Starting phenix.real_space_refine on Tue Aug 26 10:10:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evp_50010/08_2025/9evp_50010_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evp_50010/08_2025/9evp_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 { model { file = "/net/cci-nas-00/data/ceres_data/9evp_50010/08_2025/9evp_50010_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evp_50010/08_2025/9evp_50010_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9evp_50010/08_2025/9evp_50010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evp_50010/08_2025/9evp_50010.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.07, per 1000 atoms: 0.20 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: 3.60 Conformation dependent library (CDL) restraints added in 987.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 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: 1.00 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: 9.15 Time building geometry restraints manager: 4.90 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: 64366 2.28 - 4.57: 1300 4.57 - 6.85: 81 6.85 - 9.13: 13 9.13 - 11.42: 10 Bond angle restraints: 65770 Sorted by residual: angle pdb=" C4' DT S 6 " pdb=" O4' DT S 6 " pdb=" C1' DT S 6 " ideal model delta sigma weight residual 109.70 102.78 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" PB ANP D 800 " pdb=" N3B ANP D 800 " pdb=" PG ANP D 800 " ideal model delta sigma weight residual 126.95 115.53 11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" N GLY F 524 " pdb=" CA GLY F 524 " pdb=" C GLY F 524 " ideal model delta sigma weight residual 111.59 117.78 -6.19 1.63e+00 3.76e-01 1.44e+01 angle pdb=" CA TRP E 599 " pdb=" CB TRP E 599 " pdb=" CG TRP E 599 " ideal model delta sigma weight residual 113.60 106.52 7.08 1.90e+00 2.77e-01 1.39e+01 angle pdb=" N GLY E 524 " pdb=" CA GLY E 524 " pdb=" C GLY E 524 " ideal model delta sigma weight residual 110.80 116.00 -5.20 1.41e+00 5.03e-01 1.36e+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 - 0.080: 2374 0.080 - 0.159: 320 0.159 - 0.239: 26 0.239 - 0.318: 5 0.318 - 0.398: 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 2.35 2.74 -0.40 2.00e-01 2.50e+01 3.95e+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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.650 Find NCS groups from input model: 0.710 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 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= 0.362 Angle : 1.007 11.417 24726 Z= 0.583 Chirality : 0.057 0.398 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 aren 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 covalent geometry : bond 0.00755 (18297) covalent geometry : angle 1.00687 (24726) hydrogen bonds : bond 0.18472 ( 995) hydrogen bonds : angle 6.68245 ( 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 : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8404 (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: 0.5109 time to fit residues: 275.0579 Evaluate side-chains 310 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 496 ASN B 513 HIS E 458 ASN F 395 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.052343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.041559 restraints weight = 133015.657| |-----------------------------------------------------------------------------| r_work (start): 0.2373 rms_B_bonded: 1.82 r_work: 0.2263 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2153 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18297 Z= 0.200 Angle : 0.695 7.791 24726 Z= 0.380 Chirality : 0.039 0.155 2728 Planarity : 0.005 0.063 3061 Dihedral : 13.451 176.130 2605 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.77 % Allowed : 4.59 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.17), residues: 2160 helix: 0.34 (0.14), residues: 1280 sheet: 0.23 (0.45), residues: 121 loop : -0.35 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 559 TYR 0.024 0.002 TYR C 314 PHE 0.024 0.002 PHE C 607 TRP 0.016 0.002 TRP F 393 HIS 0.009 0.002 HIS F 513 Details of bonding type rmsd covalent geometry : bond 0.00451 (18297) covalent geometry : angle 0.69507 (24726) hydrogen bonds : bond 0.06487 ( 995) hydrogen bonds : angle 5.33210 ( 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 343 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 328 time to evaluate : 1.009 