Starting phenix.real_space_refine on Tue May 7 13:26:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x51_38058/05_2024/8x51_38058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x51_38058/05_2024/8x51_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x51_38058/05_2024/8x51_38058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x51_38058/05_2024/8x51_38058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x51_38058/05_2024/8x51_38058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x51_38058/05_2024/8x51_38058.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/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: 4.98, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 2.97 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: 2.71 Time building geometry restraints manager: 3.56 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=" N VAL B 375 " pdb=" CA VAL B 375 " ideal model delta sigma weight residual 1.458 1.498 -0.039 1.17e-02 7.31e+03 1.14e+01 bond pdb=" C3' DT E 20 " pdb=" O3' DT E 20 " ideal model delta sigma weight residual 1.422 1.505 -0.083 3.00e-02 1.11e+03 7.68e+00 bond pdb=" N LEU B 376 " pdb=" CA LEU B 376 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" N ARG B 374 " pdb=" CA ARG B 374 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.26e+00 bond pdb=" C3' DT F 6 " pdb=" O3' DT F 6 " ideal model delta sigma weight residual 1.422 1.493 -0.071 3.00e-02 1.11e+03 5.67e+00 ... (remaining 8313 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.43: 264 105.43 - 112.54: 3930 112.54 - 119.66: 3433 119.66 - 126.77: 3527 126.77 - 133.89: 205 Bond angle restraints: 11359 Sorted by residual: 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=" 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 angle pdb=" CA TYR A 113 " pdb=" CB TYR A 113 " pdb=" CG TYR A 113 " ideal model delta sigma weight residual 113.90 124.06 -10.16 1.80e+00 3.09e-01 3.19e+01 angle pdb=" C LYS B 341 " pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta sigma weight residual 121.97 132.08 -10.11 1.80e+00 3.09e-01 3.15e+01 angle pdb=" C LEU B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.10e+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 - 0.123: 1186 0.123 - 0.247: 70 0.247 - 0.370: 9 0.370 - 0.493: 2 0.493 - 0.617: 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 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.51e+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 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.33e+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 2.440 nonbonded pdb=" O LYS B 24 " pdb=" OG1 THR B 331 " model vdw 2.356 2.440 nonbonded pdb=" OH TYR B 153 " pdb=" OE1 GLU B 288 " model vdw 2.383 2.440 nonbonded pdb=" OE1 GLU B 291 " pdb=" OG1 THR B 319 " model vdw 2.413 2.440 nonbonded pdb=" NZ LYS A 439 " pdb=" O2 DT F 17 " model vdw 2.432 2.520 ... (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 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: 2.880 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: 0.010 Extract box with map and model: 12.030 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.030 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 0.083 8318 Z= 0.465 Angle : 1.266 13.740 11359 Z= 0.689 Chirality : 0.074 0.617 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.005 TRP A 126 HIS 0.010 0.002 HIS A 320 PHE 0.036 0.003 PHE A 315 TYR 0.041 0.003 TYR A 113 ARG 0.007 0.001 ARG B 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7808 (ptmm) cc_final: 0.7432 (tttp) REVERT: A 58 SER cc_start: 0.6720 (p) cc_final: 0.6486 (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: 0.7113 (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 479 LYS cc_start: 0.5949 (ttpp) cc_final: 0.5590 (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: 1.1474 time to fit residues: 209.8693 Evaluate side-chains 104 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.0020 chunk 83 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 551 ASN B 295 HIS B 337 HIS B 495 ASN B 514 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8318 Z= 0.190 Angle : 0.629 7.333 11359 Z= 0.348 Chirality : 0.045 0.175 1269 Planarity : 0.003 0.033 1297 Dihedral : 20.516 177.152 1423 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer: Outliers : 2.70 % Allowed : 12.15 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.26), residues: 873 helix: -2.31 (0.23), residues: 301 sheet: 0.30 (0.39), residues: 205 loop : -2.00 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 126 HIS 0.004 0.001 HIS A 415 PHE 0.019 0.001 PHE B 11 TYR 0.024 0.002 TYR A 113 ARG 0.005 0.001 ARG B 51 *********************** 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 132 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7908 (ptmm) cc_final: 0.7391 (tttp) REVERT: A 58 SER cc_start: 0.6831 (p) cc_final: 0.6539 (m) REVERT: A 298 MET cc_start: 0.5786 (mtp) cc_final: 0.5453 (tmm) REVERT: A 541 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6925 (tttp) REVERT: A 547 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: B 2 LYS cc_start: 0.7345 (pttp) cc_final: 0.6990 (pttt) REVERT: B 48 LYS cc_start: 0.7220 (mtmm) cc_final: 0.6869 (mtmm) REVERT: B 49 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7802 (mm-30) REVERT: B 68 LYS cc_start: 0.7071 (tppt) cc_final: 0.6742 (tppp) REVERT: B 305 GLN cc_start: 0.6696 (mt0) cc_final: 0.6206 (tt0) REVERT: B 367 SER cc_start: 0.8501 (p) cc_final: 0.8266 (p) REVERT: B 479 LYS cc_start: 0.6125 (ttpp) cc_final: 0.5682 (tppt) REVERT: B 545 MET cc_start: 0.6601 (tpp) cc_final: 0.6052 (tpp) outliers start: 22 outliers final: 6 residues processed: 120 average time/residue: 1.0555 time to fit residues: 135.9313 Evaluate side-chains 103 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR 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 128 SER Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 468 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 415 HIS A 551 ASN B 455 ASN B 538 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8318 Z= 0.307 Angle : 0.702 10.541 11359 Z= 0.383 Chirality : 0.048 0.172 1269 Planarity : 0.004 0.033 1297 Dihedral : 20.551 176.800 1423 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer: Outliers : 4.54 % Allowed : 13.99 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.27), residues: 873 helix: -1.22 (0.28), residues: 301 sheet: 0.53 (0.39), residues: 199 loop : -1.90 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 126 HIS 0.008 0.001 HIS B 295 PHE 0.019 0.002 PHE A 490 TYR 0.022 0.002 TYR A 113 ARG 0.005 0.001 ARG A 332 *********************** 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 129 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 0.916 Fit side-chains REVERT: A 22 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6940 (p0) REVERT: A 48 LYS cc_start: 0.7846 (ptmm) cc_final: 0.7357 (tttp) REVERT: A 58 SER cc_start: 0.6879 (p) cc_final: 0.6513 (m) REVERT: A 298 MET cc_start: 0.5946 (mtp) cc_final: 0.5426 (tmm) REVERT: A 324 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8181 (mt) REVERT: A 327 GLU cc_start: 0.7414 (pm20) cc_final: 0.6907 (tp30) REVERT: A 532 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: B 21 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6860 (pp) REVERT: B 48 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7336 (mtmm) REVERT: B 49 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 68 LYS cc_start: 0.7078 (tppt) cc_final: 0.6850 (tppt) REVERT: B 130 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7493 (tm) REVERT: B 143 ASN cc_start: 0.7146 (OUTLIER) cc_final: 0.6791 (m-40) REVERT: B 305 GLN cc_start: 0.6833 (mt0) cc_final: 0.6306 (tt0) REVERT: B 367 SER cc_start: 0.8414 (p) cc_final: 0.8157 (p) REVERT: B 468 ASP cc_start: 0.7230 (t70) cc_final: 0.6952 (t0) REVERT: B 479 LYS cc_start: 0.6142 (ttpp) cc_final: 0.5577 (tppt) outliers start: 37 outliers final: 13 residues processed: 114 average time/residue: 1.0816 time to fit residues: 131.8289 Evaluate side-chains 101 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 386 LEU 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 36 THR 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 143 ASN 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 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 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8318 Z= 0.212 Angle : 0.613 7.773 11359 Z= 0.338 Chirality : 0.045 0.165 1269 Planarity : 0.003 0.022 1297 Dihedral : 20.525 173.859 