb=" O VAL F 470 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE F 472 " --> pdb=" O THR F 527 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP F 422 " --> pdb=" O GLY F 524 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TYR F 421 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE F 545 " --> pdb=" O TYR F 421 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU F 423 " --> pdb=" O ILE F 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 507 through 509 953 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 7.81 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18190 1.03 - 1.23: 123 1.23 - 1.42: 7677 1.42 - 1.62: 10824 1.62 - 1.81: 204 Bond restraints: 37018 Sorted by residual: bond pdb=" N LYS B 266 " pdb=" H1 LYS B 266 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N LYS A 266 " pdb=" H1 LYS A 266 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" N LYS E 266 " pdb=" H1 LYS E 266 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" N LYS D 266 " pdb=" H1 LYS D 266 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" N LYS F 266 " pdb=" H1 LYS F 266 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 37013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 64547 1.74 - 3.48: 2381 3.48 - 5.21: 131 5.21 - 6.95: 27 6.95 - 8.69: 4 Bond angle restraints: 67090 Sorted by residual: angle pdb=" C4' DT T -1 " pdb=" O4' DT T -1 " pdb=" C1' DT T -1 " ideal model delta sigma weight residual 110.10 104.50 5.60 1.00e+00 1.00e+00 3.13e+01 angle pdb=" C4' DA P 5 " pdb=" O4' DA P 5 " pdb=" C1' DA P 5 " ideal model delta sigma weight residual 110.10 104.51 5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" O4' DA P 5 " pdb=" C1' DA P 5 " pdb=" N9 DA P 5 " ideal model delta sigma weight residual 108.00 111.50 -3.50 7.00e-01 2.04e+00 2.51e+01 angle pdb=" CA PRO B 523 " pdb=" C PRO B 523 " pdb=" N GLY B 524 " ideal model delta sigma weight residual 115.12 120.74 -5.62 1.25e+00 6.40e-01 2.02e+01 angle pdb=" N3 DT T -9 " pdb=" C4 DT T -9 " pdb=" O4 DT T -9 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 ... (remaining 67085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15616 17.91 - 35.82: 836 35.82 - 53.73: 447 53.73 - 71.64: 299 71.64 - 89.56: 39 Dihedral angle restraints: 17237 sinusoidal: 9698 harmonic: 7539 Sorted by residual: dihedral pdb=" CA LEU D 469 " pdb=" C LEU D 469 " pdb=" N VAL D 470 " pdb=" CA VAL D 470 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LEU E 469 " pdb=" C LEU E 469 " pdb=" N VAL E 470 " pdb=" CA VAL E 470 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA LEU F 469 " pdb=" C LEU F 469 " pdb=" N VAL F 470 " pdb=" CA VAL F 470 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 17234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2002 0.050 - 0.101: 646 0.101 - 0.151: 131 0.151 - 0.202: 27 0.202 - 0.252: 6 Chirality restraints: 2812 Sorted by residual: chirality pdb=" C3' DT T 0 " pdb=" C4' DT T 0 " pdb=" O3' DT T 0 " pdb=" C2' DT T 0 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3' DT T -1 " pdb=" C4' DT T -1 " pdb=" O3' DT T -1 " pdb=" C2' DT T -1 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -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 -2.49 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2809 not shown) Planarity restraints: 5193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 602 " -0.518 9.50e-02 1.11e+02 1.80e-01 9.11e+01 pdb=" NE ARG F 602 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 602 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG F 602 " 0.078 2.00e-02 2.50e+03 pdb=" NH2 ARG F 602 " 0.071 2.00e-02 2.50e+03 pdb="HH11 ARG F 602 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG F 602 " -0.064 2.00e-02 2.50e+03 pdb="HH21 ARG F 602 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG F 602 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 540 " 0.560 9.50e-02 1.11e+02 1.90e-01 6.23e+01 pdb=" NE ARG D 540 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG D 540 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG D 540 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG D 540 " -0.070 2.00e-02 2.50e+03 pdb="HH11 ARG D 540 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG D 540 " 0.003 2.00e-02 2.50e+03 pdb="HH21 ARG D 540 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 540 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 570 " -0.044 2.00e-02 2.50e+03 5.36e-02 4.30e+01 pdb=" CD GLN A 570 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLN A 570 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 570 " 0.084 2.00e-02 2.50e+03 pdb="HE21 GLN A 570 " 0.005 2.00e-02 2.50e+03 