Starting phenix.real_space_refine on Sun Aug 9 14:42:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evp_50010/08_2026/9evp_50010_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evp_50010/08_2026/9evp_50010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9evp_50010/08_2026/9evp_50010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evp_50010/08_2026/9evp_50010.map" model { file = "/net/cci-nas-00/data/ceres_data/9evp_50010/08_2026/9evp_50010_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evp_50010/08_2026/9evp_50010_trim.cif" } resolution = 3.12 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= 0.076 sd= 0.781 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 25 5.49 5 Mg 6 5.21 5 S 126 5.16 5 C 11458 2.51 5 N 3008 2.21 5 O 3301 1.98 5 H 17997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35921 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5918 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "B" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5917 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "C" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5917 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "D" Number of atoms: 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: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5917 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "F" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5917 Classifications: {'peptide': 362} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "S" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 225 Classifications: {'DNA': 7} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 6} 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: 5.30, per 1000 atoms: 0.15 Number of scatterers: 35921 At special positions: 0 Unit cell: (142.29, 133.92, 96.72, 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 25 15.00 Mg 6 11.99 O 3301 8.00 N 3008 7.00 C 11458 6.00 H 17997 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 977.6 milliseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 12 sheets defined 69.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.821A 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: 5.219A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASN A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.632A 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 377 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 400 through 414 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 456 through 462 removed outlier: 4.095A 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 592 through 607 Processing helix chain 'A' and resid 608 through 621 Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.594A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.881A pdb=" N PHE B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 297 No H-bonds generated for 'chain 'B' and resid 296 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 329 removed outlier: 5.443A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASN B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 355 Processing helix chain 'B' and resid 356 through 377 Processing helix chain 'B' and resid 383 through 396 Processing helix chain 'B' and resid 400 through 415 Processing helix chain 'B' and resid 431 through 444 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 456 through 462 removed outlier: 3.967A pdb=" N GLU B 460 " --> pdb=" O ARG B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 480 through 484 Processing helix chain 'B' and resid 489 through 497 Processing helix chain 'B' and resid 497 through 503 Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 589 through 607 removed outlier: 4.465A pdb=" N SER B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.567A 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 302 through 308 Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 316 through 329 removed outlier: 5.303A pdb=" N ALA C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 3.640A 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 376 Processing helix chain 'C' and resid 383 through 398 removed outlier: 3.675A pdb=" N TRP C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 397 " --> pdb=" O TRP C 393 " (cutoff:3.500A) removed outlier: 4.188A 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: 3.837A 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 Processing helix chain 'C' and resid 497 through 503 removed outlier: 3.630A 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 567 through 570 Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.565A pdb=" N LEU C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 589 through 607 removed outlier: 4.430A pdb=" N SER C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 621 Processing helix chain 'D' and resid 269 through 281 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 302 through 308 Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 316 through 329 removed outlier: 5.251A pdb=" N ALA D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASN D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 355 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 383 through 396 removed outlier: 3.515A pdb=" N TRP D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 453 through 462 