Starting phenix.real_space_refine on Mon Mar 11 05:19:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/03_2024/6npk_0472.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/03_2024/6npk_0472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/03_2024/6npk_0472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/03_2024/6npk_0472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/03_2024/6npk_0472.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/03_2024/6npk_0472.pdb" } resolution = 3.6 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= 0.014 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4722 2.51 5 N 1112 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 216": "NH1" <-> "NH2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 630": "NH1" <-> "NH2" Residue "A TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 630": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7134 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3567 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain: "B" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3567 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Time building chain proxies: 4.88, per 1000 atoms: 0.68 Number of scatterers: 7134 At special positions: 0 Unit cell: (102.335, 75.96, 92.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1254 8.00 N 1112 7.00 C 4722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 507 " distance=2.03 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 1 sheets defined 70.1% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.577A pdb=" N TRP A 222 " --> pdb=" O MET A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 238 through 265 removed outlier: 3.619A pdb=" N ILE A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.652A pdb=" N LEU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 318 removed outlier: 3.944A pdb=" N ALA A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.624A pdb=" N ILE A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 377 removed outlier: 3.633A pdb=" N GLU A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 421 through 425 removed outlier: 4.273A pdb=" N GLY A 425 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 463 removed outlier: 3.884A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 3.999A pdb=" N LEU A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 546 through 557 removed outlier: 3.624A pdb=" N VAL A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.754A pdb=" N ILE A 563 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 577 through 592 removed outlier: 3.874A pdb=" N LEU A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 625 Proline residue: A 601 - end of helix removed outlier: 3.624A pdb=" N ASN A 605 " --> pdb=" O PRO A 601 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 615 " --> pdb=" O TYR A 611 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 619 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 removed outlier: 3.663A pdb=" N SER A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 676 removed outlier: 3.536A pdb=" N TYR A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 removed outlier: 5.302A pdb=" N VAL B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 222 " --> pdb=" O MET B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 238 through 265 removed outlier: 3.543A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.816A pdb=" N ILE B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 320 removed outlier: 3.752A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 349 removed outlier: 3.602A pdb=" N ILE B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 377 removed outlier: 3.629A pdb=" N GLU B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 377 " --> pdb=" O ILE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 421 through 425 removed outlier: 4.200A pdb=" N GLY B 425 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 463 removed outlier: 3.664A pdb=" N ILE B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Proline residue: B 440 - end of helix removed outlier: 3.675A pdb=" N LEU B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 522 removed outlier: 3.972A pdb=" N VAL B 520 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 545 removed outlier: 4.143A pdb=" N SER B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.612A pdb=" N VAL B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 removed outlier: 3.681A pdb=" N ILE B 563 " --> pdb=" O TYR B 