Starting phenix.real_space_refine on Tue Aug 26 11:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kak_62209/08_2025/9kak_62209_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kak_62209/08_2025/9kak_62209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kak_62209/08_2025/9kak_62209_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kak_62209/08_2025/9kak_62209_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kak_62209/08_2025/9kak_62209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kak_62209/08_2025/9kak_62209.map" } resolution = 3.1 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= -0.006 sd= 0.563 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: 7 Type Number sf(0) Gaussians P 43 5.49 5 Mg 6 5.21 5 S 126 5.16 5 C 11638 2.51 5 N 3074 2.21 5 O 3407 1.98 5 H 18197 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36491 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "B" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 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: 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: "E" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 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: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 321 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 481 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.93, per 1000 atoms: 0.19 Number of scatterers: 36491 At special positions: 0 Unit cell: (101.37, 123.69, 142.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 126 16.00 P 43 15.00 Mg 6 11.99 O 3407 8.00 N 3074 7.00 C 11638 6.00 H 18197 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: 3.52 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 12 sheets defined 69.5% alpha, 6.3% beta 10 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 6.71 Creating SS restraints... Processing helix chain 'A' and resid 269 through 281 removed outlier: 3.665A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.774A pdb=" N PHE A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.618A pdb=" N LYS A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 5.291A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASN A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.597A 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 377 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 400 through 414 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 456 through 462 removed outlier: 4.027A pdb=" N GLU A 460 " --> pdb=" O ARG A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 481 through 485 removed outlier: 4.014A pdb=" N LEU A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 497 through 503 removed outlier: 3.666A pdb=" N LEU A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 567 through 570 removed outlier: 3.600A pdb=" N GLN A 570 " --> pdb=" O ARG A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 570' Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.535A 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: 3.563A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 302 through 308 Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 316 through 330 removed outlier: 5.261A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 355 Processing helix chain 'B' and resid 356 through 376 Processing helix chain 'B' and resid 383 through 396 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: 3.843A pdb=" N ASN B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 460 " --> pdb=" O ARG B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 480 through 484 Processing helix chain 'B' and resid 489 through 497 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 560 Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 567 through 570 Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 589 through 607 removed outlier: 4.493A pdb=" N SER B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 4.908A 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: 3.634A pdb=" N VAL C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 removed outlier: 3.856A 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 330 removed outlier: 5.029A pdb=" N ALA C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 355 Processing helix chain 'C' and resid 356 through 377 Processing helix chain 'C' and resid 383 through 398 removed outlier: 4.262A 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 Processing helix chain 'C' and resid 456 through 462 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 480 through 484 Processing helix chain 'C' and resid 489 through 497 Processing helix chain 'C' and resid 497 through 503 removed outlier: 3.578A pdb=" N GLY C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 561 through 566 Processing helix chain 'C' and resid 571 through 583 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 592 through 607 Processing helix chain 'C' and resid 608 through 621 Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.724A pdb=" N VAL D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 298 through 301 removed outlier: 3.833A pdb=" N MET D 301 " --> pdb=" O SER D 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 302 through 308 Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 316 through 330 removed outlier: 5.259A pdb=" N ALA D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASN D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 355 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 