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: A 412 MET cc_start: 0.8949 (mmp) cc_final: 0.8379 (mmt) REVERT: A 484 ASP cc_start: 0.8671 (t0) cc_final: 0.8316 (t70) REVERT: A 606 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8565 (mm-30) REVERT: B 412 MET cc_start: 0.9075 (mmp) cc_final: 0.8073 (mmt) REVERT: B 614 LYS cc_start: 0.5835 (tttt) cc_final: 0.4982 (tttt) REVERT: C 484 ASP cc_start: 0.8879 (t0) cc_final: 0.8604 (t0) REVERT: D 550 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8356 (mmmm) REVERT: E 473 GLU cc_start: 0.7897 (pm20) cc_final: 0.7359 (pm20) REVERT: E 474 ASP cc_start: 0.8674 (t0) cc_final: 0.8472 (m-30) REVERT: E 484 ASP cc_start: 0.8766 (t0) cc_final: 0.8273 (t0) REVERT: F 358 GLU cc_start: 0.8140 (mp0) cc_final: 0.7856 (mp0) REVERT: F 473 GLU cc_start: 0.8449 (pt0) cc_final: 0.8177 (pm20) REVERT: F 617 PHE cc_start: 0.8882 (t80) cc_final: 0.8581 (t80) outliers start: 15 outliers final: 10 residues processed: 331 average time/residue: 0.4613 time to fit residues: 211.2396 Evaluate side-chains 321 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 311 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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: 0.9980 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: 4.9990 chunk 163 optimal weight: 5.9990 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: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 395 HIS E 458 ASN E 496 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.050807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.040120 restraints weight = 133876.345| |-----------------------------------------------------------------------------| r_work (start): 0.2331 rms_B_bonded: 1.80 r_work: 0.2222 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2112 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18297 Z= 0.270 Angle : 0.668 7.641 24726 Z= 0.368 Chirality : 0.040 0.161 2728 Planarity : 0.005 0.057 3061 Dihedral : 12.809 179.526 2605 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.03 % Allowed : 6.19 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2160 helix: 0.52 (0.14), residues: 1279 sheet: -0.12 (0.41), residues: 140 loop : -0.53 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 420 TYR 0.026 0.002 TYR C 314 PHE 0.018 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 covalent geometry : bond 0.00633 (18297) covalent geometry : angle 0.66827 (24726) hydrogen bonds : bond 0.06283 ( 995) hydrogen bonds : angle 5.09354 ( 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 335 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8979 (mmp) cc_final: 0.8403 (mmt) REVERT: A 484 ASP cc_start: 0.8657 (t0) cc_final: 0.8260 (t0) REVERT: B 412 MET cc_start: 0.9039 (mmp) cc_final: 0.8007 (mmt) REVERT: B 614 LYS cc_start: 0.5929 (tttt) cc_final: 0.4970 (tttt) REVERT: C 484 ASP cc_start: 0.8886 (t0) cc_final: 0.8667 (t0) REVERT: D 528 MET cc_start: 0.5950 (ttm) cc_final: 0.5659 (ttm) REVERT: E 473 GLU cc_start: 0.7886 (pm20) cc_final: 0.7420 (pm20) REVERT: E 484 ASP cc_start: 0.8738 (t0) cc_final: 0.8237 (t0) REVERT: F 358 GLU cc_start: 0.8120 (mp0) cc_final: 0.7765 (mp0) REVERT: F 617 PHE cc_start: 0.8933 (t80) cc_final: 0.8695 (t80) outliers start: 20 outliers final: 18 residues processed: 319 average time/residue: 0.4414 time to fit residues: 196.5756 Evaluate side-chains 324 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 306 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 557 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 75 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.051862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.041111 restraints weight = 132646.671| |-----------------------------------------------------------------------------| r_work (start): 0.2359 rms_B_bonded: 1.81 r_work: 0.2253 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2144 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18297 Z= 0.173 Angle : 0.589 5.621 24726 Z= 0.324 Chirality : 0.036 0.146 2728 Planarity : 0.005 0.059 3061 Dihedral : 12.260 177.914 2605 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.98 % Allowed : 7.28 % 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 aren not related in a simple way. whole: 0.32 (0.17), residues: 2160 helix: 0.77 (0.14), residues: 1280 sheet: -0.27 (0.44), residues: 130 loop : -0.52 