Starting phenix.real_space_refine on Sat Mar 16 14:29:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fak_28959/03_2024/8fak_28959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fak_28959/03_2024/8fak_28959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fak_28959/03_2024/8fak_28959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fak_28959/03_2024/8fak_28959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fak_28959/03_2024/8fak_28959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fak_28959/03_2024/8fak_28959.pdb" } resolution = 3.22 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= 0.003 sd= 0.500 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 57 5.49 5 S 28 5.16 5 C 4696 2.51 5 N 1434 2.21 5 O 1498 1.98 5 H 7248 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 14963 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1519 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "B" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1503 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 723 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "H" Number of atoms: 10134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 10134 Classifications: {'peptide': 643} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 602} Chain breaks: 1 Chain: "J" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 733 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "Z" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 349 Classifications: {'DNA': 11} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9326 SG CYS H 445 37.544 61.957 59.870 1.00 87.36 S ATOM 9374 SG CYS H 448 37.228 58.300 58.786 1.00 80.81 S ATOM 9626 SG CYS H 463 40.304 59.457 60.738 1.00 91.68 S ATOM 9670 SG CYS H 466 39.744 60.511 57.131 1.00 88.01 S ATOM 9202 SG CYS H 436 36.878 71.412 76.767 1.00 66.12 S ATOM 9241 SG CYS H 439 33.163 71.157 75.929 1.00 60.08 S ATOM 9829 SG CYS H 476 35.613 72.552 73.377 1.00 81.61 S ATOM 9864 SG CYS H 479 34.712 74.555 76.479 1.00 75.40 S Time building chain proxies: 6.80, per 1000 atoms: 0.45 Number of scatterers: 14963 At special positions: 0 Unit cell: (83.083, 103.584, 125.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 57 15.00 O 1498 8.00 N 1434 7.00 C 4696 6.00 H 7248 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS B 48 " 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: 12.07 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 801 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 466 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 448 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 463 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 445 " pdb=" ZN H 802 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 439 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 476 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 479 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 436 " Number of angles added : 12 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1562 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 32.4% alpha, 20.7% beta 19 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 6.55 Creating SS restraints... Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.911A pdb=" N ALA A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 62 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 66 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 91 through 99 removed outlier: 3.632A pdb=" N ALA H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 removed outlier: 4.035A pdb=" N GLN H 106 " --> pdb=" O ILE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 213 Processing helix chain 'H' and resid 229 through 243 Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 257 through 269 removed outlier: 3.605A pdb=" N THR H 261 " --> pdb=" O LEU H 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG H 264 " --> pdb=" O GLN H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 295 Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.971A pdb=" N PHE H 308 " --> pdb=" O SER H 305 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR H 309 " --> pdb=" O ALA H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 328 removed outlier: 3.697A pdb=" N TYR H 327 " --> pdb=" O ASP H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 349 Processing helix chain 'H' and resid 360 through 369 Processing