383 through 396 Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 456 through 462 removed outlier: 4.099A pdb=" N GLU D 460 " --> pdb=" O ARG D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 480 through 484 Processing helix chain 'D' and resid 489 through 497 Processing helix chain 'D' and resid 497 through 502 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 567 through 570 removed outlier: 3.543A pdb=" N GLN D 570 " --> pdb=" O ARG D 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 567 through 570' Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.512A 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: 4.384A pdb=" N SER D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ARG D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 621 Processing helix chain 'E' and resid 269 through 281 removed outlier: 3.588A pdb=" N VAL E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 295 removed outlier: 3.666A pdb=" N PHE E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) 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: 5.252A pdb=" N ALA E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN E 323 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 3.579A 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 377 Processing helix chain 'E' and resid 383 through 396 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 462 removed outlier: 3.727A pdb=" N LEU E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN E 458 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.227A pdb=" N GLU E 481 " --> pdb=" O THR E 478 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER E 482 " --> pdb=" O GLY E 479 " (cutoff:3.500A) 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 567 through 570 Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.648A 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 Processing helix chain 'E' and resid 608 through 621 Processing helix chain 'F' and resid 269 through 281 removed outlier: 3.597A pdb=" N VAL F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 294 Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 298 through 301 removed outlier: 3.636A pdb=" N MET F 301 " --> pdb=" O SER F 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 298 through 301' Processing helix chain 'F' and resid 302 through 308 Processing helix chain 'F' and resid 310 through 315 Processing helix chain 'F' and resid 316 through 330 removed outlier: 5.059A pdb=" N ALA F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN F 323 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP F 329 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 355 Processing helix chain 'F' and resid 356 through 376 removed outlier: 3.528A pdb=" N LEU F 361 " --> pdb=" O ARG F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 396 removed outlier: 3.675A pdb=" N CYS F 396 " --> pdb=" O ALA F 392 " (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 456 Processing helix chain 'F' and resid 457 through 462 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 removed outlier: 4.402A pdb=" N SER F 482 " --> pdb=" O GLY F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 496 Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 550 through 559 Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'F' and resid 571 through 583 Processing helix chain 'F' and resid 584 through 588 Processing helix chain 'F' and resid 592 through 607 removed outlier: 4.204A pdb=" N GLU F 598 " --> pdb=" O SER F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 621 Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 448 removed outlier: 7.238A pdb=" N TYR A 421 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ILE A 545 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 6.534A 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 511 removed outlier: 5.116A pdb=" N LYS A 511 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASN A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 448 removed outlier: 7.138A pdb=" N TYR B 421 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ILE B 545 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 423 " --> pdb=" O ILE B 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 507 through 509 Processing sheet with id=AA5, first strand: chain 'C' and resid 445 through 448 removed outlier: 3.561A pdb=" N LYS C 446 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR C 421 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE C 545 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 423 " --> pdb=" O ILE C 545 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 507 through 509 Processing sheet with id=AA7, first strand: chain 'D' and resid 445 through 448 removed outlier: 7.434A pdb=" N TYR D 421 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE D 545 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.633A 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: 6.570A pdb=" N TYR E 421 " --> pdb=" O PHE E 541 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS E 543 " --> pdb=" O TYR E 421 " (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 447 removed outlier: 6.698A pdb=" N LYS F 446 " --> pdb=" O VAL F 471 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR F 421 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N ILE F 545 " --> pdb=" O TYR F 421 " (cutoff:3.500A) removed outlier: 6.603A 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 509 988 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 