560 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 564 " --> pdb=" O PRO B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 564' Processing helix chain 'B' and resid 576 through 592 removed outlier: 3.617A pdb=" N PHE B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 625 Proline residue: B 601 - end of helix removed outlier: 3.599A pdb=" N ASN B 605 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 615 " --> pdb=" O TYR B 611 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.813A pdb=" N SER B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 653 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 676 removed outlier: 3.856A pdb=" N VAL B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 569 through 570 421 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2144 1.34 - 1.46: 1856 1.46 - 1.58: 3236 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 7306 Sorted by residual: bond pdb=" C ALA A 600 " pdb=" N PRO A 601 " ideal model delta sigma weight residual 1.337 1.373 -0.036 9.80e-03 1.04e+04 1.38e+01 bond pdb=" C ALA B 600 " pdb=" N PRO B 601 " ideal model delta sigma weight residual 1.337 1.372 -0.036 9.80e-03 1.04e+04 1.33e+01 bond pdb=" C SER B 525 " pdb=" N PRO B 526 " ideal model delta sigma weight residual 1.337 1.354 -0.017 1.11e-02 8.12e+03 2.46e+00 bond pdb=" CA VAL A 234 " pdb=" C VAL A 234 " ideal model delta sigma weight residual 1.519 1.535 -0.016 1.14e-02 7.69e+03 1.86e+00 bond pdb=" CA VAL B 234 " pdb=" C VAL B 234 " ideal model delta sigma weight residual 1.519 1.533 -0.014 1.14e-02 7.69e+03 1.52e+00 ... (remaining 7301 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.12: 128 106.12 - 113.09: 3876 113.09 - 120.05: 2790 120.05 - 127.02: 3068 127.02 - 133.99: 76 Bond angle restraints: 9938 Sorted by residual: angle pdb=" C LYS B 383 " pdb=" N LYS B 384 " pdb=" CA LYS B 384 " ideal model delta sigma weight residual 121.54 133.33 -11.79 1.91e+00 2.74e-01 3.81e+01 angle pdb=" C LYS A 383 " pdb=" N LYS A 384 " pdb=" CA LYS A 384 " ideal model delta sigma weight residual 121.54 133.29 -11.75 1.91e+00 2.74e-01 3.79e+01 angle pdb=" N ILE B 563 " pdb=" CA ILE B 563 " pdb=" C ILE B 563 " ideal model delta sigma weight residual 113.53 108.82 4.71 9.80e-01 1.04e+00 2.31e+01 angle pdb=" C GLY B 490 " pdb=" N TYR B 491 " pdb=" CA TYR B 491 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C GLY A 490 " pdb=" N TYR A 491 " pdb=" CA TYR A 491 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.38e+01 ... (remaining 9933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.77: 3516 11.77 - 23.53: 459 23.53 - 35.30: 135 35.30 - 47.06: 42 47.06 - 58.83: 24 Dihedral angle restraints: 4176 sinusoidal: 1490 harmonic: 2686 Sorted by residual: dihedral pdb=" CA SER B 525 " pdb=" C SER B 525 " pdb=" N PRO B 526 " pdb=" CA PRO B 526 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER A 525 " pdb=" C SER A 525 " pdb=" N PRO A 526 " pdb=" CA PRO A 526 " ideal model delta harmonic sigma weight residual -180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LYS A 488 " pdb=" C LYS A 488 " pdb=" N TYR A 489 " pdb=" CA TYR A 489 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 4173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 693 0.039 - 0.078: 350 0.078 - 0.117: 93 0.117 - 0.155: 30 0.155 - 0.194: 4 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA SER B 525 " pdb=" N SER B 525 " pdb=" C SER B 525 " pdb=" CB SER B 525 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA SER A 525 " pdb=" N SER A 525 " pdb=" C SER A 525 " pdb=" CB SER A 525 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CG LEU B 317 " pdb=" CB LEU B 317 " pdb=" CD1 LEU B 317 " pdb=" CD2 LEU B 317 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 1167 not shown) Planarity restraints: 1222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 630 " 0.213 9.50e-02 1.11e+02 9.82e-02 1.19e+01 pdb=" NE ARG B 630 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 630 " -0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG B 630 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 630 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 416 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO B 417 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 417 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 417 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 416 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO A 417 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " 0.042 5.00e-02 4.00e+02 ... (remaining 1219 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2420 2.84 - 3.35: 6620 3.35 - 3.87: 11790 3.87 - 4.38: 13789 4.38 - 4.90: 23855 Nonbonded interactions: 58474 Sorted by model distance: nonbonded pdb=" O THR B 250 " pdb=" OG1 THR B 254 " model vdw 2.320 2.440 nonbonded pdb=" O VAL B 362 " pdb=" OG1 THR B 366 " model vdw 2.324 2.440 nonbonded pdb=" O TYR A 611 " pdb=" ND2 ASN A 615 " model vdw 2.325 2.520 nonbonded pdb=" O LEU B 613 " pdb=" OG SER B 617 " model vdw 2.329 2.440 nonbonded pdb=" O TYR B 611 " pdb=" ND2 ASN B 615 " model vdw 2.329 2.520 ... (remaining 58469 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' } 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 group one per residue 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: 0.350 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: 1.910 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.480 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.004 0.051 7306 Z= 0.274 Angle : 0.824 11.789 9938 Z= 0.476 Chirality : 0.050 0.194 1170 Planarity : 0.008 0.098 1222 Dihedral : 13.018 58.825 2462 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.13 % Allowed : 8.27 % Favored : 85.60 % 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: -5.05 (0.19), residues: 940 helix: -2.94 (0.14), residues: 620 sheet: None (None), residues: 0 loop : -3.92 (0.26), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 658 HIS 0.001 0.001 HIS A 512 PHE 0.029 0.002 PHE A 387 TYR 0.019 0.002 TYR B 305 ARG 0.044 0.002 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 161 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8630 (tttm) cc_final: 0.8305 (ttpp) REVERT: A 318 MET cc_start: 0.7573 (mtm) cc_final: 0.7235 (mtp) REVERT: A 337 ILE cc_start: 0.8728 (mm) cc_final: 0.8460 (mt) REVERT: A 436 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7792 (mm-40) REVERT: A 441 LYS cc_start: 0.8453 (tttt) cc_final: 0.8113 (ttmm) REVERT: A 497 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7606 (mtt180) REVERT: A 634 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7877 (mmmm) REVERT: A 662 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7394 (tp) REVERT: B 275 TYR cc_start: 0.7916 (t80) cc_final: 0.7421 (t80) REVERT: B 337 ILE cc_start: 0.8737 (mm) cc_final: 0.8446 (mt) REVERT: B 436 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: B 441 LYS cc_start: 0.7863 (tttp) cc_final: 0.7264 (mtpp) REVERT: B 489 TYR cc_start: 0.6832 (m-80) cc_final: 0.6622 (m-80) REVERT: B 516 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7187 (mm110) REVERT: B 541 LEU cc_start: 0.8207 (tp) cc_final: 0.7981 (mt) outliers start: 46 outliers final: 9 residues processed: 193 average time/residue: 0.1898 time to fit residues: 48.7505 Evaluate side-chains 111 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 436 GLN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 557 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 298 ASN A 327 GLN B 220 ASN B 298 ASN B 327 GLN B 357 GLN B 552 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7306 Z= 0.185 Angle : 0.531 5.874 9938 Z= 0.291 Chirality : 0.041 0.131 1170 Planarity : 0.004 0.049 1222 Dihedral : 7.122 56.581 1021 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.07 % Allowed : 12.80 % Favored : 82.13 % 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: -2.73 (0.25), residues: 940 helix: -1.00 (0.19), residues: 630 sheet: None (None), residues: 0 loop : -3.41 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 658 HIS 0.003 0.001 HIS B 620 PHE 0.021 0.001 PHE B 509 TYR 0.015 0.001 TYR B 636 ARG 0.003 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8475 (t80) cc_final: 0.7027 (t80) REVERT: A 318 MET cc_start: 0.7528 (mtm) cc_final: 0.7322 (mtp) REVERT: A 331 ILE cc_start: 0.8305 (mp) cc_final: 0.8060 (mp) REVERT: A 337 ILE cc_start: 0.8462 (mm) cc_final: 0.8190 (mt) REVERT: A 441 LYS cc_start: 0.8493 (tttt) cc_final: 0.7733 (mtpp) REVERT: A 497 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7736 (ttm170) REVERT: B 337 ILE cc_start: 0.8487 (mm) cc_final: 0.8223 (mt) REVERT: B 376 PHE cc_start: 0.8200 (m-10) cc_final: 0.7745 (m-10) REVERT: B 436 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: B 441 LYS cc_start: 0.7940 (tttp) cc_final: 0.7379 (mtpp) outliers start: 38 outliers final: 24 residues processed: 134 average time/residue: 0.1867 time to fit residues: 34.2768 Evaluate side-chains 117 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 