Starting phenix.real_space_refine on Wed Aug 5 01:38:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x51_38058/08_2026/8x51_38058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x51_38058/08_2026/8x51_38058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x51_38058/08_2026/8x51_38058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x51_38058/08_2026/8x51_38058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x51_38058/08_2026/8x51_38058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x51_38058/08_2026/8x51_38058.map" } resolution = 2.92 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= 0.000 sd= 0.031 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 40 5.49 5 S 24 5.16 5 C 5064 2.51 5 N 1346 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8095 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3598 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 8, 'TRANS': 431} Chain breaks: 2 Chain: "B" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3640 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 2 Chain: "E" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 423 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "F" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.18 Number of scatterers: 8095 At special positions: 0 Unit cell: (117.6, 78.96, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 24 16.00 P 40 15.00 O 1619 8.00 N 1346 7.00 C 5064 6.00 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: 0.62 Conformation dependent library (CDL) restraints added in 382.6 milliseconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 39.9% alpha, 15.8% beta 20 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.721A pdb=" N VAL A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.971A pdb=" N PHE A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.710A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.753A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.914A pdb=" N CYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.728A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.650A pdb=" N GLU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 502 Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.861A pdb=" N ASP A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 529 removed outlier: 7.394A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 528 " --> pdb=" O MET A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.589A pdb=" N LYS A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 3.601A pdb=" N GLU A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.551A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.954A pdb=" N VAL B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.785A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 325 " --> pdb=" O PRO B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 325' Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.989A pdb=" N ALA B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.853A pdb=" N PHE B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.870A pdb=" N LEU B 420 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 421' Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.639A pdb=" N ARG B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 removed outlier: 3.697A pdb=" N ARG B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 487 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 511 through 516 removed outlier: 4.014A pdb=" N ASP B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 528 removed outlier: 7.635A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 528 " --> pdb=" O MET B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.708A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 551 removed outlier: 3.851A pdb=" N GLU B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.691A pdb=" N PHE B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS B 563 " --> pdb=" O ASP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 567 through 574 removed outlier: 3.660A pdb=" N GLU B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 572 " --> pdb=" O CYS B 568 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.374A pdb=" N LYS A 150 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU A 286 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 152 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU A 288 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 154 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 283 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 8.545A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 6.465A pdb=" N LYS B 150 