Starting phenix.real_space_refine on Tue Aug 26 11:54:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kae_62206/08_2025/9kae_62206_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kae_62206/08_2025/9kae_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_62206/08_2025/9kae_62206_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kae_62206/08_2025/9kae_62206_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kae_62206/08_2025/9kae_62206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kae_62206/08_2025/9kae_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36491 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "B" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "C" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5917 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "D" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5918 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "E" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5915 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "F" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5917 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 321 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 481 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.48, per 1000 atoms: 0.20 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: 3.46 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 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: 6.10 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: 9.57 Time building geometry restraints manager: 4.83 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: 65169 2.16 - 4.32: 1593 4.32 - 6.48: 113 6.48 - 8.65: 11 8.65 - 10.81: 7 Bond angle restraints: 66893 Sorted by residual: 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=" 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 angle pdb=" O3' DA P 1 " pdb=" C3' DA P 1 " pdb=" C2' DA P 1 " ideal model delta sigma weight residual 111.50 117.42 -5.92 1.50e+00 4.44e-01 1.56e+01 angle pdb=" CA TRP E 599 " pdb=" CB TRP E 599 " pdb=" CG TRP E 599 " ideal model delta sigma weight residual 113.60 106.75 6.85 1.90e+00 2.77e-01 1.30e+01 angle pdb=" O1B ANP F 800 " pdb=" PB ANP F 800 " pdb=" O3A ANP F 800 " ideal model delta sigma weight residual 103.40 114.21 -10.81 3.00e+00 1.11e-01 1.30e+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 - 0.067: 2234 0.067 - 0.133: 483 0.133 - 0.200: 70 0.200 - 0.267: 6 0.267 - 0.333: 7 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 -2.66 -2.33 -0.33 2.00e-01 2.50e+01 2.78e+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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.280 Extract box with map and model: 0.560 Check model and map are aligned: 0.150 Set scattering table: 0.150 Process input model: 41.290 Find NCS groups from input model: 0.680 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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= 0.363 Angle : 1.007 10.807 25364 Z= 0.585 Chirality : 0.057 0.333 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 aren 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 covalent geometry : bond 0.00760 (18712) covalent geometry : angle 1.00713 (25364) hydrogen bonds : bond 0.18416 ( 1009) hydrogen bonds : angle 7.01653 ( 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 : 1.020 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: 0.4440 time to fit residues: 240.3705 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 : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 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... Flipped N/Q/H residues before XYZ refinement: A 458 ASN B 354 GLN D 458 ASN D 496 ASN E 323 ASN ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.062905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.049301 restraints weight = 120293.613| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 1.66 r_work: 0.2310 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2198 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18712 Z= 0.183 Angle : 0.683 6.994 25364 Z= 0.372 Chirality : 0.039 0.168 2800 Planarity : 0.005 0.064 3079 Dihedral : 14.069 167.365 2822 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.57 % Allowed : 5.57 % Favored : 93.86 % 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 aren not related in a simple way. whole: -0.14 (0.17), residues: 2160 helix: 0.26 (0.14), residues: 1283 sheet: -0.24 (0.38), residues: 179 loop : -0.46 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 420 TYR 0.032 0.002 TYR E 314 PHE 0.020 0.002 PHE D 617 TRP 0.019 0.001 TRP E 599 HIS 0.008 0.002 HIS E 395 Details of bonding type rmsd covalent geometry : bond 0.00412 (18712) covalent geometry : angle 0.68296 (25364) hydrogen bonds : bond 0.05888 ( 1009) hydrogen bonds : angle 5.39828 ( 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 333 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 322 time to evaluate : 0.875 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: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.8758 (mmt) cc_final: 0.8508 (mmt) REVERT: C 412 MET cc_start: 0.9054 (mmp) cc_final: 0.8194 (mmp) REVERT: C 484 ASP cc_start: 0.8613 (t0) cc_final: 0.8338 (t0) REVERT: D 298 SER cc_start: 0.9179 (m) cc_final: 0.8791 (p) REVERT: D 498 ARG cc_start: 0.8491 (tmt-80) cc_final: 0.8285 (ttt-90) REVERT: D 559 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8441 (mtt-85) REVERT: D 590 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8980 (mm-40) REVERT: E 451 ASN cc_start: 0.7370 (m-40) cc_final: 0.7147 (m110) REVERT: E 484 ASP cc_start: 0.8404 (t0) cc_final: 0.8184 (t0) REVERT: F 300 GLU cc_start: 0.8316 (pp20) cc_final: 0.8000 (pp20) REVERT: F 415 ASN cc_start: 0.8524 (t0) cc_final: 0.8237 (t0) REVERT: F 558 GLU cc_start: 0.8656 (tt0) cc_final: 0.8329 (tp30) outliers start: 11 outliers final: 3 residues processed: 327 average time/residue: 0.4056 time to fit residues: 183.1711 Evaluate side-chains 305 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 302 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain E residue 485 LEU 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: 2.9990 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2732 r_free = 0.2732 target = 0.060737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.047152 restraints weight = 120922.767| |-----------------------------------------------------------------------------| r_work (start): 0.2361 rms_B_bonded: 1.64 r_work: 0.2261 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2149 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 18712 Z= 0.268 Angle : 0.672 6.907 25364 Z= 0.369 Chirality : 0.041 0.170 2800 Planarity : 0.005 0.080 3079 Dihedral : 13.889 171.665 2822 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.03 % Allowed : 6.86 % Favored : 92.11 % 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 aren not related in a simple way. whole: -0.09 (0.17), residues: 2160 helix: 0.36 (0.14), residues: 1312 sheet: 0.30 (0.45), residues: 129 loop : -0.72 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 517 TYR 0.023 0.002 TYR E 314 PHE 0.017 0.002 PHE F 607 TRP 0.015 0.002 TRP D 387 HIS 0.008 0.002 HIS E 395 Details of bonding type rmsd covalent geometry : bond 0.00631 (18712) covalent geometry : angle 0.67156 (25364) hydrogen bonds : bond 0.06146 ( 1009) hydrogen bonds : angle 5.19838 ( 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: 20 poor density : 300 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.9048 (mt) cc_final: 0.8829 (mt) REVERT: B 548 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8495 (mtm110) REVERT: C 412 MET cc_start: 0.9085 (mmp) cc_final: 0.8129 (mmp) REVERT: C 484 ASP cc_start: 0.8653 (t0) cc_final: 0.8416 (t0) REVERT: D 300 GLU cc_start: 0.8552 (pm20) cc_final: 0.8314 (pm20) REVERT: D 559 ARG cc_start: 0.8818 (ttm-80) cc_final: 0.8425 (mtt-85) REVERT: E 552 TYR cc_start: 0.8676 (p90) cc_final: 0.7943 (p90) REVERT: E 553 LEU cc_start: 0.8915 (mt) cc_final: 0.8554 (mp) REVERT: F 300 GLU cc_start: 0.8319 (pp20) cc_final: 0.7756 (pp20) REVERT: F 353 LEU cc_start: 0.9398 (mt) cc_final: 0.9107 (mt) REVERT: F 558 GLU cc_start: 0.8681 (tt0) cc_final: 0.8372 (tp30) outliers start: 20 outliers final: 13 residues processed: 309 average time/residue: 0.4470 time to fit residues: 192.7843 Evaluate side-chains 305 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 292 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 D residue 307 LYS Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 485 LEU 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 528 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: 0.7980 chunk 83 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 0.0270 chunk 58 optimal weight: 