removed outlier: 3.904A pdb=" N ASN D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY D 462 " --> pdb=" O ASN D 458 " (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 496 removed outlier: 3.595A pdb=" N ASN D 496 " --> pdb=" O ASN D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.538A pdb=" N LYS D 554 " --> pdb=" O LYS D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 566 Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.600A pdb=" N LEU D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 588 Processing helix chain 'D' and resid 589 through 607 removed outlier: 4.463A pdb=" N SER D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 598 " --> pdb=" O SER D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 622 Processing helix chain 'E' and resid 269 through 281 removed outlier: 3.591A 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 329 removed outlier: 5.289A pdb=" N ALA E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASN E 323 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 355 Processing helix chain 'E' and resid 356 through 377 Processing helix chain 'E' and resid 383 through 398 removed outlier: 4.173A 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: 3.582A pdb=" N GLU E 460 " --> pdb=" O ARG E 456 " (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 480 through 484 Processing helix chain 'E' and resid 489 through 497 Processing helix chain 'E' and resid 497 through 503 removed outlier: 3.582A pdb=" N GLY E 503 " --> pdb=" O ASP E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 550 through 560 removed outlier: 3.595A pdb=" N ARG E 559 " --> pdb=" O HIS E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.623A 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 589 through 607 removed outlier: 4.583A pdb=" N SER E 594 " --> pdb=" O GLN E 590 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG E 595 " --> pdb=" O SER E 591 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU E 598 " --> pdb=" O SER E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 622 Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 284 through 295 removed outlier: 3.846A pdb=" N PHE F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) 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 329 removed outlier: 5.050A pdb=" N ALA F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN F 323 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.520A 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 398 removed outlier: 3.752A pdb=" N TRP F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 415 Processing helix chain 'F' and resid 431 through 444 removed outlier: 3.802A pdb=" N GLU F 441 " --> pdb=" O ALA F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 462 through 465 Processing helix chain 'F' and resid 480 through 484 Processing helix chain 'F' and resid 489 through 497 removed outlier: 3.809A pdb=" N ASN F 496 " --> pdb=" O ASN F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'F' and resid 534 through 540 Processing helix chain 'F' and resid 550 through 559 removed outlier: 3.573A pdb=" N GLU F 558 " --> pdb=" O LYS F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 568 removed outlier: 4.487A pdb=" N GLU F 565 " --> pdb=" O PHE F 562 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYS F 566 " --> pdb=" O LEU F 563 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 583 removed outlier: 3.539A pdb=" N LEU F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 588 Processing helix chain 'F' and resid 589 through 607 removed outlier: 4.382A pdb=" N SER F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG F 595 " --> pdb=" O SER F 591 " (cutoff:3.500A) removed outlier: 3.819A 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: 6.998A pdb=" N TYR A 421 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.272A 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: 7.054A pdb=" N TYR B 421 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE B 545 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 423 " --> pdb=" O ILE B 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 507 through 509 Processing sheet with id=AA5, first strand: chain 'C' and resid 446 through 448 removed outlier: 7.211A pdb=" N TYR C 421 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N ILE C 545 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.609A 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 421 through 425 removed outlier: 6.507A pdb=" N VAL D 470 " --> pdb=" O ILE D 525 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N THR D 527 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE D 472 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 507 through 511 removed outlier: 5.935A pdb=" N LYS D 511 " --> pdb=" O ASN D 515 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN D 515 " --> pdb=" O LYS D 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 445 through 448 removed outlier: 3.539A pdb=" N LYS E 446 " --> pdb=" O LEU E 469 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR E 421 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ILE E 545 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 6.349A 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 511 removed outlier: 5.542A pdb=" N LYS E 511 " --> pdb=" O ASN E 515 