9.56 Time building geometry restraints manager: 4.88 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: 18155 1.03 - 1.23: 209 1.23 - 1.42: 7547 1.42 - 1.62: 10792 1.62 - 1.81: 206 Bond restraints: 36909 Sorted by residual: bond pdb=" N3B ANP F 800 " pdb=" PG ANP F 800 " ideal model delta sigma weight residual 1.795 1.611 0.184 2.00e-02 2.50e+03 8.45e+01 bond pdb=" N3B ANP C 802 " pdb=" PG ANP C 802 " ideal model delta sigma weight residual 1.795 1.614 0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" N3B ANP A 800 " pdb=" PG ANP A 800 " ideal model delta sigma weight residual 1.795 1.614 0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" N3B ANP E 800 " pdb=" PG ANP E 800 " ideal model delta sigma weight residual 1.795 1.616 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" N3B ANP D 802 " pdb=" PG ANP D 802 " ideal model delta sigma weight residual 1.795 1.617 0.178 2.00e-02 2.50e+03 7.89e+01 ... (remaining 36904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 66617 3.48 - 6.95: 258 6.95 - 10.43: 10 10.43 - 13.91: 7 13.91 - 17.38: 1 Bond angle restraints: 66893 Sorted by residual: angle pdb=" PB ANP F 800 " pdb=" N3B ANP F 800 " pdb=" PG ANP F 800 " ideal model delta sigma weight residual 126.95 109.57 17.38 3.00e+00 1.11e-01 3.36e+01 angle pdb=" N GLY C 490 " pdb=" CA GLY C 490 " pdb=" C GLY C 490 " ideal model delta sigma weight residual 112.64 117.76 -5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" N GLY E 524 " pdb=" CA GLY E 524 " pdb=" C GLY E 524 " ideal model delta sigma weight residual 110.80 116.60 -5.80 1.41e+00 5.03e-01 1.69e+01 angle pdb=" CA TYR D 552 " pdb=" CB TYR D 552 " pdb=" CG TYR D 552 " ideal model delta sigma weight residual 113.90 121.18 -7.28 1.80e+00 3.09e-01 1.64e+01 angle pdb=" N PRO B 417 " pdb=" CA PRO B 417 " pdb=" C PRO B 417 " ideal model delta sigma weight residual 112.47 120.33 -7.86 2.06e+00 2.36e-01 1.45e+01 ... (remaining 66888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 16372 33.50 - 67.00: 756 67.00 - 100.50: 50 100.50 - 134.00: 0 134.00 - 167.50: 2 Dihedral angle restraints: 17180 sinusoidal: 9643 harmonic: 7537 Sorted by residual: dihedral pdb=" CA LEU C 469 " pdb=" C LEU C 469 " pdb=" N VAL C 470 " pdb=" CA VAL C 470 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LYS E 419 " pdb=" C LYS E 419 " pdb=" N ARG E 420 " pdb=" CA ARG E 420 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.19e+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 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 17177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2256 0.066 - 0.131: 465 0.131 - 0.197: 65 0.197 - 0.263: 7 0.263 - 0.329: 7 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C3' ANP F 800 " pdb=" C2' ANP F 800 " pdb=" C4' ANP F 800 " pdb=" O3' ANP F 800 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C3' ANP B 802 " pdb=" C2' ANP B 802 " pdb=" C4' ANP B 802 " pdb=" O3' ANP B 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C3' ANP A 800 " pdb=" C2' ANP A 800 " pdb=" C4' ANP A 800 " pdb=" O3' ANP A 800 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2797 not shown) Planarity restraints: 5189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP A 800 " 0.200 2.00e-02 2.50e+03 8.42e-02 1.95e+02 pdb=" C2 ANP A 800 " -0.017 2.00e-02 2.50e+03 pdb=" C4 ANP A 800 " -0.079 2.00e-02 2.50e+03 pdb=" C5 ANP A 800 " -0.059 2.00e-02 2.50e+03 pdb=" C6 ANP A 800 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ANP A 800 " -0.039 2.00e-02 2.50e+03 pdb=" N1 ANP A 800 " 0.028 2.00e-02 2.50e+03 pdb=" N3 ANP A 800 " -0.058 2.00e-02 2.50e+03 pdb=" N6 ANP A 800 " 0.129 2.00e-02 2.50e+03 pdb=" N7 ANP A 800 " -0.046 2.00e-02 2.50e+03 pdb=" N9 ANP A 800 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP E 800 " -0.187 2.00e-02 2.50e+03 8.04e-02 1.78e+02 pdb=" C2 ANP E 800 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ANP E 800 " 0.085 2.00e-02 2.50e+03 pdb=" C5 ANP E 800 " 0.068 2.00e-02 2.50e+03 pdb=" C6 ANP E 800 " 0.001 2.00e-02 2.50e+03 pdb=" C8 ANP E 800 " 0.023 2.00e-02 2.50e+03 pdb=" N1 ANP E 800 " -0.033 2.00e-02 2.50e+03 pdb=" N3 ANP E 800 " 0.070 2.00e-02 2.50e+03 pdb=" N6 ANP E 800 " -0.116 2.00e-02 2.50e+03 pdb=" N7 ANP E 800 " 0.037 2.00e-02 2.50e+03 pdb=" N9 ANP E 800 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP F 800 " -0.174 2.00e-02 2.50e+03 7.36e-02 1.49e+02 pdb=" C2 ANP F 800 " 0.006 2.00e-02 2.50e+03 pdb=" C4 ANP F 800 " 0.070 2.00e-02 2.50e+03 pdb=" C5 ANP F 800 " 0.056 2.00e-02 2.50e+03 pdb=" C6 ANP F 800 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ANP F 800 " 0.026 2.00e-02 2.50e+03 pdb=" N1 ANP F 800 " -0.028 2.00e-02 2.50e+03 pdb=" N3 ANP F 800 " 0.061 2.00e-02 2.50e+03 pdb=" N6 ANP F 800 " -0.109 2.00e-02 2.50e+03 pdb=" N7 ANP F 800 " 0.040 2.00e-02 2.50e+03 pdb=" N9 ANP F 800 " 0.053 2.00e-02 2.50e+03 ... (remaining 5186 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1308 2.17 - 2.77: 70200 2.77 - 3.38: 103240 3.38 - 3.99: 132348 3.99 - 4.60: 211408 Nonbonded interactions: 518504 Sorted by model distance: nonbonded pdb="MG MG D 801 " pdb=" O2G ANP D 802 " model vdw 1.557 2.050 nonbonded pdb=" O GLY E 431 " pdb=" HG1 THR E 434 " model vdw 1.612 2.450 nonbonded pdb=" HG1 THR A 433 " pdb=" OE2 GLU A 473 " model vdw 1.616 2.450 nonbonded pdb="HH22 ARG A 420 " pdb=" O PHE A 521 " model vdw 1.650 2.450 nonbonded pdb=" HZ1 LYS F 512 " pdb=" OP1 DT T 1 " model vdw 1.686 2.450 ... (remaining 518499 