1423 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer: Outliers : 4.29 % Allowed : 15.46 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.28), residues: 873 helix: -0.66 (0.29), residues: 310 sheet: 0.42 (0.39), residues: 197 loop : -1.77 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 126 HIS 0.006 0.001 HIS A 415 PHE 0.014 0.001 PHE A 315 TYR 0.021 0.001 TYR A 113 ARG 0.003 0.000 ARG B 51 *********************** 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 123 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 0.906 Fit side-chains REVERT: A 22 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6797 (p0) REVERT: A 48 LYS cc_start: 0.7875 (ptmm) cc_final: 0.7341 (tttp) REVERT: A 58 SER cc_start: 0.6829 (p) cc_final: 0.6440 (m) REVERT: A 327 GLU cc_start: 0.7342 (pm20) cc_final: 0.6960 (tp30) REVERT: A 532 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: A 549 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7135 (m) REVERT: B 21 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6805 (pp) REVERT: B 49 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7773 (mm-30) REVERT: B 68 LYS cc_start: 0.7027 (tppt) cc_final: 0.6779 (tppt) REVERT: B 97 ARG cc_start: 0.5717 (mmm160) cc_final: 0.5440 (mmm160) REVERT: B 130 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7526 (tm) REVERT: B 305 GLN cc_start: 0.6886 (mt0) cc_final: 0.6354 (tt0) REVERT: B 367 SER cc_start: 0.8367 (p) cc_final: 0.8143 (p) REVERT: B 383 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4714 (pm20) REVERT: B 468 ASP cc_start: 0.7108 (t70) cc_final: 0.6835 (t0) REVERT: B 479 LYS cc_start: 0.6098 (ttpp) cc_final: 0.5549 (tppt) outliers start: 35 outliers final: 12 residues processed: 108 average time/residue: 1.1685 time to fit residues: 134.7093 Evaluate side-chains 93 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 386 LEU 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 A residue 554 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 ASN 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 465 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS B 121 ASN B 550 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8318 Z= 0.285 Angle : 0.666 6.928 11359 Z= 0.364 Chirality : 0.047 0.158 1269 Planarity : 0.003 0.026 1297 Dihedral : 20.483 175.833 1423 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.99 % Favored : 92.67 % Rotamer: Outliers : 5.15 % Allowed : 16.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.28), residues: 873 helix: -0.39 (0.30), residues: 306 sheet: 0.40 (0.41), residues: 189 loop : -1.56 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 126 HIS 0.005 0.001 HIS A 415 PHE 0.017 0.002 PHE A 490 TYR 0.020 0.002 TYR A 113 ARG 0.005 0.001 ARG A 332 *********************** 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 123 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 81 time to evaluate : 0.930 Fit side-chains REVERT: A 22 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6973 (p0) REVERT: A 48 LYS cc_start: 0.7897 (ptmm) cc_final: 0.7350 (tttp) REVERT: A 58 SER cc_start: 0.6863 (p) cc_final: 0.6447 (m) REVERT: A 289 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: A 324 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8233 (mt) REVERT: A 327 GLU cc_start: 0.7396 (pm20) cc_final: 0.7081 (tp30) REVERT: A 526 ARG cc_start: 0.6666 (ttp-110) cc_final: 0.6362 (mtm110) REVERT: A 532 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: B 21 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6817 (pp) REVERT: B 48 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7286 (mtmm) REVERT: B 49 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7716 (mm-30) REVERT: B 68 LYS cc_start: 0.7206 (tppt) cc_final: 0.6956 (tppt) REVERT: B 130 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7471 (tm) REVERT: B 305 GLN cc_start: 0.6913 (mt0) cc_final: 0.6344 (tt0) REVERT: B 363 ASN cc_start: 0.6762 (m-40) cc_final: 0.6313 (m-40) REVERT: B 367 SER cc_start: 0.8367 (p) cc_final: 0.8142 (p) REVERT: B 468 ASP cc_start: 0.7147 (t70) cc_final: 0.6871 (t0) REVERT: B 479 LYS cc_start: 0.6195 (ttpp) cc_final: 0.5580 (tppt) REVERT: B 503 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6410 (tm-30) REVERT: B 551 ASN cc_start: 