helix chain 'H' and resid 379 through 384 removed outlier: 3.988A pdb=" N ASN H 383 " --> pdb=" O ARG H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 417 Processing helix chain 'H' and resid 490 through 502 removed outlier: 4.006A pdb=" N ALA H 499 " --> pdb=" O GLU H 495 " (cutoff:3.500A) Proline residue: H 500 - end of helix Processing helix chain 'H' and resid 517 through 530 removed outlier: 3.523A pdb=" N LEU H 521 " --> pdb=" O ARG H 517 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU H 522 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 544 Processing helix chain 'H' and resid 569 through 583 Processing helix chain 'H' and resid 603 through 612 Processing helix chain 'H' and resid 613 through 628 removed outlier: 3.552A pdb=" N PHE H 617 " --> pdb=" O GLY H 613 " (cutoff:3.500A) Processing helix chain 'H' and resid 647 through 662 removed outlier: 4.262A pdb=" N LEU H 651 " --> pdb=" O GLN H 647 " (cutoff:3.500A) Processing helix chain 'H' and resid 697 through 711 Processing helix chain 'H' and resid 712 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 19 removed outlier: 15.809A pdb=" N VAL A 6 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 13.405A pdb=" N GLU A 38 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N SER A 8 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL A 36 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR A 10 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG A 34 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N CYS A 12 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLU A 32 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA A 14 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL A 30 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 48 " --> pdb=" O HIS A 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 42 through 54 current: chain 'A' and resid 96 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 96 through 99 current: chain 'B' and resid 26 through 38 removed outlier: 3.596A pdb=" N HIS B 33 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS B 48 " --> pdb=" O HIS B 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 43 through 48 current: chain 'B' and resid 90 through 97 Processing sheet with id=AA2, first strand: chain 'H' and resid 16 through 19 removed outlier: 6.759A pdb=" N VAL H 3 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL H 49 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS H 5 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN H 40 " --> pdb=" O PHE H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 273 through 276 removed outlier: 6.293A pdb=" N GLU H 274 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN H 247 " --> pdb=" O VAL H 316 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL H 318 " --> pdb=" O GLN H 247 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU H 249 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASP H 320 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET H 251 " --> pdb=" O ASP H 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 388 through 393 removed outlier: 6.048A pdb=" N ILE H 388 " --> pdb=" O VAL H 594 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU H 596 " --> pdb=" O ILE H 388 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS H 390 " --> pdb=" O LEU H 596 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR H 598 " --> pdb=" O HIS H 390 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU H 392 " --> pdb=" O THR H 598 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR H 552 " --> pdb=" O GLU H 593 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL H 595 " --> pdb=" O THR H 552 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL H 554 " --> pdb=" O VAL H 595 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLN H 597 " --> pdb=" O VAL H 554 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU H 556 " --> pdb=" O GLN H 597 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN H 420 " --> pdb=" O VAL H 551 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU H 553 " --> pdb=" O GLN H 420 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY H 538 " --> pdb=" O LEU H 423 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 433 through 436 removed outlier: 3.661A pdb=" N ALA H 433 " --> pdb=" O VAL H 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 453 