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 627) selection = (chain 'B' and resid 266 through 627) selection = (chain 'C' and (resid 266 through 301 or (resid 302 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 303 through 304 or (resid 305 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 306 through 627)) selection = (chain 'D' and (resid 266 through 301 or (resid 302 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 303 through 304 or (resid 305 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 306 through 312 or (resid 313 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 3 \ 14 through 627)) selection = (chain 'E' and resid 266 through 627) selection = (chain 'F' and (resid 266 through 301 or (resid 302 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 303 through 304 or (resid 305 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 306 through 627)) } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 41.720 Find NCS groups from input model: 0.720 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: 47.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 : 0.007 0.184 18712 Z= 0.354 Angle : 1.003 17.383 25364 Z= 0.581 Chirality : 0.057 0.329 2800 Planarity : 0.012 0.276 3079 Dihedral : 15.296 167.504 7274 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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 aren not related in a simple way. whole: -1.11 (0.15), residues: 2160 helix: -0.70 (0.12), residues: 1285 sheet: -0.18 (0.42), residues: 161 loop : -0.58 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG F 498 TYR 0.030 0.006 TYR D 552 PHE 0.025 0.004 PHE F 521 TRP 0.025 0.005 TRP E 599 HIS 0.011 0.004 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00739 (18712) covalent geometry : angle 1.00319 (25364) hydrogen bonds : bond 0.19027 ( 1008) hydrogen bonds : angle 6.64282 ( 2896) *********************** 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 360 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 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: 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 299 PHE cc_start: 0.8604 (p90) cc_final: 0.8244 (p90) REVERT: B 484 ASP cc_start: 0.8917 (t0) cc_final: 0.8682 (t0) REVERT: B 502 ASP cc_start: 0.8530 (m-30) cc_final: 0.8152 (m-30) REVERT: C 412 MET cc_start: 0.8858 (mmp) cc_final: 0.8515 (mmp) REVERT: C 484 ASP cc_start: 0.8634 (t0) cc_final: 0.8408 (t0) REVERT: C 614 LYS cc_start: 0.8708 (tppt) cc_final: 0.8167 (ttpt) REVERT: D 484 ASP cc_start: 0.8608 (t0) cc_final: 0.8315 (t0) REVERT: E 396 CYS cc_start: 0.8857 (t) cc_final: 0.8477 (t) REVERT: E 474 ASP cc_start: 0.8417 (t0) cc_final: 0.8176 (p0) REVERT: E 540 ARG cc_start: 0.8870 (mtt-85) cc_final: 0.8499 (mtt-85) REVERT: E 615 MET cc_start: 0.7934 (mtm) cc_final: 0.7590 (mtm) REVERT: F 401 MET cc_start: 0.9240 (tpp) cc_final: 0.8889 (tpt) REVERT: F 502 ASP cc_start: 0.8520 (m-30) cc_final: 0.8319 (m-30) REVERT: F 511 LYS cc_start: 0.9020 (tttt) cc_final: 0.8647 (ttmm) REVERT: F 558 GLU cc_start: 0.8736 (tt0) cc_final: 0.8417 (tp30) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.4966 time to fit residues: 242.8080 Evaluate side-chains 273 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 20.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 GLN E 323 ASN E 513 HIS F 267 GLN F 467 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.064404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.050347 restraints weight = 123568.747| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 1.76 r_work: 0.2354 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2236 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18712 Z= 0.195 Angle : 0.679 6.852 25364 Z= 0.377 Chirality : 0.040 0.187 2800 Planarity : 0.006 0.104 3079 Dihedral : 14.519 170.798 2822 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.21 % Allowed : 4.64 % 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: -0.19 (0.16), residues: 2160 helix: 0.24 (0.14), residues: 1283 sheet: 0.00 (0.42), residues: 157 loop : -0.60 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 498 TYR 0.025 0.002 TYR D 552 PHE 0.014 0.002 PHE E 327 TRP 0.013 0.001 TRP E 599 HIS 0.006 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00437 (18712) covalent geometry : angle 0.67926 (25364) hydrogen bonds : bond 0.06625 ( 1008) hydrogen bonds : angle 5.16939 ( 2896) *********************** 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 297 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 293 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8587 (p90) cc_final: 0.8296 (p90) REVERT: A 548 ARG cc_start: 0.8819 (ttm-80) cc_final: 0.8424 (mtm-85) REVERT: B 401 MET cc_start: 0.8987 (tpt) cc_final: 0.8538 (tpt) REVERT: B 484 ASP cc_start: 0.8893 (t0) cc_final: 0.8498 (t0) REVERT: C 278 MET cc_start: 0.9198 (mmm) cc_final: 0.8555 (mmm) REVERT: C 412 MET cc_start: 0.8783 (mmp) cc_final: 0.8314 (mmp) REVERT: C 614 LYS cc_start: 0.8772 (tppt) cc_final: 0.8204 (ttpt) REVERT: D 484 ASP cc_start: 0.8733 (t0) cc_final: 0.8302 (t0) REVERT: D 578 MET cc_start: 0.9074 (ttm) cc_final: 0.8841 (ttp) REVERT: E 396 CYS cc_start: 0.8925 (t) cc_final: 0.8617 (t) REVERT: E 474 ASP cc_start: 0.8512 (t0) cc_final: 0.8147 (p0) REVERT: F 454 LEU cc_start: 0.8145 (tp) cc_final: 0.7838 (tt) REVERT: F 511 LYS cc_start: 0.8921 (tttt) cc_final: 0.8612 (ttmm) REVERT: F 558 GLU cc_start: 0.8740 (tt0) cc_final: 0.8449 (tp30) outliers start: 4 outliers final: 0 residues processed: 