Starting phenix.real_space_refine on Mon Jul 6 15:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kae_62206/07_2026/9kae_62206_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kae_62206/07_2026/9kae_62206.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/9kae_62206/07_2026/9kae_62206_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kae_62206/07_2026/9kae_62206_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kae_62206/07_2026/9kae_62206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kae_62206/07_2026/9kae_62206.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= -0.004 sd= 0.577 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 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.72, per 1000 atoms: 0.18 Number of scatterers: 36491 At special positions: 0 Unit cell: (99.51, 130.2, 141.36, 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: 3.53 Conformation dependent library (CDL) restraints added in 981.6 milliseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 12 sheets defined 69.5% alpha, 7.0% beta 10 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'A' and resid 269 through 281 removed outlier: 3.613A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.871A 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 Processing helix chain 'A' and resid 316 through 330 removed outlier: 5.165A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 355 Processing helix chain 'A' and resid 356 through 376 Processing helix chain 'A' and resid 383 through 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: 3.797A pdb=" N GLU A 460 " --> pdb=" O ARG A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 589 through 607 removed outlier: 4.285A pdb=" N SER A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 622 removed outlier: 3.609A pdb=" N TYR A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.729A 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 298 through 301 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: 5.279A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 355 Processing helix chain 'B' and resid 356 through 376 Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.547A pdb=" N LEU B 397 " --> pdb=" O TRP B 393 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 415 Processing helix chain 'B' and resid 431 through 444 Processing helix chain 'B' and resid 456 through 462 removed outlier: 3.851A 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 removed outlier: 3.925A pdb=" N GLY B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 561 through 566 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: 4.378A pdb=" N SER B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.576A pdb=" N VAL C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 298 through 301 removed outlier: 3.591A pdb=" N MET C 301 " --> pdb=" O SER C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 310 through 329 removed outlier: 3.667A pdb=" N TYR C 314 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLU C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LYS C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ALA C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.696A 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: 4.102A 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 removed outlier: 3.702A pdb=" N GLU C 460 " --> pdb=" O ARG C 456 " (cutoff:3.500A) 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 removed outlier: 3.542A pdb=" N LEU C 497 " --> pdb=" O ASN C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 503 removed outlier: 3.668A pdb=" N GLY C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 550 through 560 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 589 through 607 removed outlier: 4.525A pdb=" N SER C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 598 " --> pdb=" O SER C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 621 removed outlier: 3.512A pdb=" N MET C 621 " --> pdb=" O PHE C 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.616A 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: 3.797A 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: 5.142A pdb=" N ALA D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 5.356A 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: 3.709A 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 398 removed outlier: 4.220A pdb=" N LEU D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 456 through 462 removed outlier: 3.698A pdb=" N GLU D 460 " --> pdb=" O ARG D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 480 through 484 Processing helix chain 'D' and resid 489 through 497 Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 561 through 566 Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.523A 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 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 592 through 