pdb="HE22 GLN A 570 " -0.083 2.00e-02 2.50e+03 ... (remaining 5190 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1288 2.16 - 2.77: 69684 2.77 - 3.38: 101482 3.38 - 3.99: 128178 3.99 - 4.60: 206750 Nonbonded interactions: 507382 Sorted by model distance: nonbonded pdb=" HG1 THR C 434 " pdb=" O1A ATP C 800 " model vdw 1.554 2.450 nonbonded pdb=" HG1 THR F 335 " pdb=" OP2 DA P 7 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP F 370 " pdb="HH22 ARG F 595 " model vdw 1.595 2.450 nonbonded pdb=" HG1 THR B 434 " pdb=" O2A ATP B 800 " model vdw 1.616 2.450 nonbonded pdb=" HG1 THR F 433 " pdb=" O1B ATP F 800 " model vdw 1.632 2.450 ... (remaining 507377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 266 through 316 or (resid 317 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 HD2 or name HE1 or nam \ e HE2)) or resid 318 through 800)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 266 through 312 or (resid 313 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 314 through 316 or (resid 317 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2 \ )) or resid 318 through 800)) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 35.440 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 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 : 0.005 0.052 18780 Z= 0.296 Angle : 0.883 8.689 25469 Z= 0.555 Chirality : 0.052 0.252 2812 Planarity : 0.010 0.206 3082 Dihedral : 15.389 89.555 7320 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2160 helix: -1.18 (0.12), residues: 1239 sheet: 1.19 (0.41), residues: 156 loop : -0.32 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 498 TYR 0.031 0.005 TYR F 582 PHE 0.021 0.003 PHE F 327 TRP 0.022 0.005 TRP F 422 HIS 0.020 0.005 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.30 (18780) covalent geometry : angle 0.88254 / 0.56 (25469) hydrogen bonds : bond 0.18571 / 11.72 ( 975) hydrogen bonds : angle 7.04741 / 5.00 ( 2786) *********************** 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 145 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 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: symmetry clash REVERT: B 299 PHE cc_start: 0.9101 (p90) cc_final: 0.8800 (p90) REVERT: B 617 PHE cc_start: 0.9099 (t80) cc_final: 0.8834 (t80) REVERT: B 621 MET cc_start: 0.9096 (mtp) cc_final: 0.8809 (mtp) REVERT: E 621 MET cc_start: 0.9086 (mmp) cc_final: 0.8871 (mmp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3487 time to fit residues: 73.0666 Evaluate side-chains 101 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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: 30.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 363 ASN C 593 GLN E 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.051973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039194 restraints weight = 234026.886| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.21 r_work: 0.2755 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18780 Z= 0.253 Angle : 0.685 7.039 25469 Z= 0.387 Chirality : 0.040 0.184 2812 Planarity : 0.005 0.091 3082 Dihedral : 15.923 89.601 2868 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.31 % Allowed : 1.65 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2160 helix: 0.01 (0.14), residues: 1240 sheet: 0.95 (0.46), residues: 137 loop : -0.49 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 483 TYR 0.017 0.002 TYR B 314 PHE 0.013 0.001 PHE B 562 TRP 0.012 0.002 TRP E 387 HIS 0.009 0.002 HIS F 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (18780) covalent geometry : angle 0.68548 / 0.39 (25469) hydrogen bonds : bond 0.06821 / 4.40 ( 975) hydrogen bonds : angle 5.38886 / 3.83 ( 2786) *********************** 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 109 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.937 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: B 299 PHE cc_start: 0.9051 (p90) cc_final: 0.8791 (p90) REVERT: B 412 MET cc_start: 0.9336 (mmp) cc_final: 0.8921 (mmt) REVERT: E 309 GLU cc_start: 0.8568 (tp30) cc_final: 0.8282 (tm-30) REVERT: E 621 MET cc_start: 0.9028 (mmp) cc_final: 0.8824 (mmp) REVERT: F 617 PHE cc_start: 0.9307 (t80) cc_final: 0.9083 (t80) outliers start: 6 outliers final: 5 residues processed: 103 average time/residue: 0.2613 time to fit residues: 42.8270 Evaluate side-chains 100 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain D residue 621 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 578 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 66 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN C 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.051535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038905 