293 average time/residue: 0.4329 time to fit residues: 176.0602 Evaluate side-chains 266 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 168 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN E 467 GLN E 613 GLN F 555 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.063878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.049866 restraints weight = 124214.106| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 1.75 r_work: 0.2341 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2224 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18712 Z= 0.200 Angle : 0.619 7.004 25364 Z= 0.341 Chirality : 0.038 0.185 2800 Planarity : 0.005 0.073 3079 Dihedral : 14.168 170.054 2822 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.52 % Allowed : 6.45 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.17), residues: 2160 helix: 0.55 (0.14), residues: 1288 sheet: 0.07 (0.43), residues: 141 loop : -0.71 (0.20), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 349 TYR 0.022 0.002 TYR C 314 PHE 0.026 0.002 PHE C 299 TRP 0.011 0.001 TRP D 387 HIS 0.005 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00463 (18712) covalent geometry : angle 0.61886 (25364) hydrogen bonds : bond 0.05759 ( 1008) hydrogen bonds : angle 4.85399 ( 2896) *********************** 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 287 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 277 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8466 (p90) cc_final: 0.8235 (p90) REVERT: A 548 ARG cc_start: 0.8844 (ttm-80) cc_final: 0.8460 (mtm-85) REVERT: B 401 MET cc_start: 0.8989 (tpt) cc_final: 0.8592 (tpt) REVERT: B 484 ASP cc_start: 0.8931 (t0) cc_final: 0.8615 (t0) REVERT: C 412 MET cc_start: 0.8800 (mmp) cc_final: 0.8257 (mmp) REVERT: C 614 LYS cc_start: 0.8792 (tppt) cc_final: 0.8218 (ttpt) REVERT: D 484 ASP cc_start: 0.8747 (t0) cc_final: 0.8346 (t0) REVERT: E 396 CYS cc_start: 0.8931 (t) cc_final: 0.8625 (t) REVERT: E 474 ASP cc_start: 0.8540 (t0) cc_final: 0.8280 (p0) REVERT: E 599 TRP cc_start: 0.8995 (m100) cc_final: 0.8680 (m100) REVERT: F 454 LEU cc_start: 0.8124 (tp) cc_final: 0.7760 (tt) REVERT: F 538 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7971 (tm-30) REVERT: F 558 GLU cc_start: 0.8711 (tt0) cc_final: 0.8495 (tp30) REVERT: F 561 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7800 (tm-30) outliers start: 10 outliers final: 7 residues processed: 282 average time/residue: 0.4635 time to fit residues: 181.8028 Evaluate side-chains 273 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 266 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain E residue 594 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 ASN F 555 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.063739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.049798 restraints weight = 124316.296| |-----------------------------------------------------------------------------| r_work (start): 0.2465 rms_B_bonded: 1.74 r_work: 0.2366 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2258 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18712 Z= 0.180 Angle : 0.585 6.687 25364 Z= 0.323 Chirality : 0.037 0.185 2800 Planarity : 0.005 0.063 3079 Dihedral : 13.949 168.533 2822 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.52 % Allowed : 7.33 % Favored : 92.16 % 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: 0.24 (0.17), residues: 2160 helix: 0.74 (0.14), residues: 1294 sheet: 0.78 (0.49), residues: 109 loop : -0.85 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 548 TYR 0.020 0.002 TYR B 314 PHE 0.015 0.001 PHE E 327 TRP 0.010 0.001 TRP D 387 HIS 0.004 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00414 (18712) covalent geometry : angle 0.58490 (25364) hydrogen bonds : bond 0.05205 ( 1008) hydrogen bonds : angle 4.70298 ( 2896) *********************** 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 283 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 273 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8534 (p90) cc_final: 0.7900 (p90) REVERT: A 353 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8883 (mp) REVERT: A 548 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.8484 (mtm-85) REVERT: B 484 ASP cc_start: 0.8927 (t0) cc_final: 0.8609 (t0) REVERT: C 412 MET cc_start: 0.8787 (mmp) cc_final: 0.8252 (mmp) REVERT: C 614 LYS cc_start: 0.8772 (tppt) cc_final: 0.8228 (ttpt) REVERT: D 484 ASP cc_start: 0.8729 (t0) cc_final: 0.8307 (t0) REVERT: E 396 CYS cc_start: 0.8908 (t) cc_final: 0.8575 (t) REVERT: E 412 MET cc_start: 0.8907 (mmp) cc_final: 0.8446 (mmp) REVERT: E 474 ASP cc_start: 0.8527 (t0) cc_final: 0.8289 (p0) REVERT: E 599 TRP cc_start: 0.9001 (m100) cc_final: 0.8681 (m100) REVERT: F 454 LEU cc_start: 0.8081 (tp) cc_final: 0.7776 (tt) REVERT: F 511 LYS cc_start: 0.8919 (tttt) cc_final: 0.8533 (ttmm) REVERT: F 538 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7921 (tm-30) outliers start: 10 outliers final: 8 residues processed: 278 average time/residue: 0.4734 time to fit residues: 182.5504 Evaluate side-chains 276 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 267 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain E residue 410 LYS Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 553 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 75 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 0.0040 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.063529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.049134 