Starting phenix.real_space_refine (version: dev) on Sun Dec 11 20:08:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/12_2022/6npk_0472.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/12_2022/6npk_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_0472/12_2022/6npk_0472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/12_2022/6npk_0472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/12_2022/6npk_0472.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npk_0472/12_2022/6npk_0472.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 4.49, per 1000 atoms: 0.63 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: 2.83 Conformation dependent library (CDL) restraints added in 1.1 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: 0.29 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: 1.99 Time building geometry restraints manager: 3.09 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 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. 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: 0.570 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: 2.410 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 22.480 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 6.13 % 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: -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 *********************** 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 : 0.790 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 9 residues processed: 193 average time/residue: 0.1819 time to fit residues: 47.1690 Evaluate side-chains 106 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0672 time to fit residues: 2.1465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 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: 1.5786 ------------------------------------------------------------------------------- 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 516 GLN B 552 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7306 Z= 0.258 Angle : 0.576 7.721 9938 Z= 0.313 Chirality : 0.043 0.142 1170 Planarity : 0.004 0.047 1222 Dihedral : 5.381 22.730 998 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 3.60 % 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: -2.83 (0.25), residues: 940 helix: -1.09 (0.19), residues: 630 sheet: None (None), residues: 0 loop : -3.41 (0.30), residues: 310 *********************** 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 129 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 0.697 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 120 average time/residue: 0.1774 time to fit residues: 29.4687 Evaluate side-chains 103 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0667 time to fit residues: 3.1629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 84 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 516 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 7306 Z= 0.290 Angle : 0.572 5.368 9938 Z= 0.308 Chirality : 0.043 0.131 1170 Planarity : 0.004 0.035 1222 Dihedral : 5.205 21.492 998 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 2.53 % 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: -2.00 (0.27), residues: 940 helix: -0.42 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -3.18 (0.32), residues: 312 *********************** 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 120 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.716 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 117 average time/residue: 0.1849 time to fit residues: 29.4133 Evaluate side-chains 105 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0995 time to fit residues: 2.5129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.0670 chunk 64 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 7306 Z= 0.142 Angle : 0.502 5.716 9938 Z= 0.269 Chirality : 0.040 0.137 1170 Planarity : 0.003 0.030 1222 Dihedral : 4.746 18.827 998 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 2.00 % 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: -1.34 (0.27), residues: 940 helix: 0.12 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -3.02 (0.33), residues: 312 *********************** 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 114 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.773 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 108 average time/residue: 0.1733 time to fit residues: 26.1078 Evaluate side-chains 96 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0709 time to fit residues: 1.8564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2730 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= 0.159 Angle : 0.496 5.403 9938 Z= 0.262 Chirality : 0.040 0.146 1170 Planarity : 0.003 0.030 1222 Dihedral : 4.587 18.831 998 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 1.20 % 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: -0.91 (0.28), residues: 940 helix: 0.41 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.78 (0.34), residues: 308 *********************** 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 103 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.774 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.1764 time to fit residues: 24.6796 Evaluate side-chains 97 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0665 time to fit residues: 1.6813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 7306 Z= 0.333 Angle : 0.589 7.427 9938 Z= 0.310 Chirality : 0.044 0.153 1170 Planarity : 0.003 0.031 1222 Dihedral : 5.044 23.374 998 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer Outliers : 1.33 % 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: -1.24 (0.27), residues: 940 helix: 0.13 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.88 (0.34), residues: 304 *********************** 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 118 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.864 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 113 average time/residue: 0.1692 time to fit residues: 26.8340 Evaluate side-chains 110 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0653 time to fit residues: 1.7929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 0.0040 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2994 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= 0.142 Angle : 0.504 7.107 9938 Z= 0.267 Chirality : 0.041 0.157 1170 Planarity : 0.003 0.030 1222 Dihedral : 4.584 18.709 998 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 0.93 % 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 (0.28), residues: 940 helix: 0.59 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.77 (0.34), residues: 310 *********************** 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 108 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.727 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 105 average time/residue: 0.1616 time to fit residues: 24.0597 Evaluate side-chains 105 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0659 time to fit residues: 1.7598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0570 chunk 17 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.0000 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.4502 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7306 Z= 0.138 Angle : 0.517 11.020 9938 Z= 0.270 Chirality : 0.041 0.206 1170 Planarity : 0.003 0.031 1222 Dihedral : 4.430 18.083 998 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.40 (0.28), residues: 940 helix: 0.87 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.78 (0.35), residues: 306 *********************** 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 105 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.777 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.1795 time to fit residues: 25.7723 Evaluate side-chains 97 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0659 time to fit residues: 1.1987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 36 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7306 Z= 0.152 Angle : 0.528 7.627 9938 Z= 0.274 Chirality : 0.041 0.155 1170 Planarity : 0.003 0.029 1222 Dihedral : 4.408 20.851 998 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.28), residues: 940 helix: 1.03 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.76 (0.35), residues: 306 *********************** 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 98 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.867 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 97 average time/residue: 0.2584 time to fit residues: 35.6090 Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0656 time to fit residues: 1.3266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 0.0770 chunk 86 optimal weight: 0.3980 chunk 74 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.0470 chunk 22 optimal weight: 6.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 7306 Z= 0.139 Angle : 0.518 7.762 9938 Z= 0.270 Chirality : 0.040 0.155 1170 Planarity : 0.003 0.031 1222 Dihedral : 4.308 19.520 998 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 0.53 % 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: -0.01 (0.28), residues: 940 helix: 1.19 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.71 (0.35), residues: 304 ********************** 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 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.702 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 100 average time/residue: 0.1559 time to fit residues: 22.6215 Evaluate side-chains 100 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0733 time to fit residues: 1.2350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.0770 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 512 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.158725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119728 restraints weight = 7319.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.122488 restraints weight = 5142.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.123742 restraints weight = 4188.504| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7306 Z= 0.208 Angle : 0.561 9.206 9938 Z= 0.290 Chirality : 0.042 0.187 1170 Planarity : 0.003 0.028 1222 Dihedral : 4.453 19.769 998 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 0.13 % 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: -0.12 (0.28), residues: 940 helix: 1.12 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.75 (0.35), residues: 308 =============================================================================== Job complete usr+sys time: 1420.04 seconds wall clock time: 26 minutes 44.27 seconds (1604.27 seconds total)