646 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 516 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7306 Z= 0.380 Angle : 0.614 7.005 9938 Z= 0.331 Chirality : 0.046 0.144 1170 Planarity : 0.004 0.036 1222 Dihedral : 6.767 49.983 1016 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.60 % Allowed : 12.53 % Favored : 81.87 % 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: -2.18 (0.26), residues: 940 helix: -0.58 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -3.24 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 658 HIS 0.002 0.001 HIS A 512 PHE 0.022 0.002 PHE A 509 TYR 0.012 0.002 TYR B 636 ARG 0.003 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 275 TYR cc_start: 0.8627 (t80) cc_final: 0.7162 (t80) REVERT: A 276 TYR cc_start: 0.7402 (t80) cc_final: 0.7125 (t80) REVERT: A 318 MET cc_start: 0.7465 (mtm) cc_final: 0.7248 (mtp) REVERT: A 331 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 337 ILE cc_start: 0.8486 (mm) cc_final: 0.8259 (mt) REVERT: A 441 LYS cc_start: 0.8398 (tttt) cc_final: 0.8153 (ttmm) REVERT: A 497 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7635 (mtt180) REVERT: A 563 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6748 (tp) REVERT: B 275 TYR cc_start: 0.8120 (t80) cc_final: 0.7827 (t80) REVERT: B 337 ILE cc_start: 0.8539 (mm) cc_final: 0.8266 (mt) REVERT: B 441 LYS cc_start: 0.7988 (tttp) cc_final: 0.7393 (mtpp) REVERT: B 568 LYS cc_start: 0.7819 (tttt) cc_final: 0.7570 (tptp) outliers start: 42 outliers final: 28 residues processed: 139 average time/residue: 0.1634 time to fit residues: 31.6666 Evaluate side-chains 130 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 646 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.0370 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7306 Z= 0.144 Angle : 0.495 6.067 9938 Z= 0.267 Chirality : 0.040 0.149 1170 Planarity : 0.003 0.031 1222 Dihedral : 6.003 52.109 1006 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.27 % Allowed : 14.27 % 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: -1.45 (0.27), residues: 940 helix: 0.04 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -3.11 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 658 HIS 0.003 0.001 HIS B 620 PHE 0.022 0.001 PHE A 509 TYR 0.011 0.001 TYR A 636 ARG 0.003 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.7908 (mmt) cc_final: 0.7611 (mmt) REVERT: A 275 TYR cc_start: 0.8612 (t80) cc_final: 0.7192 (t80) REVERT: A 318 MET cc_start: 0.7414 (mtm) cc_final: 0.7209 (mtp) REVERT: A 324 MET cc_start: 0.4215 (tpp) cc_final: 0.3791 (tpp) REVERT: A 331 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8197 (mt) REVERT: A 337 ILE cc_start: 0.8484 (mm) cc_final: 0.8269 (mt) REVERT: A 350 MET cc_start: 0.7559 (mtp) cc_final: 0.7140 (mtm) REVERT: A 441 LYS cc_start: 0.8419 (tttt) cc_final: 0.7731 (mtpp) REVERT: A 497 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7623 (mtt180) REVERT: B 331 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8244 (mt) REVERT: B 337 ILE cc_start: 0.8487 (mm) cc_final: 0.8210 (mt) REVERT: B 441 LYS cc_start: 0.7855 (tttp) cc_final: 0.7313 (mtpp) REVERT: B 568 LYS cc_start: 0.7748 (tttt) cc_final: 0.7520 (tptp) outliers start: 32 outliers final: 22 residues processed: 117 average time/residue: 0.2024 time to fit residues: 33.0482 Evaluate side-chains 110 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 557 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 77 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7306 Z= 0.155 Angle : 0.484 5.310 9938 Z= 0.258 Chirality : 0.040 0.149 1170 Planarity : 0.003 0.031 1222 Dihedral : 5.839 53.561 1006 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.27 % Allowed : 15.60 % Favored : 80.13 % 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: -0.95 (0.28), residues: 940 helix: 0.40 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.90 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 639 HIS 0.002 0.000 HIS B 620 PHE 0.022 0.001 PHE B 509 TYR 0.009 0.001 TYR B 636 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.7859 (mmt) cc_final: 0.7627 (mmt) REVERT: A 324 MET cc_start: 0.4231 (tpp) cc_final: 0.3820 (tpp) REVERT: A 331 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 337 ILE cc_start: 0.8471 (mm) cc_final: 0.8249 (mt) REVERT: A 441 LYS cc_start: 0.8372 (tttt) cc_final: 0.7703 (mtpp) REVERT: A 497 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7646 (mtt180) REVERT: B 