0.6980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.061892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.047965 restraints weight = 119593.452| |-----------------------------------------------------------------------------| r_work (start): 0.2425 rms_B_bonded: 1.73 r_work: 0.2323 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2211 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18712 Z= 0.127 Angle : 0.565 6.616 25364 Z= 0.308 Chirality : 0.036 0.151 2800 Planarity : 0.004 0.058 3079 Dihedral : 13.400 163.215 2822 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.72 % Allowed : 7.84 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.17), residues: 2160 helix: 0.79 (0.14), residues: 1311 sheet: -0.41 (0.38), residues: 170 loop : -0.56 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 540 TYR 0.024 0.002 TYR E 314 PHE 0.038 0.001 PHE D 617 TRP 0.014 0.001 TRP E 599 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00275 (18712) covalent geometry : angle 0.56490 (25364) hydrogen bonds : bond 0.04564 ( 1009) hydrogen bonds : angle 4.88711 ( 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 315 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 301 time to evaluate : 1.051 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: B 412 MET cc_start: 0.8794 (mmt) cc_final: 0.8242 (mmt) REVERT: B 548 ARG cc_start: 0.8725 (ttm110) cc_final: 0.8453 (mtm110) REVERT: B 613 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: C 412 MET cc_start: 0.9050 (mmp) cc_final: 0.8163 (mmp) REVERT: C 484 ASP cc_start: 0.8626 (t0) cc_final: 0.8346 (t0) REVERT: D 298 SER cc_start: 0.9268 (m) cc_final: 0.8716 (p) REVERT: D 300 GLU cc_start: 0.8488 (pm20) cc_final: 0.8273 (pm20) REVERT: D 590 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: E 552 TYR cc_start: 0.8653 (p90) cc_final: 0.7906 (p90) REVERT: E 553 LEU cc_start: 0.8876 (mt) cc_final: 0.8502 (mp) REVERT: E 599 TRP cc_start: 0.8759 (m100) cc_final: 0.8339 (m100) REVERT: F 300 GLU cc_start: 0.8339 (pp20) cc_final: 0.8042 (pp20) REVERT: F 353 LEU cc_start: 0.9337 (mt) cc_final: 0.9079 (mt) REVERT: F 558 GLU cc_start: 0.8601 (tt0) cc_final: 0.8312 (tp30) outliers start: 14 outliers final: 10 residues processed: 307 average time/residue: 0.4699 time to fit residues: 201.2800 Evaluate side-chains 307 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 295 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 613 GLN Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain F residue 375 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=3.50 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.061041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.047470 restraints weight = 120673.093| |-----------------------------------------------------------------------------| r_work (start): 0.2373 rms_B_bonded: 1.65 r_work: 0.2274 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2163 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18712 Z= 0.226 Angle : 0.608 7.898 25364 Z= 0.333 Chirality : 0.038 0.163 2800 Planarity : 0.005 0.062 3079 Dihedral : 13.607 168.898 2822 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.83 % Allowed : 8.57 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.17), residues: 2160 helix: 0.66 (0.14), residues: 1320 sheet: 0.17 (0.44), residues: 128 loop : -0.92 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 483 TYR 0.021 0.002 TYR B 552 PHE 0.029 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 covalent geometry : bond 0.00526 (18712) covalent geometry : angle 0.60806 (25364) hydrogen bonds : bond 0.05272 ( 1009) hydrogen bonds : angle 4.93107 ( 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 313 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 297 time to evaluate : 1.066 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 412 MET cc_start: 0.8834 (mmt) cc_final: 0.8465 (mmt) REVERT: C 412 MET cc_start: 0.9077 (mmp) cc_final: 0.8138 (mmp) REVERT: D 298 SER cc_start: 0.9290 (m) cc_final: 0.8672 (p) REVERT: D 300 GLU cc_start: 0.8492 (pm20) cc_final: 0.8255 (pm20) REVERT: E 401 MET cc_start: 0.8607 (tpp) cc_final: 0.8397 (tpt) REVERT: E 552 TYR cc_start: 0.8639 (p90) cc_final: 0.7958 (p90) REVERT: E 553 LEU cc_start: 0.8923 (mt) cc_final: 0.8544 (mp) REVERT: F 353 LEU cc_start: 0.9388 (mt) cc_final: 0.9071 (mt) REVERT: F 558 GLU cc_start: 0.8617 (tt0) cc_final: 0.8337 (tp30) outliers start: 16 outliers final: 11 residues processed: 303 average