through 455 Processing sheet with id=AA7, first strand: chain 'H' and resid 635 through 643 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 635 through 643 current: chain 'H' and resid 687 through 695 No H-bonds generated for sheet with id=AA7 223 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7240 1.04 - 1.23: 133 1.23 - 1.43: 3340 1.43 - 1.62: 4500 1.62 - 1.82: 38 Bond restraints: 15251 Sorted by residual: bond pdb=" N ARG H 108 " pdb=" CA ARG H 108 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.37e-02 5.33e+03 5.68e+00 bond pdb=" C ASN H 706 " pdb=" N GLY H 707 " ideal model delta sigma weight residual 1.334 1.362 -0.028 1.32e-02 5.74e+03 4.54e+00 bond pdb=" N ALA H 110 " pdb=" CA ALA H 110 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.23e-02 6.61e+03 3.27e+00 bond pdb=" C PRO H 109 " pdb=" O PRO H 109 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.30e-02 5.92e+03 2.12e+00 bond pdb=" O3' DT Z 12 " pdb=" P DC Z 13 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.50e-02 4.44e+03 2.01e+00 ... (remaining 15246 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.18: 2361 107.18 - 113.88: 16090 113.88 - 120.58: 5033 120.58 - 127.28: 3946 127.28 - 133.98: 203 Bond angle restraints: 27633 Sorted by residual: angle pdb=" O4' DA J 35 " pdb=" C4' DA J 35 " pdb=" H4' DA J 35 " ideal model delta sigma weight residual 109.00 115.87 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C4' DA J 35 " pdb=" C3' DA J 35 " pdb=" H3' DA J 35 " ideal model delta sigma weight residual 109.00 115.42 -6.42 1.50e+00 4.44e-01 1.83e+01 angle pdb=" O4' DT J 33 " pdb=" C1' DT J 33 " pdb=" H1' DT J 33 " ideal model delta sigma weight residual 109.00 115.11 -6.11 1.50e+00 4.44e-01 1.66e+01 angle pdb=" C4' DA G 7 " pdb=" C3' DA G 7 " pdb=" H3' DA G 7 " ideal model delta sigma weight residual 109.00 115.03 -6.03 1.50e+00 4.44e-01 1.62e+01 angle pdb=" O4' DT G 13 " pdb=" C4' DT G 13 " pdb=" H4' DT G 13 " ideal model delta sigma weight residual 109.00 114.97 -5.97 1.50e+00 4.44e-01 1.58e+01 ... (remaining 27628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 6375 30.75 - 61.49: 516 61.49 - 92.24: 19 92.24 - 122.98: 0 122.98 - 153.73: 2 Dihedral angle restraints: 6912 sinusoidal: 4120 harmonic: 2792 Sorted by residual: dihedral pdb=" C4' DC J 32 " pdb=" C3' DC J 32 " pdb=" O3' DC J 32 " pdb=" P DT J 33 " ideal model delta sinusoidal sigma weight residual 220.00 66.27 153.73 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" C4' DG J 34 " pdb=" C3' DG J 34 " pdb=" O3' DG J 34 " pdb=" P DA J 35 " ideal model delta sinusoidal sigma weight residual 220.00 80.20 139.80 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA CYS A 80 " pdb=" CB CYS A 80 " pdb=" SG CYS A 80 " pdb=" SG CYS B 48 " ideal model delta sinusoidal sigma weight residual -73.00 -14.90 -58.10 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 6909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 835 0.030 - 0.060: 294 0.060 - 0.091: 55 0.091 - 0.121: 70 0.121 - 0.151: 6 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ARG H 108 " pdb=" N ARG H 108 " pdb=" C ARG H 108 " pdb=" CB ARG H 108 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE H 691 " pdb=" N ILE H 691 " pdb=" C ILE H 691 " pdb=" CB ILE H 691 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA THR H 258 " pdb=" N THR H 258 " pdb=" C THR H 258 " pdb=" CB THR H 258 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1257 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 631 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO H 632 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 632 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 632 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC Z 11 " -0.014 2.00e-02 2.50e+03 1.01e-02 2.78e+00 pdb=" N1 DC Z 11 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DC Z 11 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DC Z 11 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC Z 11 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC Z 11 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC Z 11 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC Z 11 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC Z 11 " 0.008 2.00e-02 2.50e+03 pdb=" H5 DC Z 11 " -0.018 2.00e-02 2.50e+03 pdb=" H6 DC Z 11 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 630 