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 483 TYR 0.021 0.002 TYR C 314 PHE 0.014 0.001 PHE A 327 TRP 0.016 0.001 TRP F 599 HIS 0.006 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00389 (18297) covalent geometry : angle 0.58893 (24726) hydrogen bonds : bond 0.05202 ( 995) hydrogen bonds : angle 4.87630 ( 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 327 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 1.047 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: 0.8950 (mmp) cc_final: 0.8393 (mmt) REVERT: A 476 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8384 (mtpt) REVERT: A 484 ASP cc_start: 0.8643 (t0) cc_final: 0.8253 (t0) REVERT: B 483 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8258 (mtt-85) REVERT: B 614 LYS cc_start: 0.5919 (tttt) cc_final: 0.4996 (tttt) REVERT: D 528 MET cc_start: 0.5849 (ttm) cc_final: 0.5546 (ttm) REVERT: E 484 ASP cc_start: 0.8721 (t0) cc_final: 0.8221 (t0) REVERT: F 358 GLU cc_start: 0.8094 (mp0) cc_final: 0.7721 (mp0) REVERT: F 385 GLU cc_start: 0.8689 (tp30) cc_final: 0.8471 (tp30) REVERT: F 617 PHE cc_start: 0.8972 (t80) cc_final: 0.8747 (t80) REVERT: F 621 MET cc_start: 0.8805 (mmm) cc_final: 0.8597 (mmp) outliers start: 19 outliers final: 12 residues processed: 313 average time/residue: 0.4442 time to fit residues: 193.5521 Evaluate side-chains 317 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 304 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 536 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: 5.9990 chunk 194 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.051939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.041205 restraints weight = 132931.498| |-----------------------------------------------------------------------------| r_work (start): 0.2363 rms_B_bonded: 1.81 r_work: 0.2256 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2147 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18297 Z= 0.168 Angle : 0.574 5.488 24726 Z= 0.314 Chirality : 0.036 0.138 2728 Planarity : 0.005 0.061 3061 Dihedral : 11.924 171.907 2605 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.83 % Allowed : 7.64 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.17), residues: 2160 helix: 0.89 (0.14), residues: 1293 sheet: -0.37 (0.44), residues: 130 loop : -0.55 (0.21), residues: 737 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 0.017 0.001 PHE F 299 TRP 0.018 0.001 TRP F 599 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00383 (18297) covalent geometry : angle 0.57369 (24726) hydrogen bonds : bond 0.05004 ( 995) hydrogen bonds : angle 4.77773 ( 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 326 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 310 time to evaluate : 1.040 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 299 PHE cc_start: 0.8730 (t80) cc_final: 0.8503 (t80) REVERT: A 412 MET cc_start: 0.8952 (mmp) cc_final: 0.8381 (mmt) REVERT: A 476 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8401 (mtpt) REVERT: B 614 LYS cc_start: 0.5944 (tttt) cc_final: 0.5016 (tttt) REVERT: D 528 MET cc_start: 0.5830 (ttm) cc_final: 0.5520 (ttm) REVERT: E 484 ASP cc_start: 0.8704 (t0) cc_final: 0.8140 (t0) REVERT: F 358 GLU cc_start: 0.8096 (mp0) cc_final: 0.7723 (mp0) REVERT: F 385 GLU cc_start: 0.8667 (tp30) cc_final: 0.8449 (tp30) REVERT: F 617 PHE cc_start: 0.8970 (t80) cc_final: 0.8768 (t80) outliers start: 16 outliers final: 13 residues processed: 314 average time/residue: 0.4492 time to fit residues: 196.0152 Evaluate side-chains 323 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 310 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 474 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 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: 2.9990 chunk 117 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 458 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.051610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.040844 restraints weight = 133405.742| |-----------------------------------------------------------------------------| r_work (start): 0.2352 rms_B_bonded: 1.81 r_work: 0.2246 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2137 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18297 Z= 0.194 Angle : 0.578 6.757 24726 Z= 0.318 Chirality : 0.036 0.136 2728 Planarity : 0.005 0.057 3061 Dihedral : 11.812 171.990 2605 