607 Processing helix chain 'D' and resid 608 through 621 Processing helix chain 'E' and resid 269 through 281 removed outlier: 3.721A pdb=" N VAL E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 295 through 297 No H-bonds generated for 'chain 'E' and resid 295 through 297' Processing helix chain 'E' and resid 302 through 308 Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 316 through 330 removed outlier: 5.356A pdb=" N ALA E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN E 323 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 355 Processing helix chain 'E' and resid 356 through 376 Processing helix chain 'E' and resid 383 through 398 removed outlier: 3.754A pdb=" N TRP E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 415 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 456 through 462 removed outlier: 3.728A pdb=" N GLY E 462 " --> pdb=" O ASN E 458 " (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 484 removed outlier: 4.344A pdb=" N GLU E 481 " --> pdb=" O THR E 478 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER E 482 " --> pdb=" O GLY E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 497 removed outlier: 3.502A pdb=" N LEU E 497 " --> pdb=" O ASN E 493 " (cutoff:3.500A) 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 558 Processing helix chain 'E' and resid 561 through 566 removed outlier: 3.853A pdb=" N GLU E 565 " --> pdb=" O GLU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.577A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 588 Processing helix chain 'E' and resid 592 through 607 removed outlier: 3.600A pdb=" N GLU E 598 " --> pdb=" O SER E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 621 removed outlier: 3.567A pdb=" N TYR E 612 " --> pdb=" O SER E 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.763A 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: 3.562A 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 328 removed outlier: 4.885A pdb=" N ALA F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN F 323 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 355 Processing helix chain 'F' and resid 356 through 376 Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.634A pdb=" N LEU F 397 " --> pdb=" O TRP F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 415 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 456 through 462 removed outlier: 4.274A pdb=" N GLU F 460 " --> pdb=" O ARG F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 479 through 484 removed outlier: 4.066A pdb=" N SER F 482 " --> pdb=" O GLY F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 497 Processing helix chain 'F' and resid 497 through 502 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 550 through 559 removed outlier: 3.517A pdb=" N LYS F 554 " --> pdb=" O LYS F 550 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS F 555 " --> pdb=" O ASP F 551 " (cutoff:3.500A) 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 589 through 605 removed outlier: 4.383A pdb=" N SER F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG F 595 " --> pdb=" O SER F 591 " (cutoff:3.500A) removed outlier: 3.940A 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: 6.833A pdb=" N TYR A 421 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 543 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 507 through 509 Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 448 removed outlier: 7.192A pdb=" N TYR B 421 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE B 545 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 423 " --> pdb=" O ILE B 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 507 through 509 Processing sheet with id=AA5, first strand: chain 'C' and resid 445 through 448 removed outlier: 7.282A pdb=" N TYR C 421 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE C 545 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.584A 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: 7.449A pdb=" N TYR D 421 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ILE D 545 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU D 423 " --> pdb=" O ILE D 545 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 507 through 509 Processing sheet with id=AA9, first strand: chain 'E' and resid 445 through 448 removed outlier: 7.241A pdb=" N TYR E 421 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ILE E 545 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU E 423 " --> pdb=" O ILE E 545 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 507 through 509 Processing sheet with id=AB2, first strand: chain 'F' and resid 446 through 448 removed outlier: 7.764A pdb=" N TYR F 421 " --> pdb=" O VAL F 542 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN F 544 " --> pdb=" O TYR F 421 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 423 " --> pdb=" O GLN F 544 