Starting phenix.real_space_refine on Mon Jul 6 16:06:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fb4_50287/07_2026/9fb4_50287_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fb4_50287/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fb4_50287/07_2026/9fb4_50287_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fb4_50287/07_2026/9fb4_50287_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fb4_50287/07_2026/9fb4_50287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fb4_50287/07_2026/9fb4_50287.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= 0.095 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-dev-6108/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: 6.27, per 1000 atoms: 0.17 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: 3.47 Conformation dependent library (CDL) restraints added in 993.9 milliseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 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: 6.03 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: 8.82 Time building geometry restraints manager: 4.77 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: 64551 1.74 - 3.48: 2378 3.48 - 5.21: 130 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: 3.720 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: 0.240 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 39.300 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.180 ------------------------------------------------------------------------------- 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 : 0.881 8.689 25469 Z= 0.553 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 0.88132 / 0.55 (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 : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.3858 time to fit residues: 81.2042 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 : 1.019 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.051927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.039187 restraints weight = 233886.921| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.20 r_work: 0.2753 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18780 Z= 0.254 Angle : 0.683 6.673 25469 Z= 0.387 Chirality : 0.040 0.169 2812 Planarity : 0.005 0.083 3082 Dihedral : 15.938 89.844 2868 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -0.26 (0.17), residues: 2160 helix: 0.03 (0.14), residues: 1240 sheet: 0.94 (0.46), residues: 137 loop : -0.49 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 483 TYR 0.017 0.002 TYR B 314 PHE 0.013 0.001 PHE B 562 TRP 0.013 0.002 TRP E 387 HIS 0.009 0.002 HIS F 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 (18780) covalent geometry : angle 0.68258 / 0.39 (25469) hydrogen bonds : bond 0.06612 / 4.27 ( 975) hydrogen bonds : angle 5.39303 / 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 : 1.030 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: B 299 PHE cc_start: 0.9043 (p90) cc_final: 0.8783 (p90) REVERT: B 412 MET cc_start: 0.9338 (mmp) cc_final: 0.8928 (mmt) REVERT: E 309 GLU cc_start: 0.8540 (tp30) cc_final: 0.8248 (tm-30) REVERT: F 617 PHE cc_start: 0.9301 (t80) cc_final: 0.9079 (t80) outliers start: 6 outliers final: 5 residues processed: 104 average time/residue: 0.3022 time to fit residues: 50.3164 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 : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 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: 3.9990 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: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.051364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.038749 restraints weight = 236153.962| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.16 r_work: 0.2740 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18780 Z= 0.272 Angle : 0.607 6.349 25469 Z= 0.343 Chirality : 0.038 0.156 2812 Planarity : 0.004 0.052 3082 Dihedral : 15.649 86.916 2868 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.26 % Allowed : 2.22 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2160 helix: 0.47 (0.14), residues: 1236 sheet: 0.63 (0.45), residues: 134 loop : -0.66 (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 0.021 0.001 PHE F 617 TRP 0.013 0.001 TRP E 387 HIS 0.008 0.001 HIS F 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.27 (18780) covalent geometry : angle 0.60726 / 0.34 (25469) hydrogen bonds : bond 0.05860 / 3.78 ( 975) hydrogen bonds : angle 5.10673 / 3.64 ( 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 103 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 1.049 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: B 299 PHE cc_start: 0.9128 (p90) cc_final: 0.8860 (p90) REVERT: B 412 MET cc_start: 0.9334 (mmp) cc_final: 0.8902 (mmt) outliers start: 5 outliers final: 4 residues processed: 99 average time/residue: 0.2976 time to fit residues: 47.8530 Evaluate side-chains 97 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 375 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: 0.1980 chunk 178 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.052115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.039438 restraints weight = 233556.229| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.15 r_work: 0.2750 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18780 Z= 0.152 Angle : 0.543 5.944 25469 Z= 0.305 Chirality : 0.036 0.155 2812 Planarity : 0.004 0.044 3082 Dihedral : 15.396 83.832 2868 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.21 % Allowed : 2.58 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2160 helix: 0.82 (0.15), residues: 1243 sheet: 0.10 (0.44), residues: 