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN E 515 " --> pdb=" O LYS E 511 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 446 through 448 removed outlier: 3.503A pdb=" N ASP F 474 " --> pdb=" O THR F 527 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU F 423 " --> pdb=" O ILE F 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 507 through 511 removed outlier: 5.379A pdb=" N LYS F 511 " --> pdb=" O ASN F 515 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASN F 515 " --> pdb=" O LYS F 511 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2865 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.03 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17949 1.03 - 1.23: 316 1.23 - 1.43: 7263 1.43 - 1.62: 10562 1.62 - 1.82: 204 Bond restraints: 36294 Sorted by residual: bond pdb=" N3B ANP C 800 " pdb=" PG ANP C 800 " ideal model delta sigma weight residual 1.795 1.609 0.186 2.00e-02 2.50e+03 8.65e+01 bond pdb=" N3B ANP B 802 " pdb=" PG ANP B 802 " ideal model delta sigma weight residual 1.795 1.610 0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" N3B ANP A 800 " pdb=" PG ANP A 800 " ideal model delta sigma weight residual 1.795 1.612 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" N3B ANP E 800 " pdb=" PG ANP E 800 " ideal model delta sigma weight residual 1.795 1.614 0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" N3B ANP D 800 " pdb=" PG ANP D 800 " ideal model delta sigma weight residual 1.795 1.617 0.178 2.00e-02 2.50e+03 7.91e+01 ... (remaining 36289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 64350 2.28 - 4.57: 1313 4.57 - 6.85: 84 6.85 - 9.13: 13 9.13 - 11.42: 10 Bond angle restraints: 65770 Sorted by residual: angle pdb=" O4' DT S 6 " pdb=" C1' DT S 6 " pdb=" N1 DT S 6 " ideal model delta sigma weight residual 108.00 113.74 -5.74 7.00e-01 2.04e+00 6.73e+01 angle pdb=" O4' DT S 7 " pdb=" C1' DT S 7 " pdb=" N1 DT S 7 " ideal model delta sigma weight residual 108.00 113.18 -5.18 7.00e-01 2.04e+00 5.48e+01 angle pdb=" C4' DT S 6 " pdb=" O4' DT S 6 " pdb=" C1' DT S 6 " ideal model delta sigma weight residual 110.10 102.78 7.32 1.00e+00 1.00e+00 5.36e+01 angle pdb=" O4' DT S 6 " pdb=" C1' DT S 6 " pdb=" C2' DT S 6 " ideal model delta sigma weight residual 105.90 101.19 4.71 8.00e-01 1.56e+00 3.46e+01 angle pdb=" O4' DT S 5 " pdb=" C1' DT S 5 " pdb=" N1 DT S 5 " ideal model delta sigma weight residual 108.00 111.35 -3.35 7.00e-01 2.04e+00 2.29e+01 ... (remaining 65765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.71: 16196 32.71 - 65.42: 668 65.42 - 98.14: 63 98.14 - 130.85: 0 130.85 - 163.56: 4 Dihedral angle restraints: 16931 sinusoidal: 9393 harmonic: 7538 Sorted by residual: dihedral pdb=" CA LEU E 469 " pdb=" C LEU E 469 " pdb=" N VAL E 470 " pdb=" CA VAL E 470 " ideal model delta harmonic sigma weight residual 180.00 151.46 28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LYS D 425 " pdb=" C LYS D 425 " pdb=" N GLY D 426 " pdb=" CA GLY D 426 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA 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 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 16928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2391 0.082 - 0.163: 307 0.163 - 0.245: 22 0.245 - 0.326: 5 0.326 - 0.408: 3 Chirality restraints: 2728 Sorted by residual: chirality pdb=" P DT S 1 " pdb=" OP1 DT S 1 " pdb=" OP2 DT S 1 " pdb=" O5' DT S 1 " both_signs ideal model delta sigma weight residual True 2.34 2.74 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA HIS F 513 " pdb=" N HIS F 513 " pdb=" C HIS F 513 " pdb=" CB HIS F 513 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C3' ANP D 800 " pdb=" C2' ANP D 800 " pdb=" C4' ANP D 800 " pdb=" O3' ANP D 800 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 2725 not shown) Planarity restraints: 5161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP E 800 " 0.209 2.00e-02 2.50e+03 8.78e-02 2.12e+02 pdb=" C2 ANP E 800 " -0.016 2.00e-02 2.50e+03 pdb=" C4 ANP E 800 " -0.077 2.00e-02 2.50e+03 pdb=" C5 ANP E 800 " -0.061 2.00e-02 2.50e+03 pdb=" C6 ANP E 800 " 0.005 2.00e-02 2.50e+03 pdb=" C8 ANP E 800 " -0.044 2.00e-02 2.50e+03 pdb=" N1 ANP E 800 " 0.030 2.00e-02 2.50e+03 pdb=" N3 ANP E 800 " -0.069 2.00e-02 2.50e+03 pdb=" N6 ANP E 800 " 0.133 2.00e-02 2.50e+03 pdb=" N7 ANP E 800 " -0.050 2.00e-02 2.50e+03 pdb=" N9 ANP E 800 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP C 800 " -0.154 2.00e-02 2.50e+03 6.58e-02 1.19e+02 pdb=" C2 ANP C 800 " 0.011 2.00e-02 2.50e+03 pdb=" C4 ANP C 800 " 0.060 2.00e-02 2.50e+03 pdb=" C5 ANP C 800 " 0.049 2.00e-02 2.50e+03 pdb=" C6 ANP C 800 " -0.002 2.00e-02 2.50e+03 pdb=" C8 ANP C 800 " 0.025 2.00e-02 2.50e+03 pdb=" N1 ANP C 800 " -0.026 2.00e-02 2.50e+03 pdb=" N3 ANP C 800 " 0.054 2.00e-02 2.50e+03 pdb=" N6 ANP C 800 " -0.100 2.00e-02 2.50e+03 pdb=" N7 ANP C 800 " 0.041 2.00e-02 2.50e+03 pdb=" N9 ANP C 800 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP A 800 " -0.155 2.00e-02 2.50e+03 6.57e-02 1.19e+02 pdb=" C2 ANP A 800 " 0.008 2.00e-02 2.50e+03 pdb=" C4 ANP A 800 " 0.063 2.00e-02 2.50e+03 pdb=" C5 ANP A 800 " 0.047 2.00e-02 2.50e+03 pdb=" C6 ANP A 800 " 0.003 2.00e-02 2.50e+03 pdb=" C8 ANP A 800 " 0.022 2.00e-02 2.50e+03 pdb=" N1 ANP A 800 " -0.030 2.00e-02 2.50e+03 pdb=" N3 ANP A 800 " 0.053 2.00e-02 2.50e+03 pdb=" N6 