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASP F 546 " --> pdb=" O LEU F 423 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS F 425 " --> pdb=" O ASP F 546 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 507 through 509 989 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: 9.04 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18155 1.03 - 1.22: 115 1.22 - 1.42: 7631 1.42 - 1.62: 10800 1.62 - 1.81: 208 Bond restraints: 36909 Sorted by residual: bond pdb=" N3B ANP E 800 " pdb=" PG ANP E 800 " ideal model delta sigma weight residual 1.795 1.611 0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" N3B ANP C 802 " pdb=" PG ANP C 802 " ideal model delta sigma weight residual 1.795 1.613 0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" N3B ANP D 802 " pdb=" PG ANP D 802 " 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 F 800 " pdb=" PG ANP F 800 " ideal model delta sigma weight residual 1.795 1.614 0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" N3B ANP B 802 " pdb=" PG ANP B 802 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.63e+01 ... (remaining 36904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 65144 2.16 - 4.32: 1607 4.32 - 6.48: 123 6.48 - 8.65: 12 8.65 - 10.81: 7 Bond angle restraints: 66893 Sorted by residual: angle pdb=" N3 DT T 0 " pdb=" C4 DT T 0 " pdb=" O4 DT T 0 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" O4 DT T 0 " pdb=" C4 DT T 0 " pdb=" C5 DT T 0 " ideal model delta sigma weight residual 124.90 121.83 3.07 7.00e-01 2.04e+00 1.92e+01 angle pdb=" N GLY E 524 " pdb=" CA GLY E 524 " pdb=" C GLY E 524 " ideal model delta sigma weight residual 111.19 117.45 -6.26 1.45e+00 4.76e-01 1.86e+01 angle pdb=" N3 DT T 1 " pdb=" C4 DT T 1 " pdb=" O4 DT T 1 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N PRO A 522 " pdb=" CA PRO A 522 " pdb=" C PRO A 522 " ideal model delta sigma weight residual 110.47 114.54 -4.07 9.60e-01 1.09e+00 1.80e+01 ... (remaining 66888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.69: 16332 31.69 - 63.37: 724 63.37 - 95.06: 122 95.06 - 126.75: 0 126.75 - 158.44: 2 Dihedral angle restraints: 17180 sinusoidal: 9643 harmonic: 7537 Sorted by residual: dihedral pdb=" CA ASN A 332 " pdb=" C ASN A 332 " pdb=" N GLN A 333 " pdb=" CA GLN A 333 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LEU A 469 " pdb=" C LEU A 469 " pdb=" N VAL A 470 " pdb=" CA VAL A 470 " ideal model delta harmonic sigma weight residual 180.00 151.06 28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASP A 495 " pdb=" C ASP A 495 " pdb=" N ASN A 496 " pdb=" CA ASN A 496 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 17177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2411 0.081 - 0.162: 351 0.162 - 0.242: 30 0.242 - 0.323: 6 0.323 - 0.404: 2 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C3' DA P 1 " pdb=" C4' DA P 1 " pdb=" O3' DA P 1 " pdb=" C2' DA P 1 " both_signs ideal model delta sigma weight residual False -2.73 -2.33 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C3' ANP E 800 " pdb=" C2' ANP E 800 " pdb=" C4' ANP E 800 " pdb=" O3' ANP E 800 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.77e+00 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 -2.68 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2797 not shown) Planarity restraints: 5189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP F 800 " 0.198 2.00e-02 2.50e+03 8.28e-02 1.88e+02 pdb=" C2 ANP F 800 " -0.018 2.00e-02 2.50e+03 pdb=" C4 ANP F 800 " -0.072 2.00e-02 2.50e+03 pdb=" C5 ANP F 800 " -0.054 2.00e-02 2.50e+03 pdb=" C6 ANP F 800 " 0.006 2.00e-02 2.50e+03 pdb=" C8 ANP F 800 " -0.045 2.00e-02 2.50e+03 pdb=" N1 ANP F 800 " 0.027 2.00e-02 2.50e+03 pdb=" N3 ANP F 800 " -0.062 2.00e-02 2.50e+03 pdb=" N6 ANP F 800 " 0.125 2.00e-02 2.50e+03 pdb=" N7 ANP F 800 " -0.047 2.00e-02 2.50e+03 pdb=" N9 ANP F 800 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP D 802 " 0.135 2.00e-02 2.50e+03 5.75e-02 9.10e+01 pdb=" C2 ANP D 802 " -0.002 2.00e-02 2.50e+03 pdb=" C4 ANP D 802 " -0.058 2.00e-02 2.50e+03 pdb=" C5 ANP D 802 " -0.046 2.00e-02 2.50e+03 pdb=" C6 ANP D 802 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ANP D 802 " -0.020 2.00e-02 2.50e+03 pdb=" N1 ANP D 802 " 0.032 2.00e-02 2.50e+03 pdb=" N3 ANP D 802 " -0.051 2.00e-02 2.50e+03 pdb=" N6 ANP D 802 " 0.080 2.00e-02 2.50e+03 pdb=" N7 ANP D 802 " -0.025 2.00e-02 2.50e+03 pdb=" N9 ANP D 802 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP A 800 " 0.133 2.00e-02 2.50e+03 5.70e-02 8.93e+01 pdb=" C2 ANP A 800 " -0.007 2.00e-02 2.50e+03 pdb=" C4 ANP A 800 " -0.056 2.00e-02 2.50e+03 pdb=" C5 ANP A 800 " -0.044 2.00e-02 2.50e+03 pdb=" C6 ANP A 800 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ANP A 800 " -0.020 2.00e-02 2.50e+03 pdb=" N1 ANP A 800 " 0.023 2.00e-02 2.50e+03 pdb=" N3 ANP A 800 " -0.043 2.00e-02 2.50e+03 pdb=" N6 ANP A 800 " 0.087 2.00e-02 2.50e+03 pdb=" N7 ANP