Starting phenix.real_space_refine on Tue Aug 26 12:36:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fb4_50287/08_2025/9fb4_50287_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fb4_50287/08_2025/9fb4_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_50287/08_2025/9fb4_50287_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fb4_50287/08_2025/9fb4_50287_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fb4_50287/08_2025/9fb4_50287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fb4_50287/08_2025/9fb4_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.55, 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: 2.82 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.4 microseconds 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: 5.41 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: 7.57 Time building geometry restraints manager: 4.11 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 - 1.54: 63439 1.54 - 3.07: 3367 3.07 - 4.61: 246 4.61 - 6.15: 29 6.15 - 7.68: 9 Bond angle restraints: 67090 Sorted by residual: 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=" O3' DT T -1 " pdb=" C3' DT T -1 " pdb=" C2' DT T -1 " ideal model delta sigma weight residual 111.50 118.09 -6.59 1.50e+00 4.44e-01 1.93e+01 angle pdb=" N GLY E 524 " pdb=" CA GLY E 524 " pdb=" C GLY E 524 " ideal model delta sigma weight residual 111.08 117.02 -5.94 1.62e+00 3.81e-01 1.35e+01 angle pdb=" C4' DT T -1 " pdb=" O4' DT T -1 " pdb=" C1' DT T -1 " ideal model delta sigma weight residual 109.70 104.50 5.20 1.50e+00 4.44e-01 1.20e+01 angle pdb=" C4' DA P 5 " pdb=" O4' DA P 5 " pdb=" C1' DA P 5 " ideal model delta sigma weight residual 109.70 104.51 5.19 1.50e+00 4.44e-01 1.20e+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 - 0.042: 1752 0.042 - 0.084: 796 0.084 - 0.126: 203 0.126 - 0.169: 50 0.169 - 0.211: 11 Chirality restraints: 2812 Sorted by residual: chirality pdb=" CA HIS E 513 " pdb=" N HIS E 513 " pdb=" C HIS E 513 " pdb=" CB HIS E 513 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" P DA P 1 " pdb=" OP1 DA P 1 " pdb=" OP2 DA P 1 " pdb=" O5' DA P 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA HIS A 513 " pdb=" N HIS A 513 " pdb=" C HIS A 513 " pdb=" CB HIS A 513 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 ... (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: 4.770 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: 0.200 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 0.050 18780 Z= 0.247 Angle : 0.871 7.683 25469 Z= 0.526 Chirality : 0.051 0.211 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 aren 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 covalent geometry : bond 0.00509 (18780) covalent geometry : angle 0.87097 (25469) hydrogen bonds : bond 0.18571 ( 975) hydrogen bonds : angle 7.04741 ( 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 : 1.041 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: 0.3344 time to fit residues: 69.7686 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 : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 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... Flipped N/Q/H residues before XYZ refinement: B 363 ASN C 339 GLN E 320 HIS E 363 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.052145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.039488 restraints weight = 234702.978| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.18 r_work: 0.2754 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18780 Z= 0.243 Angle : 0.612 5.763 25469 Z= 0.346 Chirality : 0.038 0.151 2812 Planarity : 0.004 0.036 3082 Dihedral : 15.434 85.035 2868 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.21 % Allowed : 1.65 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.17), residues: 2160 helix: 0.49 (0.14), residues: 1232 sheet: 0.72 (0.44), residues: 143 loop : -0.27 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 548 TYR 0.020 0.002 TYR D 314 PHE 0.014 0.001 PHE A 327 TRP 0.013 0.001 TRP F 581 HIS 0.007 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00545 (18780) covalent geometry : angle 0.61248 (25469) hydrogen bonds : bond 0.05270 ( 975) hydrogen bonds : angle 5.07396 ( 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 108 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.903 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 414 TYR cc_start: 0.8822 (m-10) cc_final: 0.8617 (m-10) REVERT: B 412 MET cc_start: 0.9334 (mmp) cc_final: 0.8918 (mmt) REVERT: D 412 MET cc_start: 0.9215 (mmt) cc_final: 0.8822 (mmt) REVERT: E 309 GLU cc_start: 0.8579 (tp30) cc_final: 0.8283 (tm-30) REVERT: E 528 MET cc_start: 0.9463 (ptp) cc_final: 0.9260 (ptp) REVERT: E 621 MET cc_start: 0.9006 (mmp) cc_final: 0.8798 (mmp) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.2402 time to fit residues: 40.9525 Evaluate side-chains 98 