ANP A 800 " -0.096 2.00e-02 2.50e+03 pdb=" N7 ANP A 800 " 0.035 2.00e-02 2.50e+03 pdb=" N9 ANP A 800 " 0.051 2.00e-02 2.50e+03 ... (remaining 5158 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 2496 2.23 - 2.82: 78302 2.82 - 3.41: 95905 3.41 - 4.01: 128426 4.01 - 4.60: 203888 Nonbonded interactions: 509017 Sorted by model distance: nonbonded pdb=" O1G ANP A 800 " pdb="MG MG A 801 " model vdw 1.634 2.050 nonbonded pdb=" OD2 ASP C 474 " pdb=" HE ARG D 498 " model vdw 1.677 2.450 nonbonded pdb="MG MG B 801 " pdb=" O2G ANP B 802 " model vdw 1.681 2.050 nonbonded pdb=" HZ1 LYS C 512 " pdb=" OE2 GLU D 510 " model vdw 1.703 2.450 nonbonded pdb="HH22 ARG D 456 " pdb=" OP2 DT S 6 " model vdw 1.703 2.450 ... (remaining 509012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 266 through 316 or (resid 317 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 318 through 627)) selection = (chain 'B' and resid 266 through 627) selection = (chain 'C' and resid 266 through 627) selection = (chain 'D' and (resid 266 through 312 or (resid 313 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 314 through 627)) selection = (chain 'E' and resid 266 through 627) selection = (chain 'F' and resid 266 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.780 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 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 0.186 18297 Z= 0.375 Angle : 1.010 11.417 24726 Z= 0.601 Chirality : 0.057 0.408 2728 Planarity : 0.011 0.148 3061 Dihedral : 14.930 163.559 7057 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2160 helix: -0.25 (0.13), residues: 1222 sheet: 0.30 (0.45), residues: 122 loop : -0.39 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG D 498 TYR 0.038 0.006 TYR D 292 PHE 0.025 0.004 PHE D 547 TRP 0.024 0.006 TRP E 599 HIS 0.017 0.005 HIS F 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.37 (18297) covalent geometry : angle 1.01009 / 0.60 (24726) hydrogen bonds : bond 0.18472 / 11.78 ( 995) hydrogen bonds : angle 6.68245 / 4.68 ( 2865) *********************** 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 401 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.835 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 412 MET cc_start: 0.9020 (mmp) cc_final: 0.8480 (mmt) REVERT: A 484 ASP cc_start: 0.8717 (t0) cc_final: 0.8425 (t70) REVERT: B 412 MET cc_start: 0.9091 (mmp) cc_final: 0.8197 (mmt) REVERT: B 614 LYS cc_start: 0.6047 (tttt) cc_final: 0.5077 (tttt) REVERT: C 484 ASP cc_start: 0.8664 (t0) cc_final: 0.8405 (t0) REVERT: E 412 MET cc_start: 0.8891 (mmp) cc_final: 0.8675 (mmp) REVERT: E 484 ASP cc_start: 0.8651 (t0) cc_final: 0.8190 (t0) REVERT: E 614 LYS cc_start: 0.7702 (tttt) cc_final: 0.7409 (tttt) REVERT: F 540 ARG cc_start: 0.8356 (mtt-85) cc_final: 0.8046 (mtt-85) REVERT: F 618 ASN cc_start: 0.8852 (m-40) cc_final: 0.8519 (m110) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.4066 time to fit residues: 222.9682 Evaluate side-chains 309 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN B 513 HIS E 458 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.052410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.041583 restraints weight = 132941.053| |-----------------------------------------------------------------------------| r_work (start): 0.2374 rms_B_bonded: 1.82 r_work: 0.2264 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2154 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18297 Z= 0.205 Angle : 0.701 8.108 24726 Z= 0.385 Chirality : 0.039 0.153 2728 Planarity : 0.005 0.066 3061 Dihedral : 13.552 176.764 2605 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.88 % Allowed : 4.39 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2160 helix: 0.32 (0.14), residues: 1280 sheet: 0.19 (0.45), residues: 121 loop : -0.37 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 498 TYR 0.023 0.002 TYR C 314 PHE 0.024 0.002 PHE C 607 TRP 0.016 0.002 TRP F 393 HIS 0.009 0.001 HIS F 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (18297) covalent geometry : angle 0.70066 / 0.38 (24726) hydrogen bonds : bond 0.06336 / 4.08 ( 995) hydrogen bonds : angle 5.35267 / 3.73 ( 2865) *********************** 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 344 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 327 time to evaluate : 0.687 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: A 412 MET cc_start: 0.8951 (mmp) cc_final: 0.8387 (mmt) REVERT: A 484 ASP cc_start: 0.8683 (t0) cc_final: 0.8329 (t70) REVERT: A 606 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8587 (mm-30) REVERT: B 412 MET cc_start: 0.9073 (mmp) cc_final: 0.8072 (mmt) REVERT: B 614 LYS cc_start: 0.5846 (tttt) cc_final: 0.4989 (tttt) REVERT: C 484 ASP cc_start: 0.8891 (t0) cc_final: 0.8619 (t0) REVERT: D 550 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8371 (mmmm) REVERT: E 473 GLU cc_start: 0.7871 (pm20) cc_final: 0.7332 (pm20) REVERT: E 474 ASP cc_start: 0.8682 (t0) cc_final: 0.8478 (m-30) REVERT: E 484 ASP cc_start: 0.8773 (t0) cc_final: 0.8277 (t0) REVERT: F 358 GLU cc_start: 0.8144 (mp0) cc_final: 0.7863 (mp0) REVERT: F 473 GLU cc_start: 0.8465 (pt0) cc_final: 0.8198 (pm20) REVERT: F 617 PHE cc_start: 0.8894 (t80) cc_final: 0.8596 (t80) outliers start: 17 outliers final: 11 residues processed: 330 average time/residue: 0.3553 