146 loop : -0.64 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 483 TYR 0.016 0.001 TYR A 314 PHE 0.011 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 0.00331 / 0.15 (18780) covalent geometry : angle 0.54293 / 0.31 (25469) hydrogen bonds : bond 0.04922 / 3.20 ( 975) hydrogen bonds : angle 4.75513 / 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 100 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 1.321 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: 0.9309 (mmp) cc_final: 0.8920 (mmt) REVERT: D 412 MET cc_start: 0.9109 (mmp) cc_final: 0.8676 (mmt) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.2910 time to fit residues: 45.8653 Evaluate side-chains 95 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 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: 8.9990 chunk 118 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.052403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040057 restraints weight = 230633.428| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.04 r_work: 0.2813 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18780 Z= 0.138 Angle : 0.513 8.172 25469 Z= 0.287 Chirality : 0.035 0.154 2812 Planarity : 0.003 0.040 3082 Dihedral : 15.050 85.211 2868 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.21 % Allowed : 2.94 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2160 helix: 1.24 (0.15), residues: 1245 sheet: 0.12 (0.44), residues: 142 loop : -0.57 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.017 0.001 TYR D 314 PHE 0.010 0.001 PHE B 617 TRP 0.009 0.001 TRP D 387 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (18780) covalent geometry : angle 0.51318 / 0.29 (25469) hydrogen bonds : bond 0.04358 / 2.84 ( 975) hydrogen bonds : angle 4.49016 / 3.21 ( 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 : 1.037 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: 0.8959 (mm-30) cc_final: 0.8664 (tp30) REVERT: B 412 MET cc_start: 0.9233 (mmp) cc_final: 0.8797 (mmt) REVERT: D 412 MET cc_start: 0.9071 (mmp) cc_final: 0.8748 (mmt) REVERT: F 412 MET cc_start: 0.8670 (mmt) cc_final: 0.8178 (mmt) outliers start: 4 outliers final: 4 residues processed: 100 average time/residue: 0.3113 time to fit residues: 49.7178 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 : 1.044 ------------------------------------------------------------------------------- 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: 1.9990 chunk 78 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.052044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.039595 restraints weight = 233019.094| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.09 r_work: 0.2797 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18780 Z= 0.181 Angle : 0.527 6.930 25469 Z= 0.294 Chirality : 0.035 0.154 2812 Planarity : 0.003 0.040 3082 Dihedral : 14.912 87.024 2868 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.26 % Allowed : 3.56 % Favored : 96.18 % 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: 0.82 (0.18), residues: 2160 helix: 1.29 (0.15), residues: 1262 sheet: 0.06 (0.41), residues: 162 loop : -0.57 (0.21), residues: 736 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 0.010 0.001 PHE B 617 TRP 0.009 0.001 TRP D 387 HIS 0.007 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (18780) covalent geometry : angle 0.52657 / 0.29 (25469) hydrogen bonds : bond 0.04309 / 2.80 ( 975) hydrogen bonds : angle 4.47356 / 3.20 ( 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 98 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.995 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: A 601 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8700 (tp30) REVERT: B 412 MET cc_start: 0.9228 (mmp) cc_final: 0.8785 (mmt) REVERT: F 372 MET cc_start: 0.7245 (mtp) cc_final: 0.7010 (mtp) outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 0.2721 time to fit residues: 42.5561 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 : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 123 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 213 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.052797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.040015 restraints weight = 232267.919| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.20 r_work: 0.2767 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18780 Z= 0.123 Angle : 0.494 7.830 25469 Z= 0.274 Chirality : 0.035 0.158 2812 Planarity : 0.003 0.037 3082 Dihedral : 14.715 89.946 2868 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.21 % Allowed : 3.82 % Favored : 95.98 % 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: 1.03 (0.18), residues: 2160 helix: 1.49 (0.15), residues: 1266 sheet: 0.23 (0.39), residues: 169 loop : -0.58 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.017 0.001 TYR D 314 PHE 0.009 0.001 PHE E 299 TRP 0.009 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (18780) covalent geometry : angle 0.49357 / 0.27 (25469) hydrogen bonds : bond 0.03991 / 2.62 ( 975) hydrogen bonds : angle 4.27578 / 3.06 ( 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 102 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.039 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: A 601 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8748 (tp30) REVERT: B 412 MET cc_start: 0.9245 (mmp) cc_final: 0.8824 (mmt) outliers start: 4 outliers final: 3 residues processed: 100 average time/residue: 0.2965 time to fit residues: 48.3160 Evaluate side-chains 99 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 133 