A 800 " -0.030 2.00e-02 2.50e+03 pdb=" N9 ANP A 800 " -0.040 2.00e-02 2.50e+03 ... (remaining 5186 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 415 2.02 - 2.67: 51883 2.67 - 3.31: 108664 3.31 - 3.96: 138060 3.96 - 4.60: 222371 Nonbonded interactions: 521393 Sorted by model distance: nonbonded pdb=" O2B ANP E 800 " pdb="MG MG E 801 " model vdw 1.378 2.050 nonbonded pdb=" HH TYR F 406 " pdb=" OE1 GLU F 587 " model vdw 1.501 2.450 nonbonded pdb=" HG1 THR E 433 " pdb=" O2B ANP E 800 " model vdw 1.567 2.450 nonbonded pdb="HH22 ARG A 420 " pdb=" O PHE A 521 " model vdw 1.592 2.450 nonbonded pdb=" HG1 THR F 335 " pdb=" OP2 DA P 7 " model vdw 1.624 2.450 ... (remaining 521388 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: 0.120 Set scattering table: 0.100 Process input model: 40.510 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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 : 0.008 0.184 18712 Z= 0.395 Angle : 1.016 10.807 25364 Z= 0.608 Chirality : 0.059 0.404 2800 Planarity : 0.012 0.179 3079 Dihedral : 15.215 158.437 7274 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.16), residues: 2160 helix: -0.84 (0.12), residues: 1303 sheet: 0.31 (0.45), residues: 133 loop : -0.51 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 456 TYR 0.038 0.007 TYR D 552 PHE 0.029 0.004 PHE F 607 TRP 0.028 0.005 TRP E 599 HIS 0.014 0.004 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.40 (18712) covalent geometry : angle 1.01607 / 0.61 (25364) hydrogen bonds : bond 0.18416 / 12.12 ( 1009) hydrogen bonds : angle 7.01653 / 5.02 ( 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 395 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.092 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: symmetry clash REVERT: B 570 GLN cc_start: 0.8469 (mt0) cc_final: 0.8210 (mt0) REVERT: D 278 MET cc_start: 0.9127 (mmm) cc_final: 0.8847 (mmm) REVERT: E 552 TYR cc_start: 0.8624 (p90) cc_final: 0.7949 (p90) REVERT: E 553 LEU cc_start: 0.8964 (mt) cc_final: 0.8682 (mp) REVERT: F 415 ASN cc_start: 0.8671 (t0) cc_final: 0.8448 (t0) REVERT: F 511 LYS cc_start: 0.8943 (tttt) cc_final: 0.8440 (ttpp) REVERT: F 558 GLU cc_start: 0.8567 (tt0) cc_final: 0.8353 (tp30) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.4586 time to fit residues: 251.3122 Evaluate side-chains 314 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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: 0.5980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN B 354 GLN D 458 ASN D 496 ASN E 323 ASN F 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.063041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.049437 restraints weight = 120150.909| |-----------------------------------------------------------------------------| r_work (start): 0.2406 rms_B_bonded: 1.66 r_work: 0.2305 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2194 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18712 Z= 0.188 Angle : 0.726 7.799 25364 Z= 0.395 Chirality : 0.040 0.242 2800 Planarity : 0.006 0.077 3079 Dihedral : 14.343 166.184 2822 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.67 % Allowed : 5.52 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2160 helix: 0.09 (0.14), residues: 1315 sheet: 0.44 (0.46), residues: 122 loop : -0.58 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 371 TYR 0.029 0.002 TYR E 314 PHE 0.019 0.002 PHE D 617 TRP 0.018 0.002 TRP E 599 HIS 0.009 0.002 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (18712) covalent geometry : angle 0.72595 / 0.39 (25364) hydrogen bonds : bond 0.06547 / 4.30 ( 1009) hydrogen bonds : angle 5.52633 / 3.97 ( 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 334 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 321 time to evaluate : 1.043 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: B 412 MET cc_start: 0.8683 (mmt) cc_final: 0.8305 (mmt) REVERT: C 412 MET cc_start: 0.9059 (mmp) cc_final: 0.8259 (mmp) REVERT: C 484 ASP cc_start: 0.8605 (t0) cc_final: 0.8321 (t0) REVERT: D 298 SER cc_start: 0.9176 (m) cc_final: 0.8761 (p) REVERT: D 498 ARG cc_start: 0.8490 (tmt-80) cc_final: 0.8287 (ttt-90) REVERT: D 559 ARG cc_start: 0.8793 (ttm-80) cc_final: 0.8461 (mtt-85) REVERT: D 590 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8979 (mm-40) REVERT: E 451 ASN cc_start: 0.7349 (m-40) cc_final: 0.7145 (m110) REVERT: E 484 ASP cc_start: 0.8413 (t0) cc_final: 0.8185 (t0) REVERT: F 300 GLU cc_start: 0.8313 (pp20) cc_final: 0.7987 (pp20) REVERT: F 415 ASN cc_start: 0.8541 (t0) cc_final: 0.8282 (t0) REVERT: F 511 LYS cc_start: 0.8836 (tttt) cc_final: 0.8586 (ttpp) REVERT: F 538 GLN cc_start: 0.9061 (tp-100) cc_final: 0.8856 (tp40) REVERT: F 558 GLU cc_start: 0.8655 (tt0) cc_final: 0.8326 (tp30) outliers start: 13 outliers final: 5 residues processed: 326 average time/residue: 0.4596 time to fit residues: 208.0712 Evaluate side-chains 308 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 303 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 619 VAL 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: 2.