time to fit residues: 166.0541 Evaluate side-chains 320 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 309 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 508 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 179 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 395 HIS C 555 HIS E 458 ASN E 496 ASN F 313 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.050334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.039686 restraints weight = 134071.135| |-----------------------------------------------------------------------------| r_work (start): 0.2318 rms_B_bonded: 1.79 r_work: 0.2210 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2101 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 18297 Z= 0.307 Angle : 0.696 7.548 24726 Z= 0.385 Chirality : 0.041 0.163 2728 Planarity : 0.005 0.059 3061 Dihedral : 12.957 179.378 2605 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.14 % Allowed : 5.88 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2160 helix: 0.43 (0.14), residues: 1279 sheet: -0.11 (0.41), residues: 140 loop : -0.58 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 420 TYR 0.027 0.003 TYR C 314 PHE 0.019 0.002 PHE A 327 TRP 0.017 0.002 TRP F 599 HIS 0.009 0.002 HIS F 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.31 (18297) covalent geometry : angle 0.69562 / 0.39 (24726) hydrogen bonds : bond 0.06611 / 4.25 ( 995) hydrogen bonds : angle 5.16004 / 3.61 ( 2865) *********************** 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 337 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 315 time to evaluate : 0.777 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: symmetry clash REVERT: A 412 MET cc_start: 0.8989 (mmp) cc_final: 0.8402 (mmt) REVERT: A 484 ASP cc_start: 0.8653 (t0) cc_final: 0.8258 (t0) REVERT: B 614 LYS cc_start: 0.5972 (tttt) cc_final: 0.4990 (tttt) REVERT: C 484 ASP cc_start: 0.8879 (t0) cc_final: 0.8662 (t0) REVERT: D 528 MET cc_start: 0.5975 (ttm) cc_final: 0.5679 (ttm) REVERT: E 309 GLU cc_start: 0.8340 (pm20) cc_final: 0.8120 (pm20) REVERT: E 473 GLU cc_start: 0.7842 (pm20) cc_final: 0.7375 (pm20) REVERT: E 484 ASP cc_start: 0.8761 (t0) cc_final: 0.8270 (t0) REVERT: F 358 GLU cc_start: 0.8121 (mp0) cc_final: 0.7765 (mp0) outliers start: 22 outliers final: 19 residues processed: 320 average time/residue: 0.3516 time to fit residues: 159.8494 Evaluate side-chains 325 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 306 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 557 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 458 ASN E 496 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.051801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.041054 restraints weight = 132963.598| |-----------------------------------------------------------------------------| r_work (start): 0.2357 rms_B_bonded: 1.81 r_work: 0.2250 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2141 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18297 Z= 0.164 Angle : 0.592 5.877 24726 Z= 0.325 Chirality : 0.037 0.148 2728 Planarity : 0.005 0.067 3061 Dihedral : 12.371 178.151 2605 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.08 % Allowed : 7.17 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2160 helix: 0.73 (0.14), residues: 1280 sheet: -0.26 (0.43), residues: 131 loop : -0.54 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 483 TYR 0.021 0.002 TYR E 314 PHE 0.017 0.001 PHE F 617 TRP 0.016 0.001 TRP F 599 HIS 0.006 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (18297) covalent geometry : angle 0.59192 / 0.33 (24726) hydrogen bonds : bond 0.05223 / 3.37 ( 995) hydrogen bonds : angle 4.89841 / 3.43 ( 2865) *********************** 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 330 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 309 time to evaluate : 0.859 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: A 412 MET cc_start: 0.8946 (mmp) cc_final: 0.8378 (mmt) REVERT: A 476 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8336 (mtpt) REVERT: A 484 ASP cc_start: 0.8653 (t0) cc_final: 0.8262 (t0) REVERT: B 483 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8256 (mtt-85) REVERT: B 614 LYS cc_start: 0.5905 (tttt) cc_final: 0.4974 (tttt) REVERT: C 484 ASP cc_start: 0.8845 (t0) cc_final: 0.8639 (t0) REVERT: D 528 MET cc_start: 0.5885 (ttm) cc_final: 0.5571 (ttm) REVERT: E 309 GLU cc_start: 0.8324 (pm20) cc_final: 0.8108 (pm20) REVERT: E 484 ASP cc_start: 0.8719 (t0) cc_final: 0.8219 (t0) REVERT: E 530 GLU cc_start: 0.7510 (mp0) cc_final: 0.7174 (mp0) REVERT: F 358 GLU cc_start: 0.8097 (mp0) cc_final: 0.7721 (mp0) outliers start: 21 outliers final: 11 residues processed: 314 average time/residue: 0.3356 time to fit residues: 150.3918 Evaluate side-chains 318 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 306 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 508 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 197 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.051513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.040797 restraints weight = 133865.697| |-----------------------------------------------------------------------------| r_work (start): 0.2352 rms_B_bonded: 1.80 r_work: 0.2244 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2135 