time/residue: 0.4866 time to fit residues: 202.8873 Evaluate side-chains 306 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 295 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 C residue 384 ILE Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 551 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 79 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 590 GLN F 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.060977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.047417 restraints weight = 121700.513| |-----------------------------------------------------------------------------| r_work (start): 0.2370 rms_B_bonded: 1.64 r_work: 0.2271 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2159 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18712 Z= 0.218 Angle : 0.604 8.421 25364 Z= 0.330 Chirality : 0.038 0.160 2800 Planarity : 0.005 0.060 3079 Dihedral : 13.630 169.462 2822 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.98 % Allowed : 8.57 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2160 helix: 0.63 (0.14), residues: 1320 sheet: 0.14 (0.44), residues: 133 loop : -0.94 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 364 TYR 0.023 0.002 TYR B 552 PHE 0.033 0.002 PHE D 617 TRP 0.013 0.001 TRP D 387 HIS 0.005 0.001 HIS E 395 Details of bonding type rmsd covalent geometry : bond 0.00508 (18712) covalent geometry : angle 0.60378 (25364) hydrogen bonds : bond 0.05186 ( 1009) hydrogen bonds : angle 4.91644 ( 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: 19 poor density : 298 time to evaluate : 0.636 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: A 300 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 412 MET cc_start: 0.8830 (mmt) cc_final: 0.8441 (mmt) REVERT: D 298 SER cc_start: 0.9300 (m) cc_final: 0.8646 (p) REVERT: D 300 GLU cc_start: 0.8494 (pm20) cc_final: 0.8233 (pm20) REVERT: D 590 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: E 401 MET cc_start: 0.8596 (tpp) cc_final: 0.8383 (tpt) REVERT: E 552 TYR cc_start: 0.8626 (p90) cc_final: 0.7974 (p90) REVERT: E 553 LEU cc_start: 0.8943 (mt) cc_final: 0.8551 (mp) REVERT: F 353 LEU cc_start: 0.9387 (mt) cc_final: 0.9064 (mt) REVERT: F 498 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6886 (ttm110) REVERT: F 558 GLU cc_start: 0.8626 (tt0) cc_final: 0.8321 (tp30) outliers start: 19 outliers final: 14 residues processed: 306 average time/residue: 0.4323 time to fit residues: 182.3500 Evaluate side-chains 310 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 295 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 301 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 217 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 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: 0.8980 chunk 163 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.060508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.047007 restraints weight = 121592.047| |-----------------------------------------------------------------------------| r_work (start): 0.2361 rms_B_bonded: 1.64 r_work: 0.2262 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2150 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18712 Z= 0.224 Angle : 0.606 8.285 25364 Z= 0.331 Chirality : 0.038 0.162 2800 Planarity : 0.005 0.061 3079 Dihedral : 13.657 170.712 2822 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.19 % Allowed : 8.82 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2160 helix: 0.62 (0.14), residues: 1321 sheet: 0.12 (0.45), residues: 133 loop : -0.93 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 456 TYR 0.023 0.002 TYR B 552 PHE 0.032 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 covalent geometry : bond 0.00525 (18712) covalent geometry : angle 0.60574 (25364) hydrogen bonds : bond 0.05212 ( 1009) hydrogen bonds : angle 4.90716 ( 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 321 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 0.927 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 412 MET cc_start: 0.8815 (mmt) cc_final: 0.8524 (mmt) REVERT: D 298 SER cc_start: 0.9310 (m) cc_final: 0.8872 (p) REVERT: D 590 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: E 396 CYS cc_start: 0.8985 (t) cc_final: 0.8232 (t) REVERT: E 401 MET cc_start: 0.8594 (tpp) cc_final: 0.8378 (tpt) REVERT: E 552 TYR cc_start: 0.8628 (p90) cc_final: 0.8001 (p90) REVERT: E 553 LEU cc_start: 0.8957 (mt) cc_final: 0.8565 (mp) REVERT: F 353 LEU cc_start: 0.9384 (mt) cc_final: 0.9059 (mt) REVERT: F 498 ARG cc_start: 0.7059 (ttm110) cc_final: 0.6858 (ttm110) outliers start: 23 outliers final: 17 residues processed: 306 average time/residue: 0.4298 time to fit residues: 181.1149 Evaluate side-chains 317 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 299 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 451 ASN Chi-restraints excluded: chain E residue 546 ASP Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 299 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 183 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.060136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.046409 restraints weight = 119908.668| |-----------------------------------------------------------------------------| r_work (start): 0.2381 rms_B_bonded: 1.70 r_work: 0.2281 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2168 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18712 Z= 0.173 Angle : 0.573 7.781 25364 Z= 0.313 Chirality : 0.036 0.159 2800 Planarity : 0.005 0.095 3079 Dihedral : 13.520 166.784 2822 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.08 % Allowed : 9.29 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.17), residues: 2160 helix: 0.77 (0.14), residues: 1321 sheet: 0.12 (0.45), residues: 133 loop : -0.88 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 559 TYR 0.020 0.002 TYR E 314 PHE 0.054 0.002 PHE D 617 TRP 0.011 0.001 TRP D 387 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00398 (18712) covalent geometry : angle 0.57320 (25364) hydrogen bonds : bond 0.04811 ( 1009) hydrogen bonds : angle 4.82030 ( 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 320 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 GLN cc_start: 0.8222 (mt0) cc_final: 0.8009 (mt0) REVERT: B 412 MET cc_start: 0.8832 (mmt) cc_final: 0.8498 (mmt) REVERT: D 298 SER cc_start: 0.9312 (m) cc_final: 0.8794 (p) REVERT: D 300 GLU cc_start: 0.8455 (pm20) cc_final: 0.8211 (pm20) REVERT: D 590 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: E 299 PHE cc_start: 0.7728 (p90) cc_final: 0.7331 (p90) REVERT: E 552 TYR cc_start: 0.8625 (p90) cc_final: 0.7992 (p90) REVERT: E 553 LEU cc_start: 0.8936 (mt) cc_final: 0.8538 (mp) REVERT: F 353 LEU cc_start: 0.9358 (mt) cc_final: 0.9023 (mt) REVERT: F 498 ARG cc_start: 0.7108 (ttm110) cc_final: 0.6883 (ttm110) REVERT: F 558 GLU cc_start: 0.8660 (tt0) cc_final: 0.8350 (tp30) outliers start: 21 outliers final: 15 residues processed: 307 average time/residue: 0.4211 time to fit residues: 178.0245 Evaluate side-chains 312 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 296 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 613 GLN 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 420 ARG Chi-restraints excluded: chain E residue 451 ASN Chi-restraints excluded: chain E residue 604 ASP Chi-restraints excluded: chain F residue 299 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 144 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.060371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.046906 restraints weight = 122462.744| |-----------------------------------------------------------------------------| r_work (start): 0.2359 rms_B_bonded: 1.64 r_work: 0.2261 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2149 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18712 Z= 0.231 Angle : 0.610 8.585 25364 Z= 0.333 Chirality : 0.038 0.163 2800 Planarity : 0.005 0.087 3079 Dihedral : 13.646 170.531 2822 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.08 % Allowed : 9.55 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2160 helix: 0.66 (0.14), residues: 1321 sheet: 0.16 (0.45), residues: 133 loop : -0.98 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 559 TYR 0.023 0.002 TYR B 552 PHE 0.021 0.002 PHE C 617 TRP 0.014 0.001 TRP D 387 HIS 0.006 0.001 HIS E 395 Details of bonding type rmsd covalent geometry : bond 0.00541 (18712) covalent geometry : angle 0.61040 (25364) hydrogen bonds : bond 0.05203 ( 1009) hydrogen bonds : angle 4.88270 ( 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 320 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 1.013 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: B 412 MET cc_start: 0.8823 (mmt) cc_final: 0.8479 (mmt) REVERT: D 298 SER cc_start: 0.9306 (m) cc_final: 0.8782 (p) REVERT: D 300 GLU cc_start: 