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.060624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.047062 restraints weight = 120960.897| |-----------------------------------------------------------------------------| r_work (start): 0.2349 rms_B_bonded: 1.64 r_work: 0.2249 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2137 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 18712 Z= 0.319 Angle : 0.732 6.224 25364 Z= 0.402 Chirality : 0.043 0.272 2800 Planarity : 0.006 0.099 3079 Dihedral : 14.203 174.628 2822 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.98 % Allowed : 6.97 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2160 helix: 0.13 (0.14), residues: 1311 sheet: 0.50 (0.46), residues: 123 loop : -0.83 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 517 TYR 0.024 0.002 TYR E 552 PHE 0.030 0.002 PHE C 617 TRP 0.016 0.002 TRP D 387 HIS 0.008 0.002 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.32 (18712) covalent geometry : angle 0.73153 / 0.40 (25364) hydrogen bonds : bond 0.06689 / 4.41 ( 1009) hydrogen bonds : angle 5.34490 / 3.85 ( 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 320 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 301 time to evaluate : 1.068 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: B 412 MET cc_start: 0.8889 (mmt) cc_final: 0.8532 (mmt) REVERT: B 548 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8516 (mtm110) REVERT: C 412 MET cc_start: 0.9094 (mmp) cc_final: 0.8161 (mmp) REVERT: C 484 ASP cc_start: 0.8652 (t0) cc_final: 0.8387 (t0) REVERT: D 559 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8438 (mtt-85) REVERT: E 484 ASP cc_start: 0.8532 (t0) cc_final: 0.8251 (t0) REVERT: E 552 TYR cc_start: 0.8534 (p90) cc_final: 0.8141 (p90) REVERT: F 300 GLU cc_start: 0.8316 (pp20) cc_final: 0.7457 (pp20) REVERT: F 558 GLU cc_start: 0.8652 (tt0) cc_final: 0.8349 (tp30) outliers start: 19 outliers final: 11 residues processed: 307 average time/residue: 0.4289 time to fit residues: 186.5885 Evaluate side-chains 305 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 294 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 590 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 36 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.062322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.048685 restraints weight = 119945.185| |-----------------------------------------------------------------------------| r_work (start): 0.2404 rms_B_bonded: 1.66 r_work: 0.2306 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2195 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18712 Z= 0.142 Angle : 0.604 8.323 25364 Z= 0.330 Chirality : 0.038 0.261 2800 Planarity : 0.005 0.067 3079 Dihedral : 13.771 165.320 2822 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.83 % Allowed : 8.15 % 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 are not related in a simple way. whole: 0.01 (0.17), residues: 2160 helix: 0.51 (0.14), residues: 1311 sheet: -0.05 (0.43), residues: 134 loop : -0.75 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 517 TYR 0.024 0.002 TYR E 314 PHE 0.032 0.002 PHE D 617 TRP 0.013 0.001 TRP E 599 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (18712) covalent geometry : angle 0.60419 / 0.33 (25364) hydrogen bonds : bond 0.05219 / 3.44 ( 1009) hydrogen bonds : angle 5.08943 / 3.66 ( 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 316 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 300 time to evaluate : 0.981 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: B 548 ARG cc_start: 0.8723 (ttm110) cc_final: 0.8461 (mtm110) REVERT: C 412 MET cc_start: 0.9063 (mmp) cc_final: 0.8153 (mmp) REVERT: C 484 ASP cc_start: 0.8616 (t0) cc_final: 0.8352 (t0) REVERT: D 298 SER cc_start: 0.9283 (m) cc_final: 0.8798 (p) REVERT: D 474 ASP cc_start: 0.8369 (t70) cc_final: 0.8135 (p0) REVERT: D 559 ARG cc_start: 0.8852 (ttm-80) cc_final: 0.8500 (mtt-85) REVERT: D 590 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: E 552 TYR cc_start: 0.8523 (p90) cc_final: 0.8135 (p90) REVERT: F 498 ARG cc_start: 0.7195 (ttm110) cc_final: 0.6862 (ttm110) REVERT: F 558 GLU cc_start: 0.8653 (tt0) cc_final: 0.8292 (tp30) outliers start: 16 outliers final: 11 residues processed: 308 average time/residue: 0.3926 time to fit residues: 171.3896 Evaluate side-chains 302 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 290 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 566 LYS Chi-restraints excluded: chain F residue 590 GLN 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: 1.