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18297 Z= 0.189 Angle : 0.588 5.814 24726 Z= 0.323 Chirality : 0.037 0.139 2728 Planarity : 0.005 0.059 3061 Dihedral : 12.107 172.414 2605 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.88 % Allowed : 7.64 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2160 helix: 0.83 (0.14), residues: 1292 sheet: -0.31 (0.44), residues: 131 loop : -0.56 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 483 TYR 0.021 0.002 TYR C 314 PHE 0.015 0.001 PHE A 327 TRP 0.017 0.002 TRP F 599 HIS 0.005 0.001 HIS F 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (18297) covalent geometry : angle 0.58781 / 0.32 (24726) hydrogen bonds : bond 0.05222 / 3.36 ( 995) hydrogen bonds : angle 4.82831 / 3.39 ( 2865) *********************** 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 329 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 312 time to evaluate : 0.946 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: A 412 MET cc_start: 0.8951 (mmp) cc_final: 0.8366 (mmt) REVERT: A 457 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8218 (mp) REVERT: A 476 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8377 (mtpt) REVERT: B 412 MET cc_start: 0.9035 (mmp) cc_final: 0.8025 (mmt) REVERT: B 483 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8271 (mtt-85) REVERT: B 614 LYS cc_start: 0.5965 (tttt) cc_final: 0.5027 (tttt) REVERT: D 528 MET cc_start: 0.5866 (ttm) cc_final: 0.5559 (ttm) REVERT: E 484 ASP cc_start: 0.8698 (t0) cc_final: 0.8131 (t0) REVERT: E 530 GLU cc_start: 0.7492 (mp0) cc_final: 0.7183 (mp0) REVERT: F 358 GLU cc_start: 0.8085 (mp0) cc_final: 0.7713 (mp0) outliers start: 17 outliers final: 14 residues processed: 316 average time/residue: 0.3575 time to fit residues: 161.4156 Evaluate side-chains 323 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 307 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain E residue 623 ILE Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 508 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 204 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 458 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.051174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.040459 restraints weight = 133629.359| |-----------------------------------------------------------------------------| r_work (start): 0.2341 rms_B_bonded: 1.80 r_work: 0.2234 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2124 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18297 Z= 0.212 Angle : 0.597 6.441 24726 Z= 0.329 Chirality : 0.037 0.137 2728 Planarity : 0.005 0.061 3061 Dihedral : 11.992 173.026 2605 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.08 % Allowed : 8.15 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2160 helix: 0.83 (0.14), residues: 1293 sheet: -0.29 (0.42), residues: 139 loop : -0.65 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 483 TYR 0.021 0.002 TYR C 314 PHE 0.016 0.002 PHE A 327 TRP 0.019 0.002 TRP F 599 HIS 0.005 0.001 HIS F 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (18297) covalent geometry : angle 0.59723 / 0.33 (24726) hydrogen bonds : bond 0.05313 / 3.42 ( 995) hydrogen bonds : angle 4.81354 / 3.38 ( 2865) *********************** 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 333 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 312 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8963 (mmp) cc_final: 0.8372 (mmt) REVERT: A 457 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 476 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8370 (mtpt) REVERT: A 484 ASP cc_start: 0.8584 (t0) cc_final: 0.8102 (t0) REVERT: B 483 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8294 (mtt-85) REVERT: B 614 LYS cc_start: 0.6004 (tttt) cc_final: 0.5057 (tttt) REVERT: D 528 MET cc_start: 0.5912 (ttm) cc_final: 0.5579 (ttm) REVERT: E 309 GLU cc_start: 0.8342 (pm20) cc_final: 0.8110 (pm20) REVERT: E 484 ASP cc_start: 0.8690 (t0) cc_final: 0.8119 (t0) REVERT: E 530 GLU cc_start: 0.7512 (mp0) cc_final: 0.7186 (mp0) REVERT: F 358 GLU cc_start: 0.8119 (mp0) cc_final: 0.7753 (mp0) outliers start: 21 outliers final: 15 residues processed: 318 average time/residue: 0.3537 time to fit residues: 160.7310 Evaluate side-chains 327 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain D residue 617 PHE Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain E residue 623 ILE Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 508 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 458 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.050596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.039948 restraints weight = 134718.902| |-----------------------------------------------------------------------------| r_work (start): 0.2325 rms_B_bonded: 1.79 r_work: 0.2219 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2110 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18297 Z= 0.244 Angle : 0.616 7.333 24726 Z= 0.340 Chirality : 0.038 0.136 2728 Planarity : 0.005 0.062 3061 Dihedral : 11.996 172.564 2605 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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 are not related in a simple way. whole: 0.28 (0.17), residues: 2160 helix: 0.82 (0.14), residues: 1276 sheet: -0.30 (0.42), residues: 139 loop : -0.69 