restraints weight = 235501.457| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.13 r_work: 0.2752 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18780 Z= 0.256 Angle : 0.600 5.965 25469 Z= 0.339 Chirality : 0.038 0.156 2812 Planarity : 0.004 0.052 3082 Dihedral : 15.638 86.957 2868 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.31 % Allowed : 2.06 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2160 helix: 0.48 (0.14), residues: 1236 sheet: 0.65 (0.45), residues: 134 loop : -0.63 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 483 TYR 0.018 0.002 TYR D 314 PHE 0.029 0.001 PHE B 617 TRP 0.012 0.001 TRP E 387 HIS 0.007 0.001 HIS F 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (18780) covalent geometry : angle 0.60011 / 0.34 (25469) hydrogen bonds : bond 0.05823 / 3.75 ( 975) hydrogen bonds : angle 5.09062 / 3.63 ( 2786) *********************** 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 105 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.075 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: B 299 PHE cc_start: 0.9127 (p90) cc_final: 0.8847 (p90) REVERT: B 412 MET cc_start: 0.9330 (mmp) cc_final: 0.8906 (mmt) REVERT: B 621 MET cc_start: 0.9020 (mtm) cc_final: 0.8293 (mtm) REVERT: E 621 MET cc_start: 0.8979 (mmp) cc_final: 0.8771 (mmp) REVERT: F 412 MET cc_start: 0.8781 (mmt) cc_final: 0.8326 (mmt) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.3064 time to fit residues: 49.9732 Evaluate side-chains 98 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 578 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 37 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 395 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.052185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.039552 restraints weight = 234277.299| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.15 r_work: 0.2751 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18780 Z= 0.159 Angle : 0.546 6.840 25469 Z= 0.306 Chirality : 0.036 0.154 2812 Planarity : 0.004 0.043 3082 Dihedral : 15.371 84.201 2868 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.26 % Allowed : 2.63 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2160 helix: 0.87 (0.15), residues: 1238 sheet: 0.08 (0.44), residues: 146 loop : -0.65 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 483 TYR 0.017 0.001 TYR D 314 PHE 0.019 0.001 PHE B 617 TRP 0.010 0.001 TRP E 387 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (18780) covalent geometry : angle 0.54552 / 0.31 (25469) hydrogen bonds : bond 0.04894 / 3.18 ( 975) hydrogen bonds : angle 4.75781 / 3.40 ( 2786) *********************** 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 102 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.142 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: B 412 MET cc_start: 0.9305 (mmp) cc_final: 0.8915 (mmt) REVERT: B 617 PHE cc_start: 0.8928 (t80) cc_final: 0.8687 (t80) REVERT: D 412 MET cc_start: 0.9149 (mmp) cc_final: 0.8667 (mmt) outliers start: 5 outliers final: 2 residues processed: 97 average time/residue: 0.3079 time to fit residues: 48.8686 Evaluate side-chains 96 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain F residue 332 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 104 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 211 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.052433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.039739 restraints weight = 232719.848| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.18 r_work: 0.2762 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18780 Z= 0.140 Angle : 0.517 6.560 25469 Z= 0.289 Chirality : 0.035 0.153 2812 Planarity : 0.003 0.040 3082 Dihedral : 15.100 85.130 2868 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.21 % Allowed : 2.99 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2160 helix: 1.16 (0.15), residues: 1249 sheet: 0.06 (0.44), residues: 146 loop : -0.60 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 420 TYR 0.017 0.001 TYR D 314 PHE 0.009 0.001 PHE F 327 TRP 0.009 0.001 TRP E 387 HIS 0.005 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (18780) covalent geometry : angle 0.51703 / 0.29 (25469) hydrogen bonds : bond 0.04501 / 2.93 ( 975) hydrogen bonds : angle 4.53924 / 3.25 ( 2786) *********************** 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 103 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 1.112 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: A 601 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8754 (tp30) REVERT: B 412 