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.061019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.047509 restraints weight = 120366.846| |-----------------------------------------------------------------------------| r_work (start): 0.2376 rms_B_bonded: 1.64 r_work: 0.2277 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2166 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18712 Z= 0.216 Angle : 0.617 6.850 25364 Z= 0.339 Chirality : 0.038 0.263 2800 Planarity : 0.005 0.065 3079 Dihedral : 13.811 168.449 2822 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.08 % Allowed : 8.36 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2160 helix: 0.58 (0.14), residues: 1312 sheet: -0.08 (0.43), residues: 134 loop : -0.80 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 517 TYR 0.021 0.002 TYR E 314 PHE 0.027 0.002 PHE C 617 TRP 0.013 0.001 TRP D 387 HIS 0.006 0.001 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (18712) covalent geometry : angle 0.61726 / 0.34 (25364) hydrogen bonds : bond 0.05421 / 3.57 ( 1009) hydrogen bonds : angle 5.01538 / 3.61 ( 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 309 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 288 time to evaluate : 0.945 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: B 412 MET cc_start: 0.8890 (mmt) cc_final: 0.8469 (mmt) REVERT: B 548 ARG cc_start: 0.8777 (ttm110) cc_final: 0.8484 (mtm110) REVERT: C 412 MET cc_start: 0.9077 (mmp) cc_final: 0.8128 (mmp) REVERT: D 559 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8434 (mtt-85) REVERT: D 590 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: E 552 TYR cc_start: 0.8570 (p90) cc_final: 0.8176 (p90) REVERT: E 601 GLU cc_start: 0.8489 (tp30) cc_final: 0.8214 (tp30) REVERT: F 558 GLU cc_start: 0.8632 (tt0) cc_final: 0.8318 (tp30) outliers start: 21 outliers final: 13 residues processed: 298 average time/residue: 0.4236 time to fit residues: 178.7316 Evaluate side-chains 306 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 292 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 546 ASP Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 566 LYS Chi-restraints excluded: chain F residue 590 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 79 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 513 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.061442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.047884 restraints weight = 121101.807| |-----------------------------------------------------------------------------| r_work (start): 0.2389 rms_B_bonded: 1.65 r_work: 0.2291 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2179 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18712 Z= 0.169 Angle : 0.581 6.375 25364 Z= 0.319 Chirality : 0.037 0.262 2800 Planarity : 0.005 0.061 3079 Dihedral : 13.713 165.954 2822 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.03 % Allowed : 8.62 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2160 helix: 0.69 (0.14), residues: 1319 sheet: -0.13 (0.44), residues: 134 loop : -0.94 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 483 TYR 0.020 0.002 TYR E 314 PHE 0.016 0.001 PHE A 299 TRP 0.012 0.001 TRP E 599 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (18712) covalent geometry : angle 0.58087 / 0.32 (25364) hydrogen bonds : bond 0.05013 / 3.30 ( 1009) hydrogen bonds : angle 4.90573 / 3.53 ( 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 317 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 1.067 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: B 300 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8305 (mm-30) REVERT: B 412 MET cc_start: 0.8878 (mmt) cc_final: 0.8476 (mmt) REVERT: B 548 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8479 (mtm110) REVERT: C 412 MET cc_start: 0.9069 (mmp) cc_final: 0.8152 (mmp) REVERT: C 484 ASP cc_start: 0.8521 (t0) cc_final: 0.8275 (t0) REVERT: D 559 ARG cc_start: 0.8845 (ttm-80) cc_final: 0.8423 (mtt-85) REVERT: D 590 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: E 601 GLU cc_start: 0.8517 (tp30) cc_final: 0.8236 (tp30) REVERT: F 558 GLU cc_start: 0.8620 (tt0) cc_final: 0.8328 (tp30) REVERT: F 559 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7911 (mtt-85) outliers start: 20 outliers final: 15 residues processed: 305 average time/residue: 0.4515 time to fit residues: 192.4460 Evaluate side-chains 302 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 286 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 604 ASP Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 566 LYS Chi-restraints excluded: chain F residue 590 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 217 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.060222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.046767 restraints weight = 121561.337| |-----------------------------------------------------------------------------| r_work (start): 0.2353 rms_B_bonded: 1.64 r_work: 0.2254 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2143 