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU B 286 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 152 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLU B 288 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 154 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 283 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.851A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 437 removed outlier: 3.752A pdb=" N ILE B 465 " --> pdb=" O TYR B 445 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1749 1.33 - 1.45: 1901 1.45 - 1.57: 4545 1.57 - 1.69: 85 1.69 - 1.81: 38 Bond restraints: 8318 Sorted by residual: bond pdb=" C1' DC E 10 " pdb=" N1 DC E 10 " ideal model delta sigma weight residual 1.468 1.553 -0.085 1.40e-02 5.10e+03 3.73e+01 bond pdb=" C3' DT E 20 " pdb=" O3' DT E 20 " ideal model delta sigma weight residual 1.435 1.505 -0.070 1.30e-02 5.92e+03 2.91e+01 bond pdb=" C3' DT F 6 " pdb=" O3' DT F 6 " ideal model delta sigma weight residual 1.435 1.493 -0.058 1.30e-02 5.92e+03 2.02e+01 bond pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.71e+01 bond pdb=" C1' DT E 18 " pdb=" N1 DT E 18 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.63e+01 ... (remaining 8313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 10863 2.75 - 5.50: 401 5.50 - 8.24: 68 8.24 - 10.99: 22 10.99 - 13.74: 5 Bond angle restraints: 11359 Sorted by residual: angle pdb=" O4' DC E 10 " pdb=" C4' DC E 10 " pdb=" C3' DC E 10 " ideal model delta sigma weight residual 106.00 101.45 4.55 6.00e-01 2.78e+00 5.75e+01 angle pdb=" C GLU A 471 " pdb=" N ASP A 472 " pdb=" CA ASP A 472 " ideal model delta sigma weight residual 121.54 133.13 -11.59 1.91e+00 2.74e-01 3.68e+01 angle pdb=" O4' DC E 11 " pdb=" C4' DC E 11 " pdb=" C3' DC E 11 " ideal model delta sigma weight residual 106.00 102.36 3.64 6.00e-01 2.78e+00 3.68e+01 angle pdb=" O4' DC E 9 " pdb=" C4' DC E 9 " pdb=" C3' DC E 9 " ideal model delta sigma weight residual 106.00 102.40 3.60 6.00e-01 2.78e+00 3.59e+01 angle pdb=" C ASP A 64 " pdb=" N THR A 65 " pdb=" CA THR A 65 " ideal model delta sigma weight residual 121.54 132.88 -11.34 1.91e+00 2.74e-01 3.52e+01 ... (remaining 11354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 4743 35.32 - 70.65: 212 70.65 - 105.97: 6 105.97 - 141.30: 1 141.30 - 176.62: 4 Dihedral angle restraints: 4966 sinusoidal: 2369 harmonic: 2597 Sorted by residual: dihedral pdb=" CA GLU B 383 " pdb=" C GLU B 383 " pdb=" N LYS B 384 " pdb=" CA LYS B 384 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual -180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA LEU A 21 " pdb=" C LEU A 21 " pdb=" N ASP A 22 " pdb=" CA ASP A 22 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 4963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1181 0.125 - 0.251: 74 0.251 - 0.376: 10 0.376 - 0.502: 2 0.502 - 0.627: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" P DA F 20 " pdb=" OP1 DA F 20 " pdb=" OP2 DA F 20 " pdb=" O5' DA F 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.83e+00 chirality pdb=" P DA F 19 " pdb=" OP1 DA F 19 " pdb=" OP2 DA F 19 " pdb=" O5' DA F 19 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" CB VAL B 342 " pdb=" CA VAL B 342 " pdb=" CG1 VAL B 342 " pdb=" CG2 VAL B 342 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 1266 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 75 " 0.024 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C LEU B 75 " -0.083 2.00e-02 2.50e+03 pdb=" O LEU B 75 " 0.031 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 374 " 0.339 9.50e-02 1.11e+02 1.52e-01 1.42e+01 pdb=" NE ARG B 374 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 374 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 374 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 374 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 468 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ASP A 468 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP A 468 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 469 " 0.015 2.00e-02 2.50e+03 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2300 2.84 - 3.36: 6286 3.36 - 3.87: 13663 3.87 - 4.39: 15708 4.39 - 4.90: 25949 Nonbonded interactions: 63906 Sorted by model distance: nonbonded pdb=" OD1 ASN B 5 " pdb=" OG1 THR B 74 " model vdw 2.328 3.040 nonbonded pdb=" O LYS B 24 " pdb=" OG1 THR B 331 " model vdw 2.356 3.040 nonbonded pdb=" OH TYR B 153 " pdb=" OE1 GLU B 288 " model vdw 2.383 3.040 nonbonded pdb=" OE1 GLU B 291 " pdb=" OG1 THR B 319 " model vdw 2.413 3.040 nonbonded pdb=" NZ LYS A 439 " pdb=" O2 DT F 17 " model vdw 2.432 3.120 ... (remaining 63901 