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO H 631 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 631 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 631 " -0.022 5.00e-02 4.00e+02 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.82: 69 1.82 - 2.52: 11091 2.52 - 3.21: 43172 3.21 - 3.91: 56309 3.91 - 4.60: 87657 Nonbonded interactions: 198298 Sorted by model distance: nonbonded pdb=" HB3 HIS H 437 " pdb=" HD2 HIS H 483 " model vdw 1.129 2.270 nonbonded pdb=" HE1 HIS B 26 " pdb=" HA HIS H 483 " model vdw 1.286 2.270 nonbonded pdb=" ND1 HIS B 26 " pdb=" HD1 HIS H 483 " model vdw 1.294 2.600 nonbonded pdb=" O ASP H 17 " pdb="HO3' DC Z 13 " model vdw 1.477 1.850 nonbonded pdb=" O GLN B 75 " pdb=" H GLU B 95 " model vdw 1.515 1.850 ... (remaining 198293 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' and (resid 2 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 49 through 98)) selection = (chain 'B' and (resid 2 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 81 through 84 or (resid 87 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 \ or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or n \ ame HD23)) or resid 88 through 98)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.210 Extract box with map and model: 2.380 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 57.920 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.002 0.039 8003 Z= 0.145 Angle : 0.461 5.623 11107 Z= 0.257 Chirality : 0.039 0.151 1260 Planarity : 0.004 0.055 1238 Dihedral : 19.105 153.728 3075 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 1.43 (0.31), residues: 827 helix: 2.49 (0.36), residues: 214 sheet: 1.38 (0.36), residues: 261 loop : -0.37 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.004 0.000 HIS H 460 PHE 0.008 0.001 PHE H 617 TYR 0.003 0.000 TYR H 87 ARG 0.002 0.000 ARG H 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.5748 (p) cc_final: 0.5335 (p) REVERT: A 90 MET cc_start: 0.6544 (mmp) cc_final: 0.6164 (mmm) REVERT: B 10 THR cc_start: 0.8218 (t) cc_final: 0.7990 (p) REVERT: H 27 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8296 (mtmm) REVERT: H 321 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7738 (mm-30) REVERT: H 472 VAL cc_start: 0.9351 (t) cc_final: 0.9148 (p) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4576 time to fit residues: 80.4715 Evaluate side-chains 93 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8003 Z= 0.218 Angle : 0.528 4.858 11107 Z= 0.289 Chirality : 0.044 0.136 1260 Planarity : 0.005 0.039 1238 Dihedral : 21.741 155.140 1510 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.42 % Allowed : 7.10 % Favored : 91.48 % 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: 1.13 (0.31), residues: 827 helix: 2.45 (0.36), residues: 216 sheet: 1.15 (0.36), residues: 241 loop : -0.56 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.009 0.001 HIS B 26 PHE 0.007 0.001 PHE H 574 TYR 0.005 0.001 TYR H 88 ARG 0.005 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.5349 (p) cc_final: 0.4636 (p) REVERT: A 90 MET cc_start: 0.6766 (mmp) cc_final: 0.6298 (mmt) REVERT: B 10 THR cc_start: 0.8246 (t) cc_final: 0.7998 (p) REVERT: B 89 LYS cc_start: 0.7236 (ptpp) cc_final: 0.6953 (pttp) REVERT: H 27 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8292 (mtmm) REVERT: H 321 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7798 (mm-30) REVERT: H 593 GLU cc_start: 0.7990 (mp0) cc_final: 0.7752 (mp0) outliers start: 10 outliers final: 8 residues processed: 98 average time/residue: 0.4623 time to fit residues: 60.3119 Evaluate side-chains 93 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain H residue 567 ASP Chi-restraints excluded: chain H residue 628 MET Chi-restraints excluded: chain H residue 644 HIS Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8003 Z= 0.255 Angle : 0.528 5.152 11107 Z= 0.292 Chirality : 0.044 0.152 1260 Planarity : 0.005 0.039 1238 Dihedral : 21.632 156.988 1510 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.70 % Allowed : 8.52 % Favored : 89.77 % 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: 0.65 (0.30), residues: 827 helix: 2.11 (0.36), residues: 226 sheet: 0.71 (0.36), residues: 236 loop : -0.84 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.014 0.001 HIS H 483 PHE 0.008 0.001 PHE H 617 TYR 0.008 0.001 TYR H 578 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7091 (mmp) cc_final: 0.6480 (mmt) REVERT: B 34 ARG cc_start: 0.5563 (mmt180) cc_final: 0.5280 (mmt180) REVERT: B 89 LYS cc_start: 0.7414 (ptpp) cc_final: 0.7059 (pttp) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.4474 time to fit residues: 54.6916 Evaluate side-chains 88 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 567 ASP Chi-restraints excluded: chain H residue 628 MET Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8003 Z= 0.268 Angle : 0.532 5.218 11107 Z= 0.294 Chirality : 0.044 0.154 1260 Planarity : 0.005 0.040 1238 Dihedral : 21.510 157.445 1510 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.99 % Allowed : 9.80 % Favored : 88.21 % 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: 0.27 (0.30), residues: 827 helix: 1.87 (0.36), residues: 226 sheet: 0.25 (0.34), residues: 242 loop : -0.96 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 289 HIS 0.007 0.001 HIS H 483 PHE 0.008 0.001 PHE H 502 TYR 0.006 0.001 TYR H 578 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7169 (mmmm) cc_final: 0.6741 (mmmm) REVERT: A 90 MET cc_start: 0.7333 (mmp) cc_final: 0.6684 (mmt) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.4624 time to fit residues: 53.8080 Evaluate side-chains 92 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 567 ASP Chi-restraints excluded: chain H residue 628 MET Chi-restraints excluded: chain H residue 708 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8003 Z= 0.218 Angle : 0.513 5.007 11107 Z= 0.284 Chirality : 0.043 0.152 1260 Planarity : 0.005 0.049 1238 Dihedral : 21.416 157.318 1510 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.85 % Allowed : 11.36 % Favored : 86.79 % 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 (0.30), residues: 827 helix: 1.92 (0.36), residues: 226 sheet: 0.12 (0.35), residues: 243 loop : -1.00 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 289 HIS 0.006 0.001 HIS H 483 PHE 0.007 0.001 PHE H 502 TYR 0.004 0.001 TYR H 343 ARG 0.011 0.000 ARG H 686 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7150 (mmp) cc_final: 0.6483 (mmt) REVERT: H 321 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7706 (mm-30) REVERT: H 593 GLU cc_start: 0.7997 (mp0) cc_final: 0.7581 (mp0) outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.4519 time to fit residues: 55.7486 Evaluate side-chains 93 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 567 ASP Chi-restraints excluded: chain H residue 708 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8003 Z= 0.343 Angle : 0.573 5.900 11107 Z= 0.318 Chirality : 0.045 0.150 1260 Planarity : 0.006 0.062 1238 Dihedral : 21.528 158.314 1510 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.84 % Allowed : 11.51 % Favored : 85.65 % 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: -0.31 (0.29), residues: 827 helix: 1.46 (0.35), residues: 225 sheet: -0.19 (0.34), residues: 235 loop : -1.27 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 289 HIS 0.007 0.001 HIS H 460 PHE 0.010 0.001 PHE H 502 TYR 0.009 0.002 TYR H 578 ARG 0.010 0.001 ARG H 686 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7277 (mmmm) cc_final: 0.7009 (mmmm) outliers start: 20 outliers final: 15 residues processed: 92 average time/residue: 0.4191 time to fit residues: 52.6581 Evaluate side-chains 95 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain H residue 567 ASP Chi-restraints excluded: chain H residue 628 MET Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.003 0.025 8003 Z= 0.186 Angle : 0.509 4.924 11107 Z= 0.281 Chirality : 0.042 0.148 1260 Planarity : 0.005 0.052 1238 Dihedral : 21.368 158.314 1510 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.42 % Allowed : 13.07 % Favored : 85.51 % 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: -0.03 (0.30), residues: 827 helix: 1.82 (0.36), residues: 226 sheet: -0.10 (0.35), residues: 239 loop : -1.14 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 289 HIS 0.005 0.001 HIS H 483 PHE 0.007 0.001 PHE H 502 TYR 0.005 0.001 TYR H 343 ARG 0.011 0.000 ARG H 686 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7247 (mmmm) cc_final: 0.6768 (mmmm) REVERT: A 90 MET cc_start: 0.7135 (mmp) cc_final: 0.6495 (mmt) REVERT: H 321 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7640 (mm-30) REVERT: H 593 GLU cc_start: 0.8036 (mp0) cc_final: 0.7523 (mp0) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.4297 