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 483 TYR 0.022 0.002 TYR C 314 PHE 0.021 0.002 PHE F 617 TRP 0.027 0.002 TRP F 599 HIS 0.006 0.001 HIS F 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (18297) covalent geometry : angle 0.61638 / 0.34 (24726) hydrogen bonds : bond 0.05504 / 3.54 ( 995) hydrogen bonds : angle 4.82866 / 3.38 ( 2865) *********************** 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 336 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 313 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8974 (mmp) cc_final: 0.8403 (mmt) REVERT: A 457 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 476 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8352 (mtpt) REVERT: B 483 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8296 (mtt-85) REVERT: B 614 LYS cc_start: 0.6152 (tttt) cc_final: 0.5182 (tttt) REVERT: D 528 MET cc_start: 0.5908 (ttm) cc_final: 0.5582 (ttm) REVERT: E 484 ASP cc_start: 0.8678 (t0) cc_final: 0.8104 (t0) REVERT: E 530 GLU cc_start: 0.7509 (mp0) cc_final: 0.7233 (mp0) REVERT: F 357 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8017 (ttt90) REVERT: F 358 GLU cc_start: 0.8097 (mp0) cc_final: 0.7727 (mp0) outliers start: 23 outliers final: 16 residues processed: 319 average time/residue: 0.3702 time to fit residues: 167.9048 Evaluate side-chains 331 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 312 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain D residue 617 PHE Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain E residue 623 ILE Chi-restraints excluded: chain F residue 357 ARG Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 508 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 162 optimal weight: 0.3980 chunk 215 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 458 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.051309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2349 r_free = 0.2349 target = 0.040620 restraints weight = 133882.741| |-----------------------------------------------------------------------------| r_work (start): 0.2344 rms_B_bonded: 1.80 r_work: 0.2238 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2129 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18297 Z= 0.181 Angle : 0.589 7.236 24726 Z= 0.324 Chirality : 0.036 0.139 2728 Planarity : 0.005 0.061 3061 Dihedral : 11.790 171.382 2605 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.88 % Allowed : 9.86 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2160 helix: 0.88 (0.14), residues: 1290 sheet: -0.35 (0.42), residues: 139 loop : -0.73 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 483 TYR 0.020 0.002 TYR B 314 PHE 0.018 0.001 PHE F 617 TRP 0.034 0.002 TRP F 599 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (18297) covalent geometry : angle 0.58949 / 0.32 (24726) hydrogen bonds : bond 0.05049 / 3.25 ( 995) hydrogen bonds : angle 4.74357 / 3.32 ( 2865) *********************** 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 329 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 312 time to evaluate : 0.975 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 412 MET cc_start: 0.8963 (mmp) cc_final: 0.8429 (mmt) REVERT: A 457 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 476 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8445 (mtpt) REVERT: A 502 ASP cc_start: 0.8597 (m-30) cc_final: 0.8322 (m-30) REVERT: B 614 LYS cc_start: 0.6133 (tttt) cc_final: 0.5178 (tttt) REVERT: D 528 MET cc_start: 0.6087 (ttm) cc_final: 0.5738 (ttm) REVERT: E 484 ASP cc_start: 0.8662 (t0) cc_final: 0.8087 (t0) REVERT: E 530 GLU cc_start: 0.7495 (mp0) cc_final: 0.7237 (mp0) REVERT: F 357 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7977 (ttt90) REVERT: F 358 GLU cc_start: 0.8113 (mp0) cc_final: 0.7745 (mp0) outliers start: 17 outliers final: 13 residues processed: 317 average time/residue: 0.3515 time to fit residues: 158.5469 Evaluate side-chains 324 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 309 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain D residue 617 PHE Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain E residue 623 ILE Chi-restraints excluded: chain F residue 357 ARG Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 508 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 458 ASN F 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.052243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.041551 restraints weight = 133270.226| |-----------------------------------------------------------------------------| r_work (start): 0.2371 rms_B_bonded: 1.80 r_work: 0.2265 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2155 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18297 Z= 0.138 Angle : 0.568 9.501 24726 Z= 0.309 Chirality : 0.035 0.139 2728 Planarity : 0.005 0.091 3061 Dihedral : 11.482 168.887 2605 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.14 % Allowed : 9.39 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2160 helix: 1.12 (0.14), residues: 1262 sheet: -0.36 (0.43), residues: 139 loop : -0.73 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 559 TYR 0.020 0.002 TYR B 314 PHE 0.017 0.001 PHE C 299 TRP 0.038 0.001 TRP F 599 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (18297) covalent geometry : angle 0.56752 / 0.31 (24726) hydrogen