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' selection = (chain 'B' and (resid 1 through 351 or resid 363 through 575)) } 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: 4.620 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 0.085 8318 Z= 0.478 Angle : 1.295 13.740 11359 Z= 0.800 Chirality : 0.076 0.627 1269 Planarity : 0.008 0.152 1297 Dihedral : 18.472 176.620 3288 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.33 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.23), residues: 873 helix: -4.10 (0.14), residues: 285 sheet: -0.00 (0.38), residues: 202 loop : -2.33 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 51 TYR 0.041 0.003 TYR A 113 PHE 0.036 0.003 PHE A 315 TRP 0.014 0.005 TRP A 126 HIS 0.010 0.002 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.48 ( 8318) covalent geometry : angle 1.29479 / 0.80 (11359) hydrogen bonds : bond 0.17076 / 10.88 ( 278) hydrogen bonds : angle 8.24472 / 5.67 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7807 (ptmm) cc_final: 0.7432 (tttp) REVERT: A 58 SER cc_start: 0.6720 (p) cc_final: 0.6485 (m) REVERT: A 298 MET cc_start: 0.5681 (mtp) cc_final: 0.5359 (tpp) REVERT: A 370 LEU cc_start: 0.8203 (mt) cc_final: 0.7932 (mt) REVERT: B 2 LYS cc_start: 0.7345 (pttp) cc_final: 0.7114 (pttp) REVERT: B 48 LYS cc_start: 0.7032 (mtmm) cc_final: 0.6704 (mtmm) REVERT: B 49 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 68 LYS cc_start: 0.6957 (tppt) cc_final: 0.6529 (mmpt) REVERT: B 285 TYR cc_start: 0.8217 (m-80) cc_final: 0.7304 (m-80) REVERT: B 468 ASP cc_start: 0.7236 (t70) cc_final: 0.7018 (OUTLIER) REVERT: B 474 LYS cc_start: 0.6755 (tttm) cc_final: 0.6549 (pttp) REVERT: B 479 LYS cc_start: 0.5949 (ttpp) cc_final: 0.5592 (tppt) REVERT: B 545 MET cc_start: 0.6642 (tpp) cc_final: 0.6262 (tpp) outliers start: 0 outliers final: 1 residues processed: 172 average time/residue: 0.4824 time to fit residues: 88.1396 Evaluate side-chains 104 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 415 HIS A 551 ASN B 121 ASN B 295 HIS B 455 ASN B 495 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.206537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.183793 restraints weight = 9615.419| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.56 r_work: 0.3856 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8318 Z= 0.169 Angle : 0.730 8.684 11359 Z= 0.405 Chirality : 0.053 0.304 1269 Planarity : 0.004 0.035 1297 Dihedral : 20.788 172.869 1423 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.19 % Favored : 93.36 % Rotamer: Outliers : 2.94 % Allowed : 11.66 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.26), residues: 873 helix: -2.56 (0.23), residues: 301 sheet: 0.20 (0.38), residues: 207 loop : -2.02 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 51 TYR 0.027 0.002 TYR A 113 PHE 0.020 0.002 PHE B 11 TRP 0.008 0.002 TRP B 126 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 8318) covalent geometry : angle 0.73035 / 0.40 (11359) hydrogen bonds : bond 0.05662 / 3.65 ( 278) hydrogen bonds : angle 5.75722 / 3.90 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.7335 (m-10) cc_final: 0.7087 (m-10) REVERT: A 48 LYS cc_start: 0.8045 (ptmm) cc_final: 0.7598 (tttp) REVERT: A 58 SER cc_start: 0.6915 (p) cc_final: 0.6655 (m) REVERT: A 298 MET cc_start: 0.5790 (mtp) cc_final: 0.5558 (tmm) REVERT: A 370 LEU cc_start: 0.8293 (mt) cc_final: 0.8085 (mt) REVERT: A 373 GLU cc_start: 0.7282 (tp30) cc_final: 0.6791 (tp30) REVERT: A 541 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6933 (tttp) REVERT: A 547 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: B 2 LYS cc_start: 0.7261 (pttp) cc_final: 0.7015 (pttt) REVERT: B 48 LYS cc_start: 0.7357 (mtmm) cc_final: 0.7078 (mtmm) REVERT: B 49 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 68 LYS cc_start: 0.7032 (tppt) cc_final: 0.6800 (tppt) REVERT: B 285 TYR cc_start: 0.8161 (m-80) cc_final: 0.7719 (m-80) REVERT: B 305 GLN cc_start: 0.6983 (mt0) cc_final: 0.6408 (tt0) REVERT: B 455 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.6809 (t0) REVERT: B 468 ASP cc_start: 0.7209 (t70) cc_final: 0.7000 (OUTLIER) REVERT: B 474 LYS cc_start: 0.6987 (tttm) cc_final: 0.6781 (pttp) REVERT: B 479 LYS cc_start: 0.6351 (ttpp) cc_final: 0.5979 (tppt) REVERT: B 545 MET cc_start: 0.6994 (tpp) cc_final: 0.6600 (tpp) outliers start: 24 outliers final: 6 residues processed: 121 average time/residue: 0.4294 time to fit residues: 55.7088 Evaluate side-chains 100 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 465 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 69 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 