331 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8236 (mt) REVERT: B 337 ILE cc_start: 0.8528 (mm) cc_final: 0.8300 (mt) REVERT: B 441 LYS cc_start: 0.7898 (tttp) cc_final: 0.7344 (mtpp) REVERT: B 563 ILE cc_start: 0.7338 (tp) cc_final: 0.7057 (tt) REVERT: B 568 LYS cc_start: 0.7817 (tttt) cc_final: 0.7530 (tptp) outliers start: 32 outliers final: 24 residues processed: 122 average time/residue: 0.1740 time to fit residues: 29.4462 Evaluate side-chains 123 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 646 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 7306 Z= 0.459 Angle : 0.657 9.025 9938 Z= 0.347 Chirality : 0.047 0.174 1170 Planarity : 0.004 0.032 1222 Dihedral : 6.322 51.732 1006 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.93 % Allowed : 16.00 % Favored : 79.07 % 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: -1.48 (0.27), residues: 940 helix: -0.02 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -3.04 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 209 HIS 0.002 0.001 HIS A 512 PHE 0.026 0.002 PHE B 509 TYR 0.023 0.002 TYR A 636 ARG 0.002 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 337 ILE cc_start: 0.8578 (mm) cc_final: 0.8377 (mt) REVERT: A 350 MET cc_start: 0.7584 (mtp) cc_final: 0.7282 (mtm) REVERT: A 441 LYS cc_start: 0.8381 (tttt) cc_final: 0.8151 (ttmm) REVERT: A 497 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7779 (mtt180) REVERT: A 563 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6735 (tp) REVERT: B 331 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B 337 ILE cc_start: 0.8640 (mm) cc_final: 0.8432 (mt) REVERT: B 441 LYS cc_start: 0.8031 (tttp) cc_final: 0.7385 (mtpp) REVERT: B 563 ILE cc_start: 0.7467 (tp) cc_final: 0.7107 (tt) outliers start: 37 outliers final: 27 residues processed: 138 average time/residue: 0.1624 time to fit residues: 31.4173 Evaluate side-chains 132 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 646 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.0870 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7306 Z= 0.157 Angle : 0.500 6.319 9938 Z= 0.268 Chirality : 0.040 0.145 1170 Planarity : 0.003 0.031 1222 Dihedral : 5.960 53.395 1006 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.13 % Allowed : 16.80 % Favored : 79.07 % 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: -0.86 (0.28), residues: 940 helix: 0.49 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.84 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 658 HIS 0.002 0.000 HIS B 620 PHE 0.026 0.001 PHE B 509 TYR 0.008 0.001 TYR B 636 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.4153 (tpp) cc_final: 0.3906 (tpp) REVERT: A 331 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8207 (mt) REVERT: A 337 ILE cc_start: 0.8505 (mm) cc_final: 0.8281 (mt) REVERT: A 441 LYS cc_start: 0.8381 (tttt) cc_final: 0.7725 (mtpp) REVERT: A 497 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7757 (mtt180) REVERT: A 676 TYR cc_start: 0.7974 (m-10) cc_final: 0.7768 (m-10) REVERT: B 331 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8259 (mt) REVERT: B 441 LYS cc_start: 0.7948 (tttp) cc_final: 0.7359 (mtpp) REVERT: B 563 ILE cc_start: 0.7397 (tp) cc_final: 0.7097 (tt) outliers start: 31 outliers final: 23 residues processed: 114 average time/residue: 0.1725 time to fit residues: 27.3293 Evaluate side-chains 119 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7306 Z= 0.144 Angle : 0.486 6.449 9938 Z= 0.260 Chirality : 0.040 0.148 1170 Planarity : 0.003 0.030 1222 Dihedral : 5.822 56.121 1006 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.73 % Allowed : 17.07 % Favored : 79.20 % 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: -0.48 (0.28), residues: 940 helix: 0.82 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.86 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 658 HIS 0.002 0.000 HIS B 620 PHE 0.025 0.001 PHE B 509 TYR 0.008 0.001 TYR B 636 ARG 0.003 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.7850 (mmt) cc_final: 0.7604 (mmt) REVERT: A 331 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8176 (mt) REVERT: A 337 ILE cc_start: 0.8527 (mm) cc_final: 0.8305 (mt) REVERT: A 350 MET cc_start: 0.7677 (mtp) cc_final: 0.7354 (mtm) REVERT: A 434 ASP cc_start: 0.7894 (t70) cc_final: 0.7501 (t70) REVERT: A 441 LYS cc_start: 0.8372 (tttt) cc_final: 0.7723 (mtpp) REVERT: A 497 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7784 (mtt180) REVERT: A 556 LYS cc_start: 0.7739 (mttm) cc_final: 0.7522 (mtpt) REVERT: A 676 TYR cc_start: 0.7913 (m-10) cc_final: 0.7707 (m-10) REVERT: B 325 ILE cc_start: 0.7473 (mp) cc_final: 0.7259 (mp) REVERT: B 331 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8252 (mt) REVERT: B 441 LYS cc_start: 0.7928 (tttp) cc_final: 0.7311 (mtpp) outliers start: 28 outliers final: 22 residues processed: 114 average time/residue: 0.1705 time to fit residues: 26.9813 Evaluate side-chains 115 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7306 Z= 0.269 Angle : 0.547 6.353 9938 Z= 0.289 Chirality : 0.043 0.146 1170 Planarity : 0.003 0.031 1222 Dihedral : 5.960 55.074 1006 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.00 % Allowed : 17.87 % Favored : 78.13 % 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: -0.71 (0.28), residues: 940 helix: 0.64 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.93 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 222 HIS 0.002 0.001 HIS A 512 PHE 0.026 0.001 PHE B 509 TYR 0.014 0.001 TYR A 636 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8230 (mt) REVERT: A 350 MET cc_start: 0.7772 (mtp) cc_final: 0.7443 (mtm) REVERT: A 441 LYS cc_start: 0.8396 (tttt) cc_final: 0.7741 (mtpp) REVERT: A 497 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7784 (mtt180) REVERT: A 556 LYS cc_start: 0.7725 (mttm) cc_final: 0.7463 (mtpt) REVERT: A 676 TYR cc_start: 0.7953 (m-10) cc_final: 0.7708 (m-10) REVERT: B 331 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8330 (mt) REVERT: B 350 MET cc_start: 0.7187 (ttt) cc_final: 0.6894 (ttm) REVERT: B 441 LYS cc_start: 0.7966 (tttp) cc_final: 0.7350 (mtpp) outliers start: 30 outliers final: 27 residues processed: 124 average time/residue: 0.1667 time to fit residues: 28.7569 Evaluate side-chains 126 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.0000 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN B 558 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7306 Z= 0.157 Angle : 0.503 8.898 9938 Z= 0.267 Chirality : 0.040 0.172 1170 Planarity : 0.003 0.029 1222 Dihedral : 5.843 55.819 1006 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.73 % Allowed : 18.40 % Favored : 77.87 % 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: -0.39 (0.28), residues: 940 helix: 0.90 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.85 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 222 HIS 0.001 0.000 HIS B 620 PHE 0.025 0.001 PHE B 509 TYR 0.007 0.001 TYR B 636 ARG 0.002 0.000 ARG A 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.7854 (mmt) cc_final: 0.7607 (mmt) REVERT: A 331 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8161 (mt) REVERT: A 350 MET cc_start: 0.7775 (mtp) cc_final: 0.7442 (mtm) REVERT: A 434 ASP cc_start: 0.7998 (t70) cc_final: 0.7730 (t70) REVERT: A 441 LYS cc_start: 0.8364 (tttt) cc_final: 0.7704 (mtpp) REVERT: A 497 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7790 (mtt180) REVERT: A 556 LYS cc_start: 0.7826 (mttm) cc_final: 0.7511 (mtpt) REVERT: A 676 TYR cc_start: 0.7968 (m-10) cc_final: 0.7674 (m-10) REVERT: B 331 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 441 LYS cc_start: 0.7955 (tttp) cc_final: 0.7328 (mtpp) outliers start: 28 outliers final: 22 residues processed: 114 average time/residue: 0.1709 time to fit residues: 27.2175 Evaluate side-chains 114 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.0970 chunk 11 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN B 558 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.155163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113602 restraints weight = 7452.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.116472 restraints weight = 5196.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.118094 restraints weight = 4256.687| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7306 Z= 0.218 Angle : 0.527 9.457 9938 Z= 0.279 Chirality : 0.042 0.176 1170 Planarity : 0.003 0.030 1222 Dihedral : 5.873 56.241 1006 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.00 % Allowed : 17.87 % Favored : 78.13 % 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: -0.44 (0.28), residues: 940 helix: 0.87 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.89 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 222 HIS 0.001 0.001 HIS B 620 PHE 0.025 0.001 PHE B 509 TYR 0.011 0.001 TYR A 636 ARG 0.002 0.000 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.15 seconds wall clock time: 28 minutes 58.14 seconds (1738.14 seconds total)