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.98 % Allowed : 8.10 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.17), residues: 2160 helix: 0.93 (0.14), residues: 1293 sheet: -0.35 (0.42), residues: 139 loop : -0.59 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 483 TYR 0.020 0.002 TYR C 314 PHE 0.018 0.001 PHE F 299 TRP 0.018 0.002 TRP F 599 HIS 0.005 0.001 HIS F 513 Details of bonding type rmsd covalent geometry : bond 0.00448 (18297) covalent geometry : angle 0.57820 (24726) hydrogen bonds : bond 0.05116 ( 995) hydrogen bonds : angle 4.75464 ( 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 328 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 309 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8718 (t80) cc_final: 0.8486 (t80) REVERT: A 412 MET cc_start: 0.8960 (mmp) cc_final: 0.8385 (mmt) REVERT: A 457 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8236 (mp) REVERT: B 483 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8265 (mtt-85) REVERT: B 614 LYS cc_start: 0.5973 (tttt) cc_final: 0.5039 (tttt) REVERT: D 528 MET cc_start: 0.5905 (ttm) cc_final: 0.5575 (ttm) REVERT: E 484 ASP cc_start: 0.8703 (t0) cc_final: 0.8133 (t0) REVERT: F 358 GLU cc_start: 0.8120 (mp0) cc_final: 0.7756 (mp0) REVERT: F 385 GLU cc_start: 0.8690 (tp30) cc_final: 0.8473 (tp30) REVERT: F 617 PHE cc_start: 0.8985 (t80) cc_final: 0.8721 (t80) outliers start: 19 outliers final: 15 residues processed: 313 average time/residue: 0.4491 time to fit residues: 195.7971 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 : 1.071 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 163 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2624 r_free = 0.2624 target = 0.050127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.039484 restraints weight = 134390.368| |-----------------------------------------------------------------------------| r_work (start): 0.2314 rms_B_bonded: 1.80 r_work: 0.2207 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2098 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 18297 Z= 0.286 Angle : 0.638 7.419 24726 Z= 0.352 Chirality : 0.039 0.134 2728 Planarity : 0.005 0.063 3061 Dihedral : 11.968 173.013 2605 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.08 % Allowed : 9.03 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2160 helix: 0.78 (0.14), residues: 1282 sheet: -0.28 (0.42), residues: 139 loop : -0.66 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 420 TYR 0.023 0.002 TYR C 314 PHE 0.020 0.002 PHE F 299 TRP 0.021 0.002 TRP F 599 HIS 0.006 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00672 (18297) covalent geometry : angle 0.63762 (24726) hydrogen bonds : bond 0.05813 ( 995) hydrogen bonds : angle 4.88481 ( 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 334 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 313 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8986 (mmp) cc_final: 0.8436 (mmt) REVERT: A 457 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8244 (mp) REVERT: B 483 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8334 (mtt-85) REVERT: B 614 LYS cc_start: 0.6165 (tttt) cc_final: 0.5182 (tttt) REVERT: D 528 MET cc_start: 0.5900 (ttm) cc_final: 0.5561 (ttm) REVERT: E 484 ASP cc_start: 0.8695 (t0) cc_final: 0.8142 (t0) REVERT: F 358 GLU cc_start: 0.8100 (mp0) cc_final: 0.7735 (mp0) REVERT: F 598 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8193 (mp0) REVERT: F 617 PHE cc_start: 0.8958 (t80) cc_final: 0.8707 (t80) REVERT: F 618 ASN cc_start: 0.8951 (m110) cc_final: 0.8654 (m-40) outliers start: 21 outliers final: 17 residues processed: 318 average time/residue: 0.4607 time to fit residues: 203.6721 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 : 1.032 ------------------------------------------------------------------------------- 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 528 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 162 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.2673 r_free = 0.2673 target = 0.052040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.041335 restraints weight = 132822.455| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 1.80 r_work: 0.2259 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2150 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18297 Z= 0.135 Angle : 0.572 7.050 24726 Z= 0.312 Chirality : 0.035 0.143 2728 Planarity : 