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 66 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN C 332 ASN E 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.051674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.039280 restraints weight = 233613.034| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.14 r_work: 0.2758 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18780 Z= 0.209 Angle : 0.540 5.376 25469 Z= 0.305 Chirality : 0.036 0.151 2812 Planarity : 0.004 0.036 3082 Dihedral : 14.939 88.968 2868 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.26 % Allowed : 2.32 % Favored : 97.42 % 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 aren not related in a simple way. whole: 0.55 (0.18), residues: 2160 helix: 0.94 (0.15), residues: 1261 sheet: 0.23 (0.44), residues: 148 loop : -0.46 (0.21), residues: 751 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 0.021 0.001 PHE B 617 TRP 0.011 0.001 TRP E 387 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00466 (18780) covalent geometry : angle 0.53978 (25469) hydrogen bonds : bond 0.04726 ( 975) hydrogen bonds : angle 4.73301 ( 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 107 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.886 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: 0.8737 (tp30) REVERT: B 412 MET cc_start: 0.9245 (mmp) cc_final: 0.8816 (mmt) outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 0.2566 time to fit residues: 42.8762 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 : 0.853 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 172 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.053029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040531 restraints weight = 232520.850| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.15 r_work: 0.2812 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18780 Z= 0.106 Angle : 0.467 5.517 25469 Z= 0.261 Chirality : 0.034 0.149 2812 Planarity : 0.003 0.032 3082 Dihedral : 14.327 89.413 2868 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.15 % Allowed : 2.79 % Favored : 97.06 % 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 aren not related in a simple way. whole: 1.08 (0.18), residues: 2160 helix: 1.48 (0.15), residues: 1264 sheet: 0.11 (0.44), residues: 145 loop : -0.39 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 420 TYR 0.018 0.001 TYR D 314 PHE 0.009 0.001 PHE E 299 TRP 0.008 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00228 (18780) covalent geometry : angle 0.46655 (25469) hydrogen bonds : bond 0.03604 ( 975) hydrogen bonds : angle 4.21862 ( 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 106 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.766 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: 0.8945 (mm-30) cc_final: 0.8674 (tp30) REVERT: B 412 MET cc_start: 0.9172 (mmp) cc_final: 0.8829 (mmt) REVERT: B 621 MET cc_start: 0.8625 (mtm) cc_final: 0.8357 (mtm) REVERT: D 412 MET cc_start: 0.9148 (mmt) cc_final: 0.8880 (mmp) outliers start: 3 outliers final: 3 residues processed: 104 average time/residue: 0.2670 time to fit residues: 44.7403 Evaluate side-chains 98 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 104 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.051417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038929 restraints weight = 234523.079| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.13 r_work: 0.2753 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18780 Z= 0.243 Angle : 0.532 5.022 25469 Z= 0.300 Chirality : 0.036 0.147 2812 Planarity : 0.003 0.032 3082 Dihedral : 14.410 89.630 2868 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.36 % Allowed : 3.30 % Favored : 96.34 % 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 aren not related in a simple way. whole: 0.86 (0.18), residues: 2160 helix: 1.35 (0.15), residues: 1276 sheet: 0.19 (0.44), residues: 147 loop : -0.66 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 540 TYR 0.014 0.001 TYR D 314 PHE 0.014 0.001 PHE F 327 TRP 0.010 0.001 TRP E 387 HIS 0.006 0.001 HIS F 313 Details of bonding type rmsd covalent geometry : bond 0.00546 (18780) covalent geometry : angle 0.53156 (25469) hydrogen bonds : bond 0.04405 ( 975) hydrogen bonds : angle 4.52443 ( 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: 7 poor density : 96 time to evaluate : 0.701 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: 0.9029 (mm-30) cc_final: 0.8779 (tp30) REVERT: B 412 MET cc_start: 0.9240 (mmp) cc_final: 0.8752 (mmt) REVERT: B 621 MET cc_start: 0.8690 (mtm) cc_final: 0.8442 (mtm) REVERT: D 412 MET cc_start: 0.9145 (mmt) cc_final: 0.8812 (mmp) REVERT: E 412 MET cc_start: 0.9313 (mmp) cc_final: 0.8722 (mmt) REVERT: F 412 MET cc_start: 0.8664 (mmt) cc_final: 0.8099 (mmt) outliers start: 7 outliers final: 6 residues processed: 99 average time/residue: 0.2323 time to fit