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 18712 Z= 0.277 Angle : 0.645 6.302 25364 Z= 0.353 Chirality : 0.040 0.266 2800 Planarity : 0.006 0.092 3079 Dihedral : 13.938 172.203 2822 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.08 % Allowed : 9.08 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2160 helix: 0.49 (0.14), residues: 1336 sheet: 0.00 (0.44), residues: 134 loop : -1.02 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 483 TYR 0.020 0.002 TYR A 552 PHE 0.029 0.002 PHE C 617 TRP 0.014 0.002 TRP D 387 HIS 0.007 0.001 HIS B 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.28 (18712) covalent geometry : angle 0.64541 / 0.35 (25364) hydrogen bonds : bond 0.05587 / 3.67 ( 1009) hydrogen bonds : angle 5.00388 / 3.62 ( 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 305 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 1.092 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: B 300 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8496 (mm-30) REVERT: B 412 MET cc_start: 0.8878 (mmt) cc_final: 0.8591 (mmt) REVERT: C 484 ASP cc_start: 0.8593 (t0) cc_final: 0.8356 (t0) REVERT: D 590 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: E 401 MET cc_start: 0.8622 (tpp) cc_final: 0.8396 (tpt) REVERT: E 552 TYR cc_start: 0.8527 (p90) cc_final: 0.7912 (p90) REVERT: E 601 GLU cc_start: 0.8525 (tp30) cc_final: 0.8248 (tp30) outliers start: 21 outliers final: 17 residues processed: 290 average time/residue: 0.4356 time to fit residues: 179.0234 Evaluate side-chains 307 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 289 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 546 ASP Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 566 LYS Chi-restraints excluded: chain F residue 590 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 183 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.060379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.046630 restraints weight = 119723.682| |-----------------------------------------------------------------------------| r_work (start): 0.2387 rms_B_bonded: 1.70 r_work: 0.2287 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2174 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18712 Z= 0.154 Angle : 0.583 10.016 25364 Z= 0.318 Chirality : 0.037 0.263 2800 Planarity : 0.005 0.071 3079 Dihedral : 13.723 166.348 2822 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.93 % Allowed : 9.29 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2160 helix: 0.74 (0.14), residues: 1320 sheet: -0.05 (0.44), residues: 133 loop : -0.94 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 483 TYR 0.021 0.002 TYR E 314 PHE 0.016 0.001 PHE F 617 TRP 0.012 0.001 TRP E 599 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18712) covalent geometry : angle 0.58258 / 0.32 (25364) hydrogen bonds : bond 0.04840 / 3.18 ( 1009) hydrogen bonds : angle 4.86169 / 3.52 ( 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 315 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 1.005 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: B 300 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8429 (mm-30) REVERT: B 412 MET cc_start: 0.8840 (mmt) cc_final: 0.8438 (mmt) REVERT: C 484 ASP cc_start: 0.8578 (t0) cc_final: 0.8344 (t0) REVERT: D 298 SER cc_start: 0.9303 (m) cc_final: 0.8779 (p) REVERT: D 590 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8350 (tm-30) REVERT: E 552 TYR cc_start: 0.8552 (p90) cc_final: 0.7902 (p90) REVERT: E 601 GLU cc_start: 0.8551 (tp30) cc_final: 0.8266 (tp30) REVERT: F 483 ARG cc_start: 0.8548 (mpp-170) cc_final: 0.8256 (mpp-170) outliers start: 18 outliers final: 15 residues processed: 302 average time/residue: 0.4381 time to fit residues: 185.3269 Evaluate side-chains 309 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 293 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 546 ASP Chi-restraints excluded: chain E residue 604 ASP Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 566 LYS 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: 3.9990 chunk 147 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.061137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.047676 restraints weight = 121935.040| |-----------------------------------------------------------------------------| r_work (start): 0.2383 rms_B_bonded: 1.65 r_work: 0.2284 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2173 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18712 Z= 0.179 Angle : 0.587 7.236 25364 Z= 0.320 Chirality : 0.037 0.263 2800 Planarity : 0.005 0.084 3079 Dihedral : 13.708 166.601 2822 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.98 % Allowed : 9.60 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2160 helix: 0.77 (0.14), residues: 1320 sheet: 0.00 (0.45), residues: 133 loop : -0.94 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 