restraints weight = 122717.044| |-----------------------------------------------------------------------------| r_work (start): 0.2479 rms_B_bonded: 1.83 r_work: 0.2376 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2259 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18712 Z= 0.143 Angle : 0.551 6.667 25364 Z= 0.303 Chirality : 0.036 0.175 2800 Planarity : 0.004 0.053 3079 Dihedral : 13.700 164.999 2822 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.62 % Allowed : 7.79 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.17), residues: 2160 helix: 1.00 (0.14), residues: 1294 sheet: 0.41 (0.47), residues: 125 loop : -0.79 (0.19), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 548 TYR 0.020 0.001 TYR C 314 PHE 0.013 0.001 PHE E 327 TRP 0.009 0.001 TRP D 387 HIS 0.004 0.001 HIS E 555 Details of bonding type rmsd covalent geometry : bond 0.00322 (18712) covalent geometry : angle 0.55063 (25364) hydrogen bonds : bond 0.04714 ( 1008) hydrogen bonds : angle 4.54396 ( 2896) *********************** 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 280 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 268 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8091 (p90) cc_final: 0.7829 (p90) REVERT: A 353 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8864 (mp) REVERT: A 548 ARG cc_start: 0.8848 (ttm-80) cc_final: 0.8520 (mtm-85) REVERT: B 484 ASP cc_start: 0.8901 (t0) cc_final: 0.8586 (t0) REVERT: C 412 MET cc_start: 0.8749 (mmp) cc_final: 0.8357 (mmt) REVERT: C 614 LYS cc_start: 0.8781 (tppt) cc_final: 0.8232 (ttpt) REVERT: D 484 ASP cc_start: 0.8715 (t0) cc_final: 0.8313 (t0) REVERT: E 396 CYS cc_start: 0.8952 (t) cc_final: 0.8643 (t) REVERT: E 412 MET cc_start: 0.8937 (mmp) cc_final: 0.8367 (mmp) REVERT: E 420 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.6799 (ttp80) REVERT: E 474 ASP cc_start: 0.8502 (t0) cc_final: 0.8271 (p0) REVERT: E 599 TRP cc_start: 0.8979 (m100) cc_final: 0.8661 (m100) REVERT: F 353 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8735 (mp) REVERT: F 454 LEU cc_start: 0.8078 (tp) cc_final: 0.7822 (tt) REVERT: F 466 ASP cc_start: 0.7627 (m-30) cc_final: 0.7315 (m-30) REVERT: F 511 LYS cc_start: 0.8941 (tttt) cc_final: 0.8533 (ttmm) REVERT: F 538 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7877 (tm-30) outliers start: 12 outliers final: 8 residues processed: 272 average time/residue: 0.4880 time to fit residues: 183.7769 Evaluate side-chains 275 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 264 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 410 LYS Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 530 GLU Chi-restraints excluded: chain E residue 553 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 79 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.2813 r_free = 0.2813 target = 0.063603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.049744 restraints weight = 124906.171| |-----------------------------------------------------------------------------| r_work (start): 0.2463 rms_B_bonded: 1.73 r_work: 0.2364 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2251 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18712 Z= 0.179 Angle : 0.561 6.427 25364 Z= 0.308 Chirality : 0.036 0.181 2800 Planarity : 0.004 0.048 3079 Dihedral : 13.681 166.151 2822 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.62 % Allowed : 7.84 % Favored : 91.54 % 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: 0.53 (0.17), residues: 2160 helix: 1.05 (0.14), residues: 1294 sheet: 0.44 (0.47), residues: 125 loop : -0.83 (0.19), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 559 TYR 0.019 0.002 TYR C 314 PHE 0.015 0.001 PHE E 327 TRP 0.010 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00413 (18712) covalent geometry : angle 0.56105 (25364) hydrogen bonds : bond 0.04868 ( 1008) hydrogen bonds : angle 4.51586 ( 2896) *********************** 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 281 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8063 (p90) cc_final: 0.7820 (p90) REVERT: A 353 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8876 (mp) REVERT: A 548 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8508 (mtm-85) REVERT: B 484 ASP cc_start: 0.8881 (t0) cc_final: 0.8558 (t0) REVERT: C 412 MET cc_start: 0.8761 (mmp) cc_final: 0.8369 (mmt) REVERT: C 614 LYS cc_start: 0.8785 (tppt) cc_final: 0.8246 (ttpt) REVERT: D 484 ASP cc_start: 0.8725 (t0) cc_final: 0.8311 (t0) REVERT: E 412 MET cc_start: 0.8938 (mmp) cc_final: 0.8430 (mmp) REVERT: E 420 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.6809 (ttp80) REVERT: E 474 ASP cc_start: 0.8482 (t0) cc_final: 0.8224 (p0) REVERT: F 353 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8730 (mp) REVERT: F 412 MET cc_start: 0.7901 (mmt) cc_final: 0.7523 (mmt) REVERT: F 454 LEU cc_start: 0.8086 (tp) cc_final: 0.7853 (tt) REVERT: F 466 ASP cc_start: 0.7575 (m-30) cc_final: 0.7317 (m-30) REVERT: F 538 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7995 (tm-30) outliers start: 12 outliers final: 6 residues processed: 272 average time/residue: 0.4759 time to fit residues: 179.7152 Evaluate side-chains 274 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 265 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 217 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.062145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.047808 restraints weight = 