residues: 37.9898 Evaluate side-chains 98 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 375 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.052856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040346 restraints weight = 232461.072| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.14 r_work: 0.2806 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18780 Z= 0.108 Angle : 0.456 5.597 25469 Z= 0.255 Chirality : 0.034 0.150 2812 Planarity : 0.003 0.031 3082 Dihedral : 13.868 85.796 2868 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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 aren not related in a simple way. whole: 1.26 (0.18), residues: 2160 helix: 1.73 (0.15), residues: 1262 sheet: 0.10 (0.44), residues: 145 loop : -0.52 (0.21), residues: 753 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 B 617 TRP 0.007 0.001 TRP D 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00236 (18780) covalent geometry : angle 0.45628 (25469) hydrogen bonds : bond 0.03487 ( 975) hydrogen bonds : angle 4.08698 ( 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 102 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.115 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: 0.8942 (mm-30) cc_final: 0.8677 (tp30) REVERT: B 412 MET cc_start: 0.9166 (mmp) cc_final: 0.8785 (mmt) REVERT: D 412 MET cc_start: 0.9139 (mmt) cc_final: 0.8838 (mmp) REVERT: F 412 MET cc_start: 0.8553 (mmt) cc_final: 0.7935 (mmt) outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.2573 time to fit residues: 42.5687 Evaluate side-chains 98 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- 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: 0.4980 chunk 210 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.052655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040113 restraints weight = 233236.961| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.14 r_work: 0.2799 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3255 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= 0.127 Angle : 0.463 5.443 25469 Z= 0.259 Chirality : 0.034 0.150 2812 Planarity : 0.003 0.030 3082 Dihedral : 13.644 85.011 2868 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.36 % Allowed : 3.97 % 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 aren not related in a simple way. whole: 1.39 (0.18), residues: 2160 helix: 1.84 (0.15), residues: 1265 sheet: 0.10 (0.44), residues: 145 loop : -0.46 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 420 TYR 0.016 0.001 TYR D 314 PHE 0.008 0.001 PHE F 327 TRP 0.009 0.001 TRP E 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00281 (18780) covalent geometry : angle 0.46277 (25469) hydrogen bonds : bond 0.03494 ( 975) hydrogen bonds : angle 4.03838 ( 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 107 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.693 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: A 601 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8690 (tp30) REVERT: B 412 MET cc_start: 0.9151 (mmp) cc_final: 0.8717 (mmt) REVERT: D 412 MET cc_start: 0.9104 (mmt) cc_final: 0.8775 (mmp) REVERT: F 412 MET cc_start: 0.8550 (mmt) cc_final: 0.7966 (mmt) outliers start: 7 outliers final: 6 residues processed: 104 average time/residue: 0.2707 time to fit residues: 45.6156 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 : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 609 LEU 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: 1.9990 chunk 136 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.052889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040398 restraints weight = 231446.058| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.14 r_work: 0.2809 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3370 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= 0.113 Angle : 0.462 7.612 25469 Z= 0.256 Chirality : 0.034 0.151 2812 Planarity : 0.003 0.029 3082 Dihedral : 13.430 84.093 2868 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.26 % Allowed : 4.44 % Favored : 95.30 % 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 aren not related in a simple way. whole: 1.56 (0.18), residues: 2160 helix: 2.00 (0.15), residues: 1266 sheet: 0.27 (0.43), residues: 152 loop : -0.47 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 420 TYR 0.016 0.001 TYR D 314 PHE 0.008 0.001 PHE E 617 TRP 0.008 0.001 TRP D 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00250 (18780) covalent geometry : angle 0.46210 (25469) hydrogen bonds : bond 0.03335 ( 975) hydrogen bonds : angle 3.94791 ( 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 102 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.621 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: 0.8961 (mm-30) cc_final: 0.8706 (tp30) REVERT: B 412 MET cc_start: 0.9138 (mmp) cc_final: 0.8754 (mmt) REVERT: D 412 MET cc_start: 