551 ASN B 337 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.206613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.180893 restraints weight = 9490.658| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.83 r_work: 0.3829 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8318 Z= 0.139 Angle : 0.657 8.850 11359 Z= 0.365 Chirality : 0.051 0.364 1269 Planarity : 0.003 0.025 1297 Dihedral : 20.663 173.925 1423 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 2.58 % Allowed : 14.72 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.27), residues: 873 helix: -1.53 (0.27), residues: 299 sheet: 0.40 (0.39), residues: 204 loop : -1.91 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 51 TYR 0.026 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 8318) covalent geometry : angle 0.65706 / 0.37 (11359) hydrogen bonds : bond 0.04912 / 3.19 ( 278) hydrogen bonds : angle 5.30524 / 3.59 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.290 Fit side-chains REVERT: A 22 ASP cc_start: 0.7088 (p0) cc_final: 0.6851 (m-30) REVERT: A 48 LYS cc_start: 0.8105 (ptmm) cc_final: 0.7626 (tttp) REVERT: A 58 SER cc_start: 0.7006 (p) cc_final: 0.6716 (m) REVERT: A 87 LYS cc_start: 0.6519 (mmtt) cc_final: 0.6250 (mmtt) REVERT: A 298 MET cc_start: 0.5806 (mtp) cc_final: 0.5526 (tmm) REVERT: A 370 LEU cc_start: 0.8265 (mt) cc_final: 0.8041 (mt) REVERT: A 373 GLU cc_start: 0.7275 (tp30) cc_final: 0.6797 (tp30) REVERT: A 541 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6877 (tttp) REVERT: A 547 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 549 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7263 (m) REVERT: B 2 LYS cc_start: 0.7287 (pttp) cc_final: 0.7061 (pttt) REVERT: B 48 LYS cc_start: 0.7501 (mtmm) cc_final: 0.7283 (mtmm) REVERT: B 49 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8022 (mm-30) REVERT: B 68 LYS cc_start: 0.7063 (tppt) cc_final: 0.6829 (tppt) REVERT: B 116 LYS cc_start: 0.5375 (mmpt) cc_final: 0.4465 (ptmm) REVERT: B 285 TYR cc_start: 0.8159 (m-80) cc_final: 0.7805 (m-80) REVERT: B 305 GLN cc_start: 0.6958 (mt0) cc_final: 0.6415 (tt0) REVERT: B 367 SER cc_start: 0.8239 (p) cc_final: 0.8035 (p) REVERT: B 383 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.4903 (pt0) REVERT: B 474 LYS cc_start: 0.6953 (tttm) cc_final: 0.6718 (pttp) REVERT: B 479 LYS cc_start: 0.6324 (ttpp) cc_final: 0.5907 (tppt) REVERT: B 537 LEU cc_start: 0.7022 (tp) cc_final: 0.6792 (tt) REVERT: B 545 MET cc_start: 0.7090 (tpp) cc_final: 0.6635 (tpp) outliers start: 21 outliers final: 7 residues processed: 112 average time/residue: 0.4331 time to fit residues: 52.2371 Evaluate side-chains 103 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.205094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.179192 restraints weight = 9660.387| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.81 r_work: 0.3822 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8318 Z= 0.139 Angle : 0.632 6.997 11359 Z= 0.352 Chirality : 0.051 0.380 1269 Planarity : 0.003 0.020 1297 Dihedral : 20.547 171.545 1423 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.07 % Favored : 93.59 % Rotamer: Outliers : 3.56 % Allowed : 14.60 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.28), residues: 873 helix: -0.80 (0.29), residues: 302 sheet: 0.42 (0.39), residues: 204 loop : -1.76 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 51 TYR 0.023 0.001 TYR A 113 PHE 0.013 0.001 PHE A 490 TRP 0.004 0.001 TRP B 126 HIS 0.007 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 8318) covalent geometry : angle 0.63177 / 0.35 (11359) hydrogen bonds : bond 0.04634 / 3.05 ( 278) hydrogen bonds : angle 4.96842 / 3.37 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.314 Fit side-chains REVERT: A 48 LYS cc_start: 0.8106 (ptmm) cc_final: 0.7604 (tttp) REVERT: A 58 SER cc_start: 0.7113 (p) cc_final: 0.6788 (m) REVERT: A 298 MET cc_start: 0.5772 (mtp) cc_final: 0.5471 (tmm) REVERT: A 370 LEU cc_start: 0.8278 (mt) cc_final: 0.8076 (mt) REVERT: A 373 GLU cc_start: 0.7287 (tp30) cc_final: 0.6789 (tp30) REVERT: A 487 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6546 (mtmp) REVERT: A 541 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6876 (tttp) REVERT: A 547 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: A 549 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7203 (m) REVERT: B 2 LYS cc_start: 0.7369 (pttp) cc_final: 0.7137 (pttt) REVERT: B 21 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7077 (pp) REVERT: B 68 LYS cc_start: 0.7121 (tppt) cc_final: 0.6850 (tppp) REVERT: B 116 LYS cc_start: 0.5323 (mmpt) cc_final: 0.4467 (ptmm) REVERT: B 285 TYR cc_start: 0.8159 (m-80) cc_final: 0.7756 (m-80) REVERT: B 305 GLN cc_start: 0.6969 (mt0) cc_final: 0.6445 (tt0) REVERT: B 383 GLU cc_start: 0.5103 (OUTLIER) cc_final: 0.4846 (pt0) REVERT: B 479 LYS cc_start: 0.6455 (ttpp) cc_final: 0.5936 (tppt) REVERT: B 524 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6725 (mmt) REVERT: B 545 MET cc_start: 0.7048 (tpp) cc_final: 0.6531 (tpp) outliers start: 29 outliers final: 11 residues processed: 119 average time/residue: 0.4464 time to fit residues: 57.1015 Evaluate side-chains 107 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 551 ASN B 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.200761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.177039 restraints weight = 9622.177| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.54 r_work: 0.3773 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8318 Z= 0.177 Angle : 0.681 8.143 11359 Z= 0.375 Chirality : 0.053 0.476 1269 Planarity : 0.003 0.025 1297 Dihedral : 20.487 171.831 1423 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 5.52 % Allowed : 13.99 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.28), residues: 873 helix: -0.40 (0.31), residues: 296 sheet: 0.36 (0.39), residues: 200 loop : -1.61 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 332 TYR 0.022 0.002 TYR A 113 PHE 0.019 0.002 PHE A 490 TRP 0.006 0.002 TRP B 126 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 8318) covalent geometry : angle 0.68140 / 0.37 (11359) hydrogen bonds : bond 0.05030 / 3.27 ( 278) hydrogen bonds : angle 4.97238 / 3.39 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 93 time to evaluate : 0.295 Fit side-chains REVERT: A 48 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7614 (tttp) REVERT: A 58 SER cc_start: 0.7151 (p) cc_final: 0.6786 (m) REVERT: A 289 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: A 298 MET cc_start: 0.5795 (mtp) cc_final: 0.5424 (tmm) REVERT: A 324 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8500 (mt) REVERT: A 327 GLU cc_start: 0.7725 (pm20) cc_final: 0.7143 (tp30) REVERT: A 373 GLU cc_start: 0.7448 (tp30) cc_final: 0.6879 (tp30) REVERT: A 487 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6542 (mtmp) REVERT: A 532 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7625 (OUTLIER) REVERT: A 541 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6817 (tttp) REVERT: A 547 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: B 2 LYS cc_start: 0.7466 (pttp) cc_final: 0.7237 (pttt) REVERT: B 21 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7051 (pp) REVERT: B 48 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7186 (mtmm) REVERT: B 68 LYS cc_start: 0.7186 (tppt) cc_final: 0.6910 (tppp) REVERT: B 97 ARG cc_start: 0.5994 (mmm160) cc_final: 0.5723 (mmm160) REVERT: B 116 LYS cc_start: 0.5252 (mmpt) cc_final: 0.4425 (ptmm) REVERT: B 130 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7643 (tm) REVERT: B 150 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7050 (ttmm) REVERT: B 305 GLN cc_start: 0.6981 (mt0) cc_final: 0.6461 (tt0) REVERT: B 363 ASN cc_start: 0.6916 (m-40) cc_final: 0.6628 (m-40) REVERT: B 479 LYS cc_start: 0.6433 (ttpp) cc_final: 0.5882 (tppt) REVERT: B 503 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: B 524 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6797 (mmt) outliers start: 45 outliers final: 12 residues processed: 121 average time/residue: 0.5296 time to fit residues: 68.1695 Evaluate side-chains 110 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.0020 chunk 68 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.203412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175629 restraints weight = 9511.997| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.25 r_work: 0.3832 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8318 Z= 0.131 Angle : 0.624 7.250 11359 Z= 0.347 Chirality : 0.050 0.394 1269 Planarity : 0.003 0.025 1297 Dihedral : 20.431 170.052 1423 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.04 % Rotamer: Outliers : 4.42 % Allowed : 15.71 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.29), residues: 873 helix: -0.10 (0.31), residues: 290 sheet: 0.28 (0.38), residues: 207 loop : -1.41 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 374 TYR 0.021 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 8318) covalent geometry : angle 0.62428 / 0.35 (11359) hydrogen bonds : bond 0.04436 / 2.93 ( 278) hydrogen bonds : angle 4.83369 / 3.30 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.231 Fit side-chains REVERT: A 48 LYS cc_start: 0.8021 (ptmm) cc_final: 