0.005 0.061 3061 Dihedral : 11.604 170.336 2605 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.14 % Allowed : 9.49 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.17), residues: 2160 helix: 0.98 (0.14), residues: 1290 sheet: -0.33 (0.43), residues: 139 loop : -0.65 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 483 TYR 0.021 0.002 TYR B 314 PHE 0.016 0.001 PHE F 299 TRP 0.037 0.001 TRP F 599 HIS 0.005 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00299 (18297) covalent geometry : angle 0.57168 (24726) hydrogen bonds : bond 0.04654 ( 995) hydrogen bonds : angle 4.69381 ( 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 336 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 314 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8958 (mmp) cc_final: 0.8407 (mmt) REVERT: A 457 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 476 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8455 (mtpt) REVERT: A 484 ASP cc_start: 0.8549 (t0) cc_final: 0.8098 (t0) REVERT: A 502 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: B 483 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8277 (mtt-85) REVERT: B 614 LYS cc_start: 0.6103 (tttt) cc_final: 0.5160 (tttt) REVERT: D 528 MET cc_start: 0.6059 (ttm) cc_final: 0.5721 (ttm) REVERT: E 375 MET cc_start: 0.9134 (ptp) cc_final: 0.8883 (ptm) REVERT: E 484 ASP cc_start: 0.8639 (t0) cc_final: 0.8078 (t0) REVERT: F 357 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7695 (mtt90) REVERT: F 358 GLU cc_start: 0.8098 (mp0) cc_final: 0.7732 (mp0) REVERT: F 385 GLU cc_start: 0.8749 (tp30) cc_final: 0.8504 (tp30) REVERT: F 617 PHE cc_start: 0.8934 (t80) cc_final: 0.8684 (t80) outliers start: 22 outliers final: 13 residues processed: 319 average time/residue: 0.4486 time to fit residues: 199.0919 Evaluate side-chains 326 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 309 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 ASP 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 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 452 LEU 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: 0.5980 chunk 18 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.052727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.041984 restraints weight = 132883.206| |-----------------------------------------------------------------------------| r_work (start): 0.2384 rms_B_bonded: 1.81 r_work: 0.2279 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2170 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18297 Z= 0.128 Angle : 0.561 10.388 24726 Z= 0.304 Chirality : 0.035 0.139 2728 Planarity : 0.005 0.092 3061 Dihedral : 11.267 167.184 2605 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.03 % Allowed : 9.70 % 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 aren not related in a simple way. whole: 0.67 (0.17), residues: 2160 helix: 1.23 (0.14), residues: 1262 sheet: -0.33 (0.45), residues: 130 loop : -0.65 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 559 TYR 0.020 0.002 TYR B 314 PHE 0.019 0.001 PHE C 299 TRP 0.045 0.001 TRP F 599 HIS 0.004 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00286 (18297) covalent geometry : angle 0.56097 (24726) hydrogen bonds : bond 0.04339 ( 995) hydrogen bonds : angle 4.57890 ( 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 327 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 1.069 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: A 299 PHE cc_start: 0.8720 (t80) cc_final: 0.8485 (t80) REVERT: A 412 MET cc_start: 0.8955 (mmp) cc_final: 0.8407 (mmt) REVERT: A 457 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 476 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8450 (mtpt) REVERT: A 502 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: B 483 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8221 (mtt-85) REVERT: B 614 LYS cc_start: 0.6148 (tttt) cc_final: 0.5223 (tttt) REVERT: D 528 MET cc_start: 0.6146 (ttm) cc_final: 0.5826 (ttm) REVERT: D 623 ILE cc_start: 0.9314 (tt) cc_final: 0.9009 (pt) REVERT: E 375 MET cc_start: 0.9103 (ptp) cc_final: 0.8874 (ptm) REVERT: E 484 ASP cc_start: 0.8668 (t0) cc_final: 0.8098 (t0) REVERT: F 357 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7693 (mtt90) REVERT: F 358 GLU cc_start: 0.8043 (mp0) cc_final: 0.7670 (mp0) REVERT: F 385 GLU cc_start: 0.8728 (tp30) cc_final: 0.8496 (tp30) REVERT: F 