0.9099 (mmt) cc_final: 0.8779 (mmp) REVERT: F 412 MET cc_start: 0.8539 (mmt) cc_final: 0.7924 (mmt) outliers start: 5 outliers final: 5 residues processed: 100 average time/residue: 0.2370 time to fit residues: 39.3371 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 : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.053019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.040822 restraints weight = 232617.699| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.07 r_work: 0.2811 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3431 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= 0.120 Angle : 0.463 7.105 25469 Z= 0.257 Chirality : 0.034 0.149 2812 Planarity : 0.003 0.029 3082 Dihedral : 13.311 83.943 2868 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.31 % Allowed : 4.44 % Favored : 95.25 % 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 aren not related in a simple way. whole: 1.64 (0.18), residues: 2160 helix: 2.08 (0.15), residues: 1266 sheet: 0.12 (0.45), residues: 147 loop : -0.42 (0.21), residues: 747 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 B 617 TRP 0.009 0.001 TRP E 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00267 (18780) covalent geometry : angle 0.46273 (25469) hydrogen bonds : bond 0.03317 ( 975) hydrogen bonds : angle 3.93994 ( 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 103 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.744 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: 0.8966 (mm-30) cc_final: 0.8727 (tp30) REVERT: B 412 MET cc_start: 0.9137 (mmp) cc_final: 0.8750 (mmt) REVERT: D 412 MET cc_start: 0.9101 (mmt) cc_final: 0.8779 (mmp) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.2410 time to fit residues: 39.9568 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 : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain F residue 332 ASN 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: 0.6980 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 189 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.053254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040691 restraints weight = 233247.820| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.16 r_work: 0.2817 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18780 Z= 0.109 Angle : 0.458 7.138 25469 Z= 0.253 Chirality : 0.034 0.150 2812 Planarity : 0.003 0.029 3082 Dihedral : 13.138 82.773 2868 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.26 % Allowed : 4.49 % Favored : 95.25 % 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 aren not related in a simple way. whole: 1.73 (0.18), residues: 2160 helix: 2.15 (0.15), residues: 1271 sheet: 0.32 (0.43), residues: 152 loop : -0.43 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 420 TYR 0.016 0.001 TYR D 314 PHE 0.007 0.001 PHE D 588 TRP 0.008 0.001 TRP E 387 HIS 0.003 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00242 (18780) covalent geometry : angle 0.45772 (25469) hydrogen bonds : bond 0.03192 ( 975) hydrogen bonds : angle 3.87134 ( 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 104 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.911 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: 0.8967 (mm-30) cc_final: 0.8763 (tp30) REVERT: B 412 MET cc_start: 0.9106 (mmp) cc_final: 0.8724 (mmt) REVERT: D 412 MET cc_start: 0.9099 (mmt) cc_final: 0.8791 (mmp) outliers start: 5 outliers final: 4 residues processed: 101 average time/residue: 0.2322 time to fit residues: 38.5324 Evaluate side-chains 101 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain F residue 332 ASN 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: 0.6980 chunk 166 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 208 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.053898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041428 restraints weight = 230992.329| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.15 r_work: 0.2841 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18780 Z= 0.092 Angle : 0.453 7.679 25469 Z= 0.248 Chirality : 0.034 0.149 2812 Planarity : 0.003 0.028 3082 Dihedral : 12.918 80.104 2868 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.26 % Allowed : 4.59 % Favored : 95.15 % 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 aren not related in a simple way. whole: 1.89 (0.18), residues: 2160 helix: 2.27 (0.15), residues: 1271 sheet: 0.31 (0.43), residues: 152 loop : -0.36 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 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 0.002 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00203 (18780) covalent geometry : angle 0.45323 (25469) hydrogen bonds : bond 0.02982 ( 975) hydrogen bonds : angle 3.73607 ( 2786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6073.70 seconds wall clock time: 104 minutes 10.31 seconds (6250.31 seconds total)