time to fit residues: 50.0522 Evaluate side-chains 89 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 628 MET Chi-restraints excluded: chain H residue 708 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8003 Z= 0.165 Angle : 0.501 4.851 11107 Z= 0.275 Chirality : 0.042 0.142 1260 Planarity : 0.005 0.061 1238 Dihedral : 21.199 159.578 1510 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.42 % Allowed : 13.64 % Favored : 84.94 % 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 (0.30), residues: 827 helix: 2.11 (0.37), residues: 226 sheet: -0.02 (0.34), residues: 249 loop : -1.03 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.004 0.001 HIS H 460 PHE 0.006 0.001 PHE H 617 TYR 0.004 0.001 TYR H 614 ARG 0.013 0.000 ARG H 686 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7325 (mmmm) cc_final: 0.7085 (mmmm) REVERT: H 321 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7614 (mm-30) REVERT: H 593 GLU cc_start: 0.8045 (mp0) cc_final: 0.7576 (mp0) outliers start: 10 outliers final: 7 residues processed: 88 average time/residue: 0.4336 time to fit residues: 52.0181 Evaluate side-chains 87 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 708 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8003 Z= 0.254 Angle : 0.535 5.435 11107 Z= 0.296 Chirality : 0.043 0.144 1260 Planarity : 0.005 0.064 1238 Dihedral : 21.255 159.151 1510 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.70 % Allowed : 14.06 % Favored : 84.23 % 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: -0.05 (0.30), residues: 827 helix: 1.85 (0.36), residues: 226 sheet: -0.14 (0.35), residues: 233 loop : -1.16 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 289 HIS 0.005 0.001 HIS H 460 PHE 0.009 0.001 PHE H 502 TYR 0.005 0.001 TYR H 88 ARG 0.014 0.001 ARG H 686 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7236 (mmmm) cc_final: 0.6922 (mmmm) REVERT: H 321 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7665 (mm-30) outliers start: 12 outliers final: 11 residues processed: 85 average time/residue: 0.4346 time to fit residues: 49.7382 Evaluate side-chains 89 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain H residue 567 ASP Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8003 Z= 0.260 Angle : 0.537 5.406 11107 Z= 0.297 Chirality : 0.044 0.143 1260 Planarity : 0.005 0.060 1238 Dihedral : 21.278 160.144 1510 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.13 % Allowed : 13.64 % Favored : 84.23 % 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: -0.22 (0.29), residues: 827 helix: 1.70 (0.36), residues: 225 sheet: -0.31 (0.35), residues: 233 loop : -1.19 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 289 HIS 0.005 0.001 HIS H 483 PHE 0.007 0.001 PHE H 502 TYR 0.005 0.001 TYR H 88 ARG 0.013 0.001 ARG H 686 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7263 (mmmm) cc_final: 0.6743 (mmmm) REVERT: A 90 MET cc_start: 0.7201 (mmp) cc_final: 0.6479 (mmt) REVERT: H 321 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7651 (mm-30) REVERT: H 587 ARG cc_start: 0.7197 (ttp80) cc_final: 0.6892 (ptm-80) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.4773 time to fit residues: 55.5592 Evaluate side-chains 90 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain H residue 567 ASP Chi-restraints excluded: chain H residue 628 MET Chi-restraints excluded: chain H residue 708 THR Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.152693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112860 restraints weight = 37398.988| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.44 r_work: 0.3390 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8003 Z= 0.221 Angle : 0.521 5.167 11107 Z= 0.289 Chirality : 0.043 0.142 1260 Planarity : 0.005 0.058 1238 Dihedral : 21.147 160.828 1510 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.56 % Allowed : 14.20 % Favored : 84.23 % 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: -0.17 (0.30), residues: 827 helix: 1.81 (0.36), residues: 221 sheet: -0.26 (0.35), residues: 233 loop : -1.19 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 289 HIS 0.004 0.001 HIS H 483 PHE 0.008 0.001 PHE H 502 TYR 0.005 0.001 TYR H 452 ARG 0.013 0.000 ARG H 686 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3795.99 seconds wall clock time: 67 minutes 46.44 seconds (4066.44 seconds total)