MET cc_start: 0.9291 (mmp) cc_final: 0.8855 (mmt) outliers start: 4 outliers final: 4 residues processed: 100 average time/residue: 0.3194 time to fit residues: 51.8694 Evaluate side-chains 99 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 578 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.052539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039823 restraints weight = 233149.820| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.18 r_work: 0.2772 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18780 Z= 0.148 Angle : 0.514 8.472 25469 Z= 0.286 Chirality : 0.035 0.157 2812 Planarity : 0.003 0.040 3082 Dihedral : 14.883 86.301 2868 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.21 % Allowed : 3.35 % Favored : 96.44 % 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: 0.83 (0.18), residues: 2160 helix: 1.30 (0.15), residues: 1269 sheet: 0.01 (0.40), residues: 162 loop : -0.56 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.016 0.001 TYR D 314 PHE 0.016 0.001 PHE B 617 TRP 0.009 0.001 TRP E 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (18780) covalent geometry : angle 0.51381 / 0.29 (25469) hydrogen bonds : bond 0.04227 / 2.76 ( 975) hydrogen bonds : angle 4.41813 / 3.16 ( 2786) *********************** 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 99 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 1.108 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: A 601 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8740 (tp30) REVERT: B 412 MET cc_start: 0.9275 (mmp) cc_final: 0.8842 (mmt) REVERT: F 412 MET cc_start: 0.8667 (mmt) cc_final: 0.8149 (mmt) outliers start: 4 outliers final: 4 residues processed: 96 average time/residue: 0.2959 time to fit residues: 47.1327 Evaluate side-chains 98 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 360 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.053061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040280 restraints weight = 232235.056| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.19 r_work: 0.2790 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18780 Z= 0.110 Angle : 0.488 7.762 25469 Z= 0.270 Chirality : 0.035 0.152 2812 Planarity : 0.003 0.037 3082 Dihedral : 14.610 89.284 2868 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.31 % Allowed : 3.46 % Favored : 96.23 % 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: 1.11 (0.18), residues: 2160 helix: 1.56 (0.15), residues: 1260 sheet: 0.19 (0.39), residues: 169 loop : -0.52 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 420 TYR 0.017 0.001 TYR D 314 PHE 0.009 0.001 PHE B 617 TRP 0.009 0.001 TRP D 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (18780) covalent geometry : angle 0.48752 / 0.27 (25469) hydrogen bonds : bond 0.03881 / 2.54 ( 975) hydrogen bonds : angle 4.21314 / 3.02 ( 2786) *********************** 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 104 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 1.133 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: A 601 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8743 (tp30) REVERT: B 412 MET cc_start: 0.9220 (mmp) cc_final: 0.8809 (mmt) REVERT: D 412 MET cc_start: 0.9163 (mmp) cc_final: 0.8905 (mmp) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.3068 time to fit residues: 50.2655 Evaluate side-chains 101 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 578 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 133 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.051999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.039276 restraints weight = 233998.637| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.21 r_work: 0.2759 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18780 Z= 0.193 Angle : 0.513 7.656 25469 Z= 0.285 Chirality : 0.035 0.152 2812 Planarity : 0.003 0.039 3082 Dihedral : 14.551 89.121 2868 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.18), residues: 2160 helix: 1.53 (0.15), residues: 1265 sheet: -0.04 (0.40), residues: 164 loop : -0.59 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 420 TYR 0.016 0.001 TYR D 314 PHE 0.011 0.001 PHE B 617 TRP 0.008 0.001 TRP E 387 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (18780) covalent geometry : angle 0.51273 / 0.28 (25469) hydrogen bonds : bond 0.04037 / 2.64 ( 975) hydrogen bonds : angle 4.34811 / 3.11 ( 2786) *********************** 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 100 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.090 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: A 601 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8762 (tp30) REVERT: B 412 MET cc_start: 0.9232 (mmp) cc_final: 0.8809 (mmt) REVERT: D 412 MET cc_start: 0.9158 (mmt) cc_final: 0.8888 (mmp) outliers start: 5 outliers final: 5 residues processed: 96 average time/residue: 0.2848 time to fit residues: 45.8433 Evaluate side-chains 100 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 578 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 163 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.052563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.039853 restraints weight = 233834.232| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.20 r_work: 0.2786 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18780 Z= 0.113 Angle : 0.484 8.283 25469 Z= 0.268 Chirality : 0.035 0.159 2812 Planarity : 0.003 0.036 3082 Dihedral : 14.405 88.787 2868 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.26 % Allowed : 4.08 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2160 helix: 1.66 (0.15), residues: 1263 sheet: 0.16 (0.43), residues: 151 loop : -0.60 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 420 TYR 0.016 0.001 TYR D 314 PHE 0.011 0.001 PHE B 617 TRP 0.009 0.001 TRP D 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18780) covalent geometry : angle 0.48403 / 0.27 (25469) hydrogen bonds : bond 0.03816 / 2.50 ( 975) hydrogen bonds : angle 4.17208 / 2.99 ( 2786) *********************** 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 101 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.079 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: A 601 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8726 (tp30) REVERT: B 412 MET cc_start: 0.9204 (mmp) cc_final: 0.8790 (mmt) REVERT: D 412 MET cc_start: 0.9131 (mmt) cc_final: 0.8869 (mmp) outliers start: 5 outliers final: 5 residues processed: 98 average time/residue: 0.2764 time to fit residues: 45.3535 Evaluate side-chains 99 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 360 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.052471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.039894 restraints weight = 232808.552| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.12 r_work: 0.2794 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18780 Z= 0.151 Angle : 0.496 8.408 25469 Z= 0.275 Chirality : 0.035 0.155 2812 Planarity : 0.003 0.038 3082 Dihedral : 14.304 87.535 2868 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.26 % Allowed : 4.18 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2160 helix: 1.68 (0.15), residues: 1268 sheet: 0.15 (0.43), residues: 151 loop : -0.66 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.016 0.001 TYR D 314 PHE 0.014 0.001 PHE B 617 TRP 0.009 0.001 TRP D 387 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (18780) covalent geometry : angle 0.49610 / 0.27 (25469) hydrogen bonds : bond 0.03849 / 2.52 ( 975) hydrogen bonds : angle 4.22716 / 3.03 ( 2786) ********************** 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 100 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.942 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: A 601 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8719 (tp30) REVERT: B 412 MET cc_start: 0.9192 (mmp) cc_final: 0.8776 (mmt) REVERT: D 412 MET cc_start: 0.9109 (mmt) cc_final: 0.8843 (mmp) outliers start: 5 outliers final: 5 residues processed: 97 average time/residue: 0.2561 time to fit residues: 41.5258 Evaluate side-chains 100 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 360 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 135 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.053089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040465 restraints weight = 230555.319| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.14 r_work: 0.2808 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18780 Z= 0.100 Angle : 0.477 8.352 25469 Z= 0.262 Chirality : 0.034 0.156 2812 Planarity : 0.003 0.034 3082 Dihedral : 14.128 85.506 2868 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.26 % Allowed : 4.18 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2160 helix: 1.83 (0.15), residues: 1261 sheet: 0.21 (0.43), residues: 151 loop : -0.53 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 420 TYR 0.016 0.001 TYR D 314 PHE 0.018 0.001 PHE B 617 TRP 0.009 0.001 TRP D 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (18780) covalent geometry : angle 0.47674 / 0.26 (25469) hydrogen bonds : bond 0.03644 / 2.39 ( 975) hydrogen bonds : angle 4.06490 / 2.91 ( 2786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7009.51 seconds wall clock time: 120 minutes 22.70 seconds (7222.70 seconds total)