0.6737 (m110) cc_final: 0.6301 (p0) outliers start: 42 outliers final: 16 residues processed: 109 average time/residue: 1.1202 time to fit residues: 130.4502 Evaluate side-chains 103 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 36 THR 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 554 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 36 THR 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 143 ASN 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 560 VAL Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8318 Z= 0.236 Angle : 0.637 7.663 11359 Z= 0.347 Chirality : 0.046 0.155 1269 Planarity : 0.003 0.021 1297 Dihedral : 20.454 174.168 1423 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.76 % Favored : 92.90 % Rotamer: Outliers : 4.66 % Allowed : 17.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.29), residues: 873 helix: -0.11 (0.31), residues: 297 sheet: 0.44 (0.41), residues: 187 loop : -1.42 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 126 HIS 0.005 0.001 HIS A 415 PHE 0.014 0.001 PHE A 315 TYR 0.020 0.002 TYR A 113 ARG 0.006 0.001 ARG B 97 *********************** 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 120 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 82 time to evaluate : 0.952 Fit side-chains REVERT: A 22 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6907 (p0) REVERT: A 48 LYS cc_start: 0.7906 (ptmm) cc_final: 0.7356 (tttp) REVERT: A 289 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: A 324 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8202 (mt) REVERT: A 327 GLU cc_start: 0.7423 (pm20) cc_final: 0.7160 (tp30) REVERT: A 526 ARG cc_start: 0.6662 (ttp-110) cc_final: 0.6347 (mtm110) REVERT: A 532 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: B 21 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6796 (pp) REVERT: B 48 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7332 (mtmm) REVERT: B 49 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 68 LYS cc_start: 0.7174 (tppt) cc_final: 0.6932 (tppt) REVERT: B 97 ARG cc_start: 0.5897 (mmm160) cc_final: 0.5537 (mmm160) REVERT: B 130 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7504 (tm) REVERT: B 305 GLN cc_start: 0.6888 (mt0) cc_final: 0.6342 (tt0) REVERT: B 363 ASN cc_start: 0.6646 (m-40) cc_final: 0.6229 (m-40) REVERT: B 367 SER cc_start: 0.8347 (p) cc_final: 0.8136 (p) REVERT: B 383 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.4956 (pm20) REVERT: B 468 ASP cc_start: 0.7104 (t70) cc_final: 0.6795 (t0) REVERT: B 479 LYS cc_start: 0.6180 (ttpp) cc_final: 0.5576 (tppt) REVERT: B 503 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6417 (tm-30) outliers start: 38 outliers final: 15 residues processed: 108 average time/residue: 1.1701 time to fit residues: 135.0764 Evaluate side-chains 96 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 36 THR 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 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 143 ASN 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 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.0000 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8318 Z= 0.167 Angle : 0.586 7.614 11359 Z= 0.320 Chirality : 0.044 0.155 1269 Planarity : 0.002 0.019 1297 Dihedral : 20.443 173.080 1423 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.19 % Favored : 93.47 % Rotamer: Outliers : 3.56 % Allowed : 19.14 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.29), residues: 873 helix: 0.17 (0.31), residues: 303 sheet: 0.27 (0.40), residues: 194 loop : -1.39 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 126 HIS 0.006 0.001 HIS A 415 PHE 0.013 0.001 PHE B 315 TYR 0.019 0.001 TYR A 113 ARG 0.004 0.000 ARG B 97 *********************** 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 110 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 81 time to evaluate : 0.887 Fit side-chains REVERT: A 22 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6808 (p0) REVERT: A 48 LYS cc_start: 0.7913 (ptmm) cc_final: 0.7361 (tttp) REVERT: A 327 GLU cc_start: 0.7530 (pm20) cc_final: 0.7274 (tp30) REVERT: A 526 ARG cc_start: 0.6623 (ttp-110) cc_final: 0.6318 (mtm110) REVERT: A 532 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: B 48 