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.051883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.039139 restraints weight = 233867.860| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.23 r_work: 0.2752 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2714 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= 0.189 Angle : 0.515 8.580 25469 Z= 0.286 Chirality : 0.035 0.152 2812 Planarity : 0.003 0.039 3082 Dihedral : 14.644 88.199 2868 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.31 % Allowed : 3.92 % Favored : 95.77 % 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: 0.95 (0.18), residues: 2160 helix: 1.47 (0.15), residues: 1265 sheet: 0.01 (0.40), residues: 164 loop : -0.63 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 420 TYR 0.015 0.001 TYR D 314 PHE 0.014 0.001 PHE A 617 TRP 0.008 0.001 TRP E 387 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (18780) covalent geometry : angle 0.51466 / 0.29 (25469) hydrogen bonds : bond 0.04100 / 2.68 ( 975) hydrogen bonds : angle 4.39150 / 3.14 ( 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 101 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8771 (tp30) REVERT: B 412 MET cc_start: 0.9235 (mmp) cc_final: 0.8802 (mmt) REVERT: D 412 MET cc_start: 0.9143 (mmt) cc_final: 0.8873 (mmp) outliers start: 6 outliers final: 6 residues processed: 97 average time/residue: 0.2681 time to fit residues: 43.3524 Evaluate side-chains 101 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 70 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.052318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.039617 restraints weight = 233695.149| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.19 r_work: 0.2768 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18780 Z= 0.127 Angle : 0.489 7.615 25469 Z= 0.271 Chirality : 0.035 0.156 2812 Planarity : 0.003 0.037 3082 Dihedral : 14.512 89.795 2868 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.31 % Allowed : 4.08 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2160 helix: 1.58 (0.15), residues: 1268 sheet: 0.16 (0.39), residues: 171 loop : -0.59 (0.22), residues: 721 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 0.008 0.001 PHE F 327 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 0.00276 / 0.13 (18780) covalent geometry : angle 0.48904 / 0.27 (25469) hydrogen bonds : bond 0.03907 / 2.56 ( 975) hydrogen bonds : angle 4.23984 / 3.04 ( 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 102 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.083 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: 0.9004 (mm-30) cc_final: 0.8740 (tp30) REVERT: B 412 MET cc_start: 0.9221 (mmp) cc_final: 0.8796 (mmt) REVERT: D 412 MET cc_start: 0.9131 (mmt) cc_final: 0.8873 (mmp) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 0.2821 time to fit residues: 46.0468 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 : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 52 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.052025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.039290 restraints weight = 234634.096| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.23 r_work: 0.2763 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18780 Z= 0.168 Angle : 0.503 8.106 25469 Z= 0.279 Chirality : 0.035 0.153 2812 Planarity : 0.003 0.038 3082 Dihedral : 14.425 89.376 2868 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.21 % Allowed : 4.28 % Favored : 95.51 % 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: 1.09 (0.18), residues: 2160 helix: 1.58 (0.15), residues: 1267 sheet: 0.13 (0.39), residues: 171 loop : -0.62 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.015 0.001 TYR D 314 PHE 0.009 0.001 PHE F 327 TRP 0.010 0.001 TRP D 387 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (18780) covalent geometry : angle 0.50284 / 0.28 (25469) hydrogen bonds : bond 0.03948 / 2.58 ( 975) hydrogen bonds : angle 4.30576 / 3.08 ( 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: 4 poor density : 96 time to evaluate : 1.056 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: 0.9010 (mm-30) cc_final: 0.8755 (tp30) REVERT: B 412 MET cc_start: 0.9220 (mmp) cc_final: 0.8794 (mmt) REVERT: D 412 MET cc_start: 0.9131 (mmt) cc_final: 0.8868 (mmp) outliers start: 4 outliers final: 3 residues processed: 98 average time/residue: 0.2794 time to fit residues: 45.6080 Evaluate side-chains 99 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 1 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 142 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.052566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039869 restraints weight = 232126.247| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.19 r_work: 0.2787 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18780 Z= 0.105 Angle : 0.475 7.673 25469 Z= 0.263 Chirality : 0.034 0.156 2812 Planarity : 0.003 0.035 3082 Dihedral : 14.279 87.003 2868 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.21 % Allowed : 4.33 % Favored : 95.46 % 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 (0.18), residues: 2160 helix: 1.74 (0.15), residues: 1266 sheet: 0.33 (0.43), residues: 149 loop : -0.58 (0.21), residues: 745 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 0.008 0.001 PHE A 617 TRP 0.010 0.001 TRP D 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (18780) covalent geometry : angle 0.47522 / 0.26 (25469) hydrogen bonds : bond 0.03746 / 2.46 ( 975) hydrogen bonds : angle 4.14173 / 2.97 ( 2786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6917.34 seconds wall clock time: 118 minutes 50.15 seconds (7130.15 seconds total)