bonds : bond 0.04537 / 2.92 ( 995) hydrogen bonds : angle 4.63755 / 3.25 ( 2865) *********************** 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 334 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 312 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8949 (mmp) cc_final: 0.8391 (mmt) REVERT: A 457 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 476 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8433 (mtpt) REVERT: A 502 ASP cc_start: 0.8593 (m-30) cc_final: 0.8318 (m-30) REVERT: A 556 CYS cc_start: 0.8310 (t) cc_final: 0.8105 (t) REVERT: B 483 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8274 (mtt-85) REVERT: B 614 LYS cc_start: 0.6162 (tttt) cc_final: 0.5221 (tttt) REVERT: D 528 MET cc_start: 0.6186 (ttm) cc_final: 0.5850 (ttm) REVERT: E 484 ASP cc_start: 0.8653 (t0) cc_final: 0.8086 (t0) REVERT: F 357 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7649 (mtt90) REVERT: F 358 GLU cc_start: 0.8047 (mp0) cc_final: 0.7672 (mp0) REVERT: F 570 GLN cc_start: 0.7954 (mt0) cc_final: 0.7569 (mm-40) outliers start: 22 outliers final: 16 residues processed: 318 average time/residue: 0.3643 time to fit residues: 165.6528 Evaluate side-chains 326 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 307 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain D residue 617 PHE Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain E residue 623 ILE Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 357 ARG Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 508 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 190 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.052755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.042009 restraints weight = 133000.357| |-----------------------------------------------------------------------------| r_work (start): 0.2384 rms_B_bonded: 1.81 r_work: 0.2280 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2172 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18297 Z= 0.128 Angle : 0.571 10.213 24726 Z= 0.309 Chirality : 0.035 0.145 2728 Planarity : 0.005 0.080 3061 Dihedral : 11.249 165.824 2605 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.93 % Allowed : 10.01 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2160 helix: 1.29 (0.15), residues: 1243 sheet: -0.39 (0.43), residues: 139 loop : -0.61 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 483 TYR 0.020 0.002 TYR B 314 PHE 0.031 0.001 PHE E 299 TRP 0.045 0.001 TRP F 599 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (18297) covalent geometry : angle 0.57078 / 0.31 (24726) hydrogen bonds : bond 0.04324 / 2.78 ( 995) hydrogen bonds : angle 4.55703 / 3.19 ( 2865) ********************** 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 328 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8717 (t80) cc_final: 0.8473 (t80) REVERT: A 412 MET cc_start: 0.8943 (mmp) cc_final: 0.8387 (mmt) REVERT: A 457 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8194 (mp) REVERT: A 476 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8421 (mtpt) REVERT: A 502 ASP cc_start: 0.8569 (m-30) cc_final: 0.8294 (m-30) REVERT: B 483 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8218 (mtt-85) REVERT: B 614 LYS cc_start: 0.6153 (tttt) cc_final: 0.5224 (tttt) REVERT: D 528 MET cc_start: 0.6136 (ttm) cc_final: 0.5864 (ttm) REVERT: E 484 ASP cc_start: 0.8657 (t0) cc_final: 0.8079 (t0) REVERT: F 357 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7690 (mtt90) REVERT: F 358 GLU cc_start: 0.8041 (mp0) cc_final: 0.7671 (mp0) outliers start: 18 outliers final: 14 residues processed: 316 average time/residue: 0.3634 time to fit residues: 163.5646 Evaluate side-chains 324 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 307 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 581 TRP Chi-restraints excluded: chain D residue 617 PHE Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain E residue 623 ILE Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 357 ARG Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 508 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 15 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2343 r_free = 0.2343 target = 0.040429 restraints weight = 133510.199| |-----------------------------------------------------------------------------| r_work (start): 0.2338 rms_B_bonded: 1.79 r_work: 0.2234 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2125 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18297 Z= 0.231 Angle : 0.616 9.486 24726 Z= 0.338 Chirality : 0.037 0.134 2728 Planarity : 0.005 0.059 3061 Dihedral : 11.480 168.226 2605 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.14 % Allowed : 10.06 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2160 helix: 1.08 (0.14), residues: 1267 sheet: -0.38 (0.43), residues: 141 loop : -0.67 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 483 TYR 0.021 0.002 TYR C 314 PHE 0.018 0.002 PHE A 327 TRP 0.043 0.002 TRP F 599 HIS 0.006 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 (18297) covalent geometry : angle 0.61615 / 0.34 (24726) hydrogen bonds : bond 0.05216 / 3.35 ( 995) hydrogen bonds : angle 4.71088 / 3.30 ( 2865) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6866.81 seconds wall clock time: 117 minutes 24.84 seconds (7044.84 seconds total)