456 TYR 0.020 0.002 TYR B 552 PHE 0.021 0.001 PHE C 617 TRP 0.011 0.001 TRP D 387 HIS 0.005 0.001 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (18712) covalent geometry : angle 0.58654 / 0.32 (25364) hydrogen bonds : bond 0.04897 / 3.21 ( 1009) hydrogen bonds : angle 4.83919 / 3.50 ( 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 312 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 293 time to evaluate : 1.058 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: B 300 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8425 (mm-30) REVERT: B 412 MET cc_start: 0.8842 (mmt) cc_final: 0.8423 (mmt) REVERT: C 484 ASP cc_start: 0.8592 (t0) cc_final: 0.8337 (t0) REVERT: D 590 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: E 601 GLU cc_start: 0.8547 (tp30) cc_final: 0.8266 (tp30) REVERT: F 483 ARG cc_start: 0.8563 (mpp-170) cc_final: 0.8247 (mpp-170) outliers start: 19 outliers final: 15 residues processed: 299 average time/residue: 0.4401 time to fit residues: 184.3472 Evaluate side-chains 310 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 546 ASP Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 566 LYS Chi-restraints excluded: chain F residue 603 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.060416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.046724 restraints weight = 120316.782| |-----------------------------------------------------------------------------| r_work (start): 0.2392 rms_B_bonded: 1.70 r_work: 0.2292 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2181 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18712 Z= 0.152 Angle : 0.576 8.289 25364 Z= 0.314 Chirality : 0.037 0.261 2800 Planarity : 0.005 0.116 3079 Dihedral : 13.623 167.001 2822 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.88 % Allowed : 9.96 % Favored : 89.16 % 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 are not related in a simple way. whole: 0.28 (0.17), residues: 2160 helix: 0.84 (0.14), residues: 1316 sheet: 0.00 (0.45), residues: 133 loop : -0.90 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 483 TYR 0.020 0.002 TYR E 314 PHE 0.025 0.001 PHE D 617 TRP 0.011 0.001 TRP D 387 HIS 0.005 0.001 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (18712) covalent geometry : angle 0.57596 / 0.31 (25364) hydrogen bonds : bond 0.04661 / 3.05 ( 1009) hydrogen bonds : angle 4.78792 / 3.45 ( 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 313 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 296 time to evaluate : 1.088 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 489 GLN cc_start: 0.8234 (mt0) cc_final: 0.8032 (mt0) REVERT: B 300 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8432 (mm-30) REVERT: B 412 MET cc_start: 0.8839 (mmt) cc_final: 0.8432 (mmt) REVERT: C 484 ASP cc_start: 0.8587 (t0) cc_final: 0.8334 (t0) REVERT: D 298 SER cc_start: 0.9303 (m) cc_final: 0.8780 (p) REVERT: D 590 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: E 552 TYR cc_start: 0.8532 (p90) cc_final: 0.7837 (p90) REVERT: E 601 GLU cc_start: 0.8558 (tp30) cc_final: 0.8280 (tp30) REVERT: F 483 ARG cc_start: 0.8565 (mpp-170) cc_final: 0.8243 (mpp-170) outliers start: 17 outliers final: 15 residues processed: 302 average time/residue: 0.4318 time to fit residues: 182.3922 Evaluate side-chains 309 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 293 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 604 ASP Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 566 LYS Chi-restraints excluded: chain F residue 603 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 192 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 177 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.061543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.047920 restraints weight = 119294.212| |-----------------------------------------------------------------------------| r_work (start): 0.2415 rms_B_bonded: 1.71 r_work: 0.2315 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2203 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18712 Z= 0.124 Angle : 0.557 7.764 25364 Z= 0.304 Chirality : 0.036 0.259 2800 Planarity : 0.005 0.079 3079 Dihedral : 13.456 167.465 2822 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.67 % Allowed : 10.22 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2160 helix: 1.01 (0.14), residues: 1311 sheet: -0.09 (0.44), residues: 138 loop : -0.83 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 559 TYR 0.021 0.001 TYR D 314 PHE 0.021 0.001 PHE C 617 TRP 0.011 0.001 TRP E 599 HIS 0.005 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (18712) covalent geometry : angle 0.55749 / 0.30 (25364) hydrogen bonds : bond 0.04323 / 2.83 ( 1009) hydrogen bonds : angle 4.70457 / 3.39 ( 2896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8574.41 seconds wall clock time: 146 minutes 34.65 seconds (8794.65 seconds total)