123387.445| |-----------------------------------------------------------------------------| r_work (start): 0.2422 rms_B_bonded: 1.80 r_work: 0.2315 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2198 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18712 Z= 0.221 Angle : 0.588 6.736 25364 Z= 0.323 Chirality : 0.038 0.186 2800 Planarity : 0.004 0.053 3079 Dihedral : 13.753 166.910 2822 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.67 % Allowed : 8.31 % Favored : 91.02 % 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: 0.42 (0.17), residues: 2160 helix: 0.94 (0.14), residues: 1288 sheet: 0.42 (0.47), residues: 125 loop : -0.82 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 420 TYR 0.020 0.002 TYR E 314 PHE 0.031 0.002 PHE C 299 TRP 0.011 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00516 (18712) covalent geometry : angle 0.58843 (25364) hydrogen bonds : bond 0.05185 ( 1008) hydrogen bonds : angle 4.58217 ( 2896) *********************** 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 286 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 273 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (mp) REVERT: A 548 ARG cc_start: 0.8929 (ttm-80) cc_final: 0.8547 (mtm-85) REVERT: B 484 ASP cc_start: 0.8898 (t0) cc_final: 0.8576 (t0) REVERT: C 412 MET cc_start: 0.8794 (mmp) cc_final: 0.8411 (mmt) REVERT: C 614 LYS cc_start: 0.8712 (tppt) cc_final: 0.8178 (ttpt) REVERT: D 484 ASP cc_start: 0.8816 (t0) cc_final: 0.8381 (t0) REVERT: E 412 MET cc_start: 0.8938 (mmp) cc_final: 0.8410 (mmp) REVERT: E 420 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.6752 (ttp80) REVERT: E 474 ASP cc_start: 0.8619 (t0) cc_final: 0.8213 (p0) REVERT: F 353 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8710 (mp) REVERT: F 412 MET cc_start: 0.8075 (mmt) cc_final: 0.7682 (mmt) REVERT: F 454 LEU cc_start: 0.8116 (tp) cc_final: 0.7878 (tt) REVERT: F 538 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8033 (tm-30) outliers start: 13 outliers final: 10 residues processed: 278 average time/residue: 0.4250 time to fit residues: 164.4257 Evaluate side-chains 281 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 268 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 183 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN E 555 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.062583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.048262 restraints weight = 123614.570| |-----------------------------------------------------------------------------| r_work (start): 0.2452 rms_B_bonded: 1.80 r_work: 0.2351 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2243 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18712 Z= 0.169 Angle : 0.563 6.979 25364 Z= 0.309 Chirality : 0.036 0.179 2800 Planarity : 0.004 0.053 3079 Dihedral : 13.611 164.187 2822 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.77 % Allowed : 8.57 % Favored : 90.66 % 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: 0.52 (0.17), residues: 2160 helix: 1.06 (0.14), residues: 1303 sheet: 0.24 (0.45), residues: 133 loop : -0.86 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 559 TYR 0.019 0.002 TYR C 314 PHE 0.027 0.002 PHE C 617 TRP 0.010 0.001 TRP D 387 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00391 (18712) covalent geometry : angle 0.56329 (25364) hydrogen bonds : bond 0.04800 ( 1008) hydrogen bonds : angle 4.51387 ( 2896) *********************** 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 284 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 269 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8881 (mp) REVERT: A 548 ARG cc_start: 0.8882 (ttm-80) cc_final: 0.8524 (mtm-85) REVERT: B 484 ASP cc_start: 0.8903 (t0) cc_final: 0.8586 (t0) REVERT: C 412 MET cc_start: 0.8778 (mmp) cc_final: 0.8363 (mmt) REVERT: C 614 LYS cc_start: 0.8746 (tppt) cc_final: 0.8214 (ttpt) REVERT: D 484 ASP cc_start: 0.8748 (t0) cc_final: 0.8334 (t0) REVERT: E 412 MET cc_start: 0.8931 (mmp) cc_final: 0.8445 (mmp) REVERT: E 420 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.6815 (ttp80) REVERT: E 474 ASP cc_start: 0.8462 (t0) cc_final: 0.8208 (p0) REVERT: F 353 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8748 (mp) REVERT: F 412 MET cc_start: 0.7991 (mmt) cc_final: 0.7641 (mmt) REVERT: F 454 LEU cc_start: 0.8085 (tp) cc_final: 0.7865 (tt) REVERT: F 538 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8056 (tm-30) outliers start: 15 outliers final: 7 residues processed: 275 average time/residue: 0.3759 time to fit residues: 144.9201 Evaluate side-chains 279 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 269 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 410 LYS Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 144 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN E 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.062150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.047728 restraints weight = 124163.006| |-----------------------------------------------------------------------------| r_work (start): 0.2429 rms_B_bonded: 1.82 r_work: 0.2322 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2204 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18712 Z= 0.192 Angle : 0.576 7.345 25364 Z= 0.314 Chirality : 0.037 0.180 2800 Planarity : 0.004 0.060 3079 Dihedral : 13.585 164.764 2822 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.57 % Allowed : 8.93 % Favored : 90.51 % 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 