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7326 (mtmm) REVERT: B 49 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 68 LYS cc_start: 0.7099 (tppt) cc_final: 0.6838 (tppt) REVERT: B 97 ARG cc_start: 0.5808 (mmm160) cc_final: 0.5534 (mmm160) REVERT: B 130 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7574 (tm) REVERT: B 305 GLN cc_start: 0.6920 (mt0) cc_final: 0.6342 (tt0) REVERT: B 363 ASN cc_start: 0.6632 (m-40) cc_final: 0.6284 (m-40) REVERT: B 383 GLU cc_start: 0.5232 (OUTLIER) cc_final: 0.4837 (pm20) REVERT: B 468 ASP cc_start: 0.7023 (t70) cc_final: 0.6759 (t0) REVERT: B 479 LYS cc_start: 0.6215 (ttpp) cc_final: 0.5599 (tppt) REVERT: B 503 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6393 (tm-30) outliers start: 29 outliers final: 12 residues processed: 101 average time/residue: 1.1828 time to fit residues: 127.6572 Evaluate side-chains 90 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 42 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 B residue 36 THR 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 143 ASN 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 503 GLU 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 26 optimal weight: 0.0010 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 43 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8318 Z= 0.143 Angle : 0.553 7.124 11359 Z= 0.304 Chirality : 0.043 0.153 1269 Planarity : 0.002 0.019 1297 Dihedral : 20.404 173.156 1423 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer: Outliers : 2.94 % Allowed : 20.00 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 873 helix: 0.46 (0.32), residues: 302 sheet: 0.26 (0.39), residues: 206 loop : -1.26 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 126 HIS 0.005 0.001 HIS A 415 PHE 0.012 0.001 PHE B 315 TYR 0.018 0.001 TYR A 113 ARG 0.003 0.000 ARG B 97 *********************** 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 112 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 0.857 Fit side-chains REVERT: A 48 LYS cc_start: 0.7857 (ptmm) cc_final: 0.7336 (tttp) REVERT: A 58 SER cc_start: 0.6731 (p) cc_final: 0.6286 (m) REVERT: A 327 GLU cc_start: 0.7504 (pm20) cc_final: 0.7101 (tm-30) REVERT: A 329 ASP cc_start: 0.7787 (t70) cc_final: 0.7192 (m-30) REVERT: A 526 ARG cc_start: 0.6657 (ttp-110) cc_final: 0.6206 (mtm110) REVERT: B 48 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7125 (ptmt) REVERT: B 49 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 68 LYS cc_start: 0.6992 (tppt) cc_final: 0.6752 (tppt) REVERT: B 130 LEU cc_start: 0.7822 (mt) cc_final: 0.7589 (tm) REVERT: B 305 GLN cc_start: 0.6946 (mt0) cc_final: 0.6322 (tt0) REVERT: B 363 ASN cc_start: 0.6563 (m-40) cc_final: 0.6283 (m-40) REVERT: B 383 GLU cc_start: 0.5057 (OUTLIER) cc_final: 0.4685 (pm20) REVERT: B 468 ASP cc_start: 0.7029 (t70) cc_final: 0.6819 (t0) REVERT: B 479 LYS cc_start: 0.6238 (ttpp) cc_final: 0.5606 (tppt) REVERT: B 485 ARG cc_start: 0.7010 (mmm-85) cc_final: 0.6653 (mmm160) REVERT: B 503 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6305 (tm-30) REVERT: B 545 MET cc_start: 0.6836 (tpp) cc_final: 0.6421 (tpp) outliers start: 24 outliers final: 7 residues processed: 105 average time/residue: 1.1888 time to fit residues: 132.9552 Evaluate side-chains 90 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 ASN 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 503 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8318 Z= 0.189 Angle : 0.591 7.040 11359 Z= 0.323 Chirality : 0.044 0.153 1269 Planarity : 0.002 0.020 1297 Dihedral : 20.418 174.708 1423 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.76 % Favored : 92.90 % Rotamer: Outliers : 2.45 % Allowed : 20.25 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.29), residues: 873 helix: 0.48 (0.31), residues: 300 sheet: 0.18 (0.39), residues: 207 loop : -1.30 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 126 HIS 0.005 0.001 HIS A 415 PHE 0.012 0.001 PHE B 315 TYR 0.018 0.001 TYR A 113 ARG 0.002 0.000 ARG B 296 *********************** 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 98 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.833 Fit side-chains REVERT: A 48 LYS cc_start: 0.7903 (ptmm) cc_final: 0.7363 (tttp) REVERT: A 324 