0.7522 (tttp) REVERT: A 58 SER cc_start: 0.7022 (p) cc_final: 0.6650 (m) REVERT: A 289 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: A 298 MET cc_start: 0.5769 (mtp) cc_final: 0.5397 (tmm) REVERT: A 324 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8426 (mt) REVERT: A 327 GLU cc_start: 0.7661 (pm20) cc_final: 0.7091 (tp30) REVERT: A 373 GLU cc_start: 0.7401 (tp30) cc_final: 0.6814 (tp30) REVERT: A 532 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7659 (OUTLIER) REVERT: A 541 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6786 (tttp) REVERT: A 549 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7185 (m) REVERT: B 2 LYS cc_start: 0.7414 (pttp) cc_final: 0.7190 (pttt) REVERT: B 21 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6951 (pp) REVERT: B 48 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7074 (mtmm) REVERT: B 68 LYS cc_start: 0.6998 (tppt) cc_final: 0.6748 (tppp) REVERT: B 97 ARG cc_start: 0.5921 (mmm160) cc_final: 0.5552 (mmm160) REVERT: B 130 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7645 (tm) REVERT: B 150 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7004 (ttmm) REVERT: B 305 GLN cc_start: 0.7027 (mt0) cc_final: 0.6464 (tt0) REVERT: B 363 ASN cc_start: 0.6893 (m-40) cc_final: 0.6559 (m-40) REVERT: B 364 LYS cc_start: 0.6342 (tptp) cc_final: 0.5917 (tppp) REVERT: B 479 LYS cc_start: 0.6348 (ttpp) cc_final: 0.5814 (tppt) REVERT: B 503 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6385 (tm-30) REVERT: B 524 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6801 (mmt) outliers start: 36 outliers final: 12 residues processed: 115 average time/residue: 0.4786 time to fit residues: 58.9304 Evaluate side-chains 104 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.202447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.175711 restraints weight = 9564.555| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.84 r_work: 0.3787 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8318 Z= 0.138 Angle : 0.628 7.409 11359 Z= 0.348 Chirality : 0.051 0.413 1269 Planarity : 0.003 0.025 1297 Dihedral : 20.349 169.502 1423 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer: Outliers : 3.56 % Allowed : 17.30 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.29), residues: 873 helix: -0.09 (0.30), residues: 300 sheet: 0.27 (0.38), residues: 203 loop : -1.43 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.020 0.001 TYR A 113 PHE 0.012 0.001 PHE A 315 TRP 0.005 0.001 TRP B 126 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 8318) covalent geometry : angle 0.62838 / 0.35 (11359) hydrogen bonds : bond 0.04490 / 2.98 ( 278) hydrogen bonds : angle 4.76859 / 3.26 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.284 Fit side-chains REVERT: A 48 LYS cc_start: 0.8058 (ptmm) cc_final: 0.7558 (tttp) REVERT: A 58 SER cc_start: 0.7019 (p) cc_final: 0.6628 (m) REVERT: A 289 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: A 298 MET cc_start: 0.5852 (mtp) cc_final: 0.5402 (tmm) REVERT: A 324 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8476 (mt) REVERT: A 327 GLU cc_start: 0.7686 (pm20) cc_final: 0.7120 (tp30) REVERT: A 373 GLU cc_start: 0.7469 (tp30) cc_final: 0.6858 (tp30) REVERT: A 532 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: A 541 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6774 (tttp) REVERT: A 549 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7140 (m) REVERT: B 2 LYS cc_start: 0.7456 (pttp) cc_final: 0.7216 (pttt) REVERT: B 21 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7023 (pp) REVERT: B 48 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7334 (mtmm) REVERT: B 68 LYS cc_start: 0.7143 (tppt) cc_final: 0.6902 (tppp) REVERT: B 97 ARG cc_start: 0.6016 (mmm160) cc_final: 0.5626 (mmm160) REVERT: B 130 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7685 (tm) REVERT: B 150 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7040 (ttmm) REVERT: B 305 GLN cc_start: 0.7028 (mt0) cc_final: 0.6477 (tt0) REVERT: B 363 ASN cc_start: 0.6909 (m-40) cc_final: 0.6512 (m-40) REVERT: B 383 GLU cc_start: 0.5074 (OUTLIER) cc_final: 0.4856 (pt0) REVERT: B 433 ASN cc_start: 0.6505 (OUTLIER) cc_final: 0.6186 (t0) REVERT: B 479 LYS cc_start: 0.6361 (ttpp) cc_final: 0.5826 (tppt) REVERT: B 503 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6518 (tm-30) REVERT: B 524 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6823 (mmt) outliers start: 29 outliers final: 11 residues processed: 108 average time/residue: 0.4373 time to fit residues: 50.5657 Evaluate side-chains 108 