0.8434 (pm20) cc_final: 0.8183 (pm20) REVERT: D 590 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: D 617 PHE cc_start: 0.8488 (t80) cc_final: 0.8208 (t80) REVERT: E 401 MET cc_start: 0.8595 (tpp) cc_final: 0.8377 (tpt) REVERT: E 552 TYR cc_start: 0.8637 (p90) cc_final: 0.8004 (p90) REVERT: E 553 LEU cc_start: 0.8969 (mt) cc_final: 0.8596 (mp) REVERT: F 353 LEU cc_start: 0.9380 (mt) cc_final: 0.9048 (mt) outliers start: 21 outliers final: 18 residues processed: 307 average time/residue: 0.3921 time to fit residues: 166.8840 Evaluate side-chains 313 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 294 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 302 CYS Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain E residue 451 ASN Chi-restraints excluded: chain E residue 546 ASP Chi-restraints excluded: chain E residue 604 ASP Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 299 PHE 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 76 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.061089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.047396 restraints weight = 120203.338| |-----------------------------------------------------------------------------| r_work (start): 0.2392 rms_B_bonded: 1.72 r_work: 0.2292 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2178 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18712 Z= 0.147 Angle : 0.571 8.412 25364 Z= 0.312 Chirality : 0.036 0.158 2800 Planarity : 0.005 0.087 3079 Dihedral : 13.409 164.547 2822 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.98 % Allowed : 9.70 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2160 helix: 0.86 (0.14), residues: 1322 sheet: 0.11 (0.44), residues: 138 loop : -0.88 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 483 TYR 0.020 0.002 TYR E 314 PHE 0.019 0.001 PHE F 617 TRP 0.011 0.001 TRP E 599 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00333 (18712) covalent geometry : angle 0.57094 (25364) hydrogen bonds : bond 0.04559 ( 1009) hydrogen bonds : angle 4.78535 ( 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 316 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 297 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 GLN cc_start: 0.8214 (mt0) cc_final: 0.8005 (mt0) REVERT: B 412 MET cc_start: 0.8827 (mmt) cc_final: 0.8446 (mmt) REVERT: D 298 SER cc_start: 0.9315 (m) cc_final: 0.8829 (p) REVERT: D 300 GLU cc_start: 0.8419 (pm20) cc_final: 0.8164 (pm20) REVERT: D 590 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: E 552 TYR cc_start: 0.8649 (p90) cc_final: 0.7977 (p90) REVERT: E 553 LEU cc_start: 0.8952 (mt) cc_final: 0.8548 (mp) REVERT: F 353 LEU cc_start: 0.9346 (mt) cc_final: 0.9000 (mt) REVERT: F 558 GLU cc_start: 0.8665 (tt0) cc_final: 0.8343 (tp30) outliers start: 19 outliers final: 14 residues processed: 304 average time/residue: 0.3984 time to fit residues: 167.4923 Evaluate side-chains 310 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 295 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 420 ARG Chi-restraints excluded: chain E residue 451 ASN Chi-restraints excluded: chain E residue 604 ASP Chi-restraints excluded: chain F residue 299 PHE 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: 3.9990 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.061518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.047765 restraints weight = 119461.138| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 1.74 r_work: 0.2305 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2192 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18712 Z= 0.138 Angle : 0.556 8.410 25364 Z= 0.303 Chirality : 0.035 0.156 2800 Planarity : 0.005 0.083 3079 Dihedral : 13.223 165.077 2822 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.88 % Allowed : 9.80 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 2160 helix: 1.01 (0.14), residues: 1316 sheet: 0.04 (0.44), residues: 138 loop : -0.85 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 498 TYR 0.020 0.001 TYR E 314 PHE 0.039 0.001 PHE D 617 TRP 0.011 0.001 TRP E 599 HIS 0.005 0.001 HIS E 395 Details of bonding type rmsd covalent geometry : bond 0.00311 (18712) covalent geometry : angle 0.55645 (25364) hydrogen bonds : bond 0.04378 ( 1009) hydrogen bonds : angle 4.70611 ( 2896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8066.42 seconds wall clock time: 137 minutes 51.19 seconds (8271.19 seconds total)