aren not related in a simple way. whole: 0.50 (0.17), residues: 2160 helix: 1.04 (0.14), residues: 1303 sheet: 0.23 (0.45), residues: 133 loop : -0.86 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.018 0.002 TYR C 314 PHE 0.021 0.002 PHE E 299 TRP 0.011 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00448 (18712) covalent geometry : angle 0.57556 (25364) hydrogen bonds : bond 0.04906 ( 1008) hydrogen bonds : angle 4.51543 ( 2896) *********************** 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 284 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 273 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7970 (p90) cc_final: 0.7661 (p90) REVERT: A 353 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8855 (mp) REVERT: A 548 ARG cc_start: 0.8920 (ttm-80) cc_final: 0.8541 (mtm-85) REVERT: B 484 ASP cc_start: 0.8896 (t0) cc_final: 0.8578 (t0) REVERT: C 412 MET cc_start: 0.8763 (mmp) cc_final: 0.8342 (mmt) REVERT: C 614 LYS cc_start: 0.8721 (tppt) cc_final: 0.8184 (ttpt) REVERT: D 484 ASP cc_start: 0.8794 (t0) cc_final: 0.8360 (t0) REVERT: E 412 MET cc_start: 0.8931 (mmp) cc_final: 0.8423 (mmp) REVERT: E 420 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.6763 (ttp80) REVERT: E 474 ASP cc_start: 0.8592 (t0) cc_final: 0.8221 (p0) REVERT: F 353 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8710 (mp) REVERT: F 412 MET cc_start: 0.8047 (mmt) cc_final: 0.7691 (mmt) REVERT: F 454 LEU cc_start: 0.8065 (tp) cc_final: 0.7849 (tt) REVERT: F 511 LYS cc_start: 0.8950 (tttt) cc_final: 0.8584 (ttmm) REVERT: F 538 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8052 (tm-30) outliers start: 11 outliers final: 8 residues processed: 277 average time/residue: 0.3784 time to fit residues: 145.9484 Evaluate side-chains 280 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 269 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.062458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.048097 restraints weight = 124260.480| |-----------------------------------------------------------------------------| r_work (start): 0.2432 rms_B_bonded: 1.83 r_work: 0.2329 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2217 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 18712 Z= 0.185 Angle : 0.735 59.193 25364 Z= 0.423 Chirality : 0.036 0.180 2800 Planarity : 0.004 0.058 3079 Dihedral : 13.574 164.572 2822 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.62 % Allowed : 8.93 % Favored : 90.45 % 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: 0.52 (0.17), residues: 2160 helix: 1.06 (0.14), residues: 1303 sheet: 0.23 (0.45), residues: 133 loop : -0.86 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.019 0.001 TYR C 314 PHE 0.018 0.001 PHE C 299 TRP 0.011 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00422 (18712) covalent geometry : angle 0.73467 (25364) hydrogen bonds : bond 0.04825 ( 1008) hydrogen bonds : angle 4.50280 ( 2896) ********************** 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 281 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 353 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8847 (mp) REVERT: A 548 ARG cc_start: 0.8929 (ttm-80) cc_final: 0.8561 (mtm-85) REVERT: B 484 ASP cc_start: 0.8870 (t0) cc_final: 0.8556 (t0) REVERT: C 412 MET cc_start: 0.8753 (mmp) cc_final: 0.8331 (mmt) REVERT: C 614 LYS cc_start: 0.8755 (tppt) cc_final: 0.8201 (ttpt) REVERT: D 484 ASP cc_start: 0.8770 (t0) cc_final: 0.8335 (t0) REVERT: E 412 MET cc_start: 0.8923 (mmp) cc_final: 0.8412 (mmp) REVERT: E 474 ASP cc_start: 0.8583 (t0) cc_final: 0.8225 (p0) REVERT: F 353 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8716 (mp) REVERT: F 412 MET cc_start: 0.8036 (mmt) cc_final: 0.7679 (mmt) REVERT: F 454 LEU cc_start: 0.8069 (tp) cc_final: 0.7845 (tt) REVERT: F 511 LYS cc_start: 0.8984 (tttt) cc_final: 0.8632 (ttmm) REVERT: F 538 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8058 (tm-30) outliers start: 12 outliers final: 9 residues processed: 273 average time/residue: 0.3732 time to fit residues: 142.7038 Evaluate side-chains 280 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 269 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 581 TRP Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 605 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 192 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.062297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.047911 restraints weight = 123424.991| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 1.81 r_work: 0.2330 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2213 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 18712 Z= 0.171 Angle : 0.732 59.198 25364 Z= 0.421 Chirality : 0.036 0.179 2800 Planarity : 0.004 0.059 3079 Dihedral : 13.572 164.544 2822 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.57 % Allowed : 9.03 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.17), residues: 2160 helix: 1.07 (0.14), residues: 1303 sheet: 0.22 (0.45), residues: 133 loop : -0.86 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 420 TYR 0.018 0.001 TYR C 314 PHE 0.016 0.001 PHE C 299 TRP 0.011 0.001 TRP D 387 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00395 (18712) covalent geometry : angle 0.73188 (25364) hydrogen bonds : bond 0.04797 ( 1008) hydrogen bonds : angle 4.50327 ( 2896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8101.57 seconds wall clock time: 138 minutes 36.22 seconds (8316.22 seconds total)