570 GLN cc_start: 0.7954 (mt0) cc_final: 0.7620 (mm-40) REVERT: F 617 PHE cc_start: 0.8941 (t80) cc_final: 0.8685 (t80) outliers start: 20 outliers final: 14 residues processed: 313 average time/residue: 0.4131 time to fit residues: 180.1472 Evaluate side-chains 321 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 607 PHE 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: 0.7980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 458 ASN F 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.052291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.041569 restraints weight = 133105.006| |-----------------------------------------------------------------------------| r_work (start): 0.2372 rms_B_bonded: 1.81 r_work: 0.2267 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2158 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18297 Z= 0.158 Angle : 0.583 10.534 24726 Z= 0.316 Chirality : 0.035 0.137 2728 Planarity : 0.005 0.081 3061 Dihedral : 11.232 165.942 2605 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.03 % Allowed : 9.91 % 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 aren not related in a simple way. whole: 0.71 (0.17), residues: 2160 helix: 1.28 (0.15), residues: 1243 sheet: -0.44 (0.43), residues: 141 loop : -0.61 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 483 TYR 0.019 0.002 TYR B 314 PHE 0.031 0.001 PHE E 299 TRP 0.043 0.001 TRP F 599 HIS 0.007 0.001 HIS F 513 Details of bonding type rmsd covalent geometry : bond 0.00361 (18297) covalent geometry : angle 0.58289 (24726) hydrogen bonds : bond 0.04561 ( 995) hydrogen bonds : angle 4.58285 ( 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 327 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 0.978 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: A 299 PHE cc_start: 0.8732 (t80) cc_final: 0.8494 (t80) REVERT: A 412 MET cc_start: 0.8961 (mmp) cc_final: 0.8416 (mmt) REVERT: A 457 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 476 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8468 (mtpt) REVERT: A 502 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: B 483 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8243 (mtt-85) REVERT: B 614 LYS cc_start: 0.6094 (tttt) cc_final: 0.5167 (tttt) REVERT: D 528 MET cc_start: 0.6142 (ttm) cc_final: 0.5872 (ttm) REVERT: E 484 ASP cc_start: 0.8666 (t0) cc_final: 0.8112 (t0) REVERT: F 357 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7704 (mtt90) REVERT: F 358 GLU cc_start: 0.8087 (mp0) cc_final: 0.7723 (mp0) REVERT: F 385 GLU cc_start: 0.8739 (tp30) cc_final: 0.8531 (tp30) REVERT: F 617 PHE cc_start: 0.8919 (t80) cc_final: 0.8716 (t80) outliers start: 20 outliers final: 14 residues processed: 313 average time/residue: 0.4377 time to fit residues: 190.8668 Evaluate side-chains 327 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 309 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain D residue 301 MET 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 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: 0.9980 chunk 126 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 458 ASN F 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.052072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.041345 restraints weight = 132319.495| |-----------------------------------------------------------------------------| r_work (start): 0.2366 rms_B_bonded: 1.81 r_work: 0.2260 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2151 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18297 Z= 0.171 Angle : 0.584 10.246 24726 Z= 0.318 Chirality : 0.036 0.136 2728 Planarity : 0.005 0.061 3061 Dihedral : 11.218 165.501 2605 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.03 % Allowed : 10.06 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.17), residues: 2160 helix: 1.27 (0.15), residues: 1243 sheet: -0.34 (0.43), residues: 139 loop : -0.64 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 483 TYR 0.020 0.002 TYR B 314 PHE 0.027 0.001 PHE E 299 TRP 0.040 0.001 TRP F 599 HIS 0.008 0.001 HIS F 513 Details of bonding type rmsd covalent geometry : bond 0.00393 (18297) covalent geometry : angle 0.58405 (24726) hydrogen bonds : bond 0.04716 ( 995) hydrogen bonds : angle 4.60258 ( 2865) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8157.10 seconds wall clock time: 139 minutes 47.66 seconds (8387.66 seconds total)