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 327 GLU cc_start: 0.7463 (pm20) cc_final: 0.7106 (tm-30) REVERT: A 329 ASP cc_start: 0.7768 (t70) cc_final: 0.7170 (m-30) REVERT: A 383 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5738 (mp0) REVERT: A 526 ARG cc_start: 0.6697 (ttp-110) cc_final: 0.6355 (mtm110) REVERT: B 48 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7450 (mtmm) REVERT: B 49 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7796 (mm-30) REVERT: B 68 LYS cc_start: 0.7257 (tppt) cc_final: 0.7004 (tppt) REVERT: B 130 LEU cc_start: 0.7806 (mt) cc_final: 0.7569 (tm) REVERT: B 305 GLN cc_start: 0.6955 (mt0) cc_final: 0.6337 (tt0) REVERT: B 363 ASN cc_start: 0.6575 (m-40) cc_final: 0.6237 (m-40) REVERT: B 383 GLU cc_start: 0.5056 (OUTLIER) cc_final: 0.4701 (pm20) REVERT: B 468 ASP cc_start: 0.7153 (t70) cc_final: 0.6868 (t0) REVERT: B 479 LYS cc_start: 0.6194 (ttpp) cc_final: 0.5629 (tppt) REVERT: B 503 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6444 (tm-30) outliers start: 20 outliers final: 10 residues processed: 94 average time/residue: 1.1612 time to fit residues: 116.8613 Evaluate side-chains 88 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 324 LEU 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 B residue 36 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 ASN 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 503 GLU Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 8318 Z= 0.403 Angle : 0.767 7.421 11359 Z= 0.412 Chirality : 0.051 0.158 1269 Planarity : 0.004 0.036 1297 Dihedral : 20.622 177.480 1423 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.99 % Favored : 92.67 % Rotamer: Outliers : 3.19 % Allowed : 20.12 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.28), residues: 873 helix: 0.07 (0.31), residues: 295 sheet: 0.34 (0.40), residues: 196 loop : -1.45 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP A 126 HIS 0.007 0.002 HIS B 415 PHE 0.023 0.002 PHE A 490 TYR 0.020 0.002 TYR A 113 ARG 0.007 0.001 ARG A 332 ********************** 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 101 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 0.887 Fit side-chains REVERT: A 48 LYS cc_start: 0.7912 (ptmm) cc_final: 0.7334 (tttp) REVERT: A 327 GLU cc_start: 0.7528 (pm20) cc_final: 0.7274 (tp30) REVERT: A 383 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: B 49 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 68 LYS cc_start: 0.7315 (tppt) cc_final: 0.7040 (tppt) REVERT: B 130 LEU cc_start: 0.7701 (mt) cc_final: 0.7455 (tm) REVERT: B 305 GLN cc_start: 0.6929 (mt0) cc_final: 0.6368 (tt0) REVERT: B 363 ASN cc_start: 0.6643 (m-40) cc_final: 0.6221 (m-40) REVERT: B 383 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.4977 (pm20) REVERT: B 397 GLU cc_start: 0.7030 (mp0) cc_final: 0.6390 (pp20) REVERT: B 468 ASP cc_start: 0.7166 (t70) cc_final: 0.6939 (t0) REVERT: B 479 LYS cc_start: 0.6256 (ttpp) cc_final: 0.5583 (tppt) REVERT: B 503 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6414 (tm-30) outliers start: 26 outliers final: 17 residues processed: 97 average time/residue: 1.2404 time to fit residues: 128.2120 Evaluate side-chains 92 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 ASN 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 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.200220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.174264 restraints weight = 9510.767| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.78 r_work: 0.3776 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8318 Z= 0.190 Angle : 0.620 7.281 11359 Z= 0.339 Chirality : 0.044 0.153 1269 Planarity : 0.003 0.021 1297 Dihedral : 20.481 172.944 1423 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.53 % Favored : 93.13 % Rotamer: Outliers : 2.94 % Allowed : 20.98 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.29), residues: 873 helix: 0.36 (0.31), residues: 302 sheet: 0.18 (0.40), residues: 200 loop : -1.48 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.014 0.001 HIS A 415 PHE 0.013 0.001 PHE A 315 TYR 0.021 0.001 TYR B 113 ARG 0.002 0.000 ARG B 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3098.68 seconds wall clock time: 56 minutes 9.76 seconds (3369.76 seconds total)