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.202412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176006 restraints weight = 9560.837| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.90 r_work: 0.3771 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8318 Z= 0.155 Angle : 0.645 7.928 11359 Z= 0.356 Chirality : 0.051 0.448 1269 Planarity : 0.003 0.026 1297 Dihedral : 20.325 169.967 1423 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer: Outliers : 4.05 % Allowed : 17.55 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.29), residues: 873 helix: 0.00 (0.31), residues: 299 sheet: 0.22 (0.39), residues: 204 loop : -1.37 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.020 0.001 TYR A 113 PHE 0.015 0.001 PHE A 490 TRP 0.004 0.001 TRP B 126 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 8318) covalent geometry : angle 0.64546 / 0.36 (11359) hydrogen bonds : bond 0.04696 / 3.09 ( 278) hydrogen bonds : angle 4.79411 / 3.28 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.310 Fit side-chains REVERT: A 48 LYS cc_start: 0.8110 (ptmm) cc_final: 0.7634 (tttp) REVERT: A 58 SER cc_start: 0.7115 (p) cc_final: 0.6687 (m) REVERT: A 289 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: A 298 MET cc_start: 0.5866 (mtp) cc_final: 0.5449 (mmm) REVERT: A 324 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8572 (mt) REVERT: A 327 GLU cc_start: 0.7669 (pm20) cc_final: 0.7291 (tp30) REVERT: A 460 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7046 (mp0) REVERT: A 504 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6720 (mpt180) REVERT: A 541 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6797 (tttp) REVERT: A 549 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7130 (p) REVERT: B 21 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7017 (pp) REVERT: B 48 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7589 (mtmm) REVERT: B 97 ARG cc_start: 0.5999 (mmm160) cc_final: 0.5750 (mmm160) REVERT: B 130 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7731 (tm) REVERT: B 150 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7114 (ttmm) REVERT: B 305 GLN cc_start: 0.7146 (mt0) cc_final: 0.6553 (tt0) REVERT: B 363 ASN cc_start: 0.7011 (m-40) cc_final: 0.6608 (m-40) REVERT: B 383 GLU cc_start: 0.5339 (OUTLIER) cc_final: 0.5089 (pt0) REVERT: B 433 ASN cc_start: 0.6653 (OUTLIER) cc_final: 0.6226 (t0) REVERT: B 479 LYS cc_start: 0.6478 (ttpp) cc_final: 0.5942 (tppt) REVERT: B 503 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: B 524 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6882 (mmt) REVERT: B 551 ASN cc_start: 0.6812 (m110) cc_final: 0.6429 (p0) outliers start: 33 outliers final: 11 residues processed: 111 average time/residue: 0.4376 time to fit residues: 51.9562 Evaluate side-chains 108 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 550 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.203659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177236 restraints weight = 9613.712| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.91 r_work: 0.3803 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.003 0.034 8318 Z= 0.134 Angle : 0.622 7.444 11359 Z= 0.344 Chirality : 0.050 0.407 1269 Planarity : 0.003 0.025 1297 Dihedral : 20.324 169.696 1423 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer: Outliers : 3.68 % Allowed : 18.40 % Favored : 77.91 % 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 are not related in a simple way. whole: -0.73 (0.29), residues: 873 helix: 0.10 (0.31), residues: 301 sheet: 0.24 (0.39), residues: 204 loop : -1.34 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.019 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 8318) covalent geometry : angle 0.62212 / 0.34 (11359) hydrogen bonds : bond 0.04402 / 2.92 ( 278) hydrogen bonds : angle 4.71304 / 3.23 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.301 Fit side-chains REVERT: A 48 LYS cc_start: 0.8086 (ptmm) cc_final: 0.7623 (tttp) REVERT: A 58 SER cc_start: 0.7074 (p) cc_final: 0.6642 (m) REVERT: A 289 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: A 298 MET cc_start: 0.5866 (mtp) cc_final: 0.5463 (mmm) REVERT: A 327 GLU cc_start: 0.7664 (pm20) cc_final: 0.6997 (tm-30) REVERT: A 383 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: A 504 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6710 (mpt180) REVERT: A 549 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7144 (p) REVERT: B 21 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7111 (pp) REVERT: B 48 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7559 (mtmm) REVERT: B 68 LYS cc_start: 0.7476 (tppp) cc_final: 0.7244 (tttm) REVERT: B 97 ARG cc_start: 0.6046 (mmm160) cc_final: 0.5814 (mmm160) REVERT: B 130 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7758 (tm) REVERT: B 141 ASN cc_start: 0.7715 (m-40) cc_final: 0.7485 (m110) REVERT: B 150 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7099 (ttmm) REVERT: B 305 GLN cc_start: 0.7171 (mt0) cc_final: 0.6559 (tt0) REVERT: B 363 ASN cc_start: 0.6969 (m-40) cc_final: 0.6601 (m-40) REVERT: B 383 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.5132 (pt0) REVERT: B 479 LYS cc_start: 0.6480 (ttpp) cc_final: 0.5942 (tppt) REVERT: B 503 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: B 524 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6845 (mmt) REVERT: B 551 ASN cc_start: 0.6854 (m110) cc_final: 0.6298 (p0) outliers start: 30 outliers final: 12 residues processed: 104 average time/residue: 0.4133 time to fit residues: 45.9188 Evaluate side-chains 104 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.203221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176621 restraints weight = 9665.501| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.95 r_work: 0.3789 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8318 Z= 0.140 Angle : 0.628 7.529 11359 Z= 0.347 Chirality : 0.050 0.412 1269 Planarity : 0.003 0.025 1297 Dihedral : 20.320 169.528 1423 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.53 % Favored : 93.13 % Rotamer: Outliers : 2.94 % Allowed : 18.90 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.29), residues: 873 helix: 0.12 (0.31), residues: 301 sheet: 0.25 (0.39), residues: 204 loop : -1.33 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 296 TYR 0.019 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.005 0.001 TRP B 126 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 8318) covalent geometry : angle 0.62804 / 0.35 (11359) hydrogen bonds : bond 0.04459 / 2.96 ( 278) hydrogen bonds : angle 4.68831 / 3.21 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.221 Fit side-chains REVERT: A 48 LYS cc_start: 0.8066 (ptmm) cc_final: 0.7606 (tttp) REVERT: A 58 SER cc_start: 0.7061 (p) cc_final: 0.6615 (m) REVERT: A 289 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: A 298 MET cc_start: 0.5856 (mtp) cc_final: 0.5452 (mmm) REVERT: A 327 GLU cc_start: 0.7636 (pm20) cc_final: 0.7117 (tm-30) REVERT: A 383 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: A 460 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7054 (mp0) REVERT: A 504 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6752 (mpt180) REVERT: A 549 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7138 (p) REVERT: B 21 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7063 (pp) REVERT: B 48 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7620 (mtmm) REVERT: B 68 LYS cc_start: 0.7432 (tppp) cc_final: 0.7211 (tttm) REVERT: B 130 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7733 (tm) REVERT: B 141 ASN cc_start: 0.7729 (m-40) cc_final: 0.7483 (m110) REVERT: B 150 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7085 (ttmm) REVERT: B 305 GLN cc_start: 0.7133 (mt0) cc_final: 0.6529 (tt0) REVERT: B 363 ASN cc_start: 0.6966 (m-40) cc_final: 0.6588 (m-40) REVERT: B 383 GLU cc_start: 0.5405 (OUTLIER) cc_final: 0.5140 (pt0) REVERT: B 479 LYS cc_start: 0.6489 (ttpp) cc_final: 0.5921 (tppt) REVERT: B 503 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: B 524 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6861 (mmt) outliers start: 24 outliers final: 11 residues processed: 101 average time/residue: 0.4731 time to fit residues: 50.9454 Evaluate side-chains 103 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.204406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.177637 restraints weight = 9574.485| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.93 r_work: 0.3835 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8318 Z= 0.129 Angle : 0.610 7.749 11359 Z= 0.338 Chirality : 0.050 0.382 1269 Planarity : 0.002 0.024 1297 Dihedral : 20.337 169.849 1423 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer: Outliers : 3.07 % Allowed : 18.90 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.29), residues: 873 helix: 0.24 (0.31), residues: 302 sheet: 0.14 (0.38), residues: 208 loop : -1.35 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.019 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 8318) covalent geometry : angle 0.61030 / 0.34 (11359) hydrogen bonds : bond 0.04300 / 2.87 ( 278) hydrogen bonds : angle 4.64122 / 3.18 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.33 seconds wall clock time: 37 minutes 57.72 seconds (2277.72 seconds total)