Starting phenix.real_space_refine on Thu Aug 6 09:32:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fak_28959/08_2026/8fak_28959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fak_28959/08_2026/8fak_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8fak_28959/08_2026/8fak_28959.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fak_28959/08_2026/8fak_28959.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fak_28959/08_2026/8fak_28959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fak_28959/08_2026/8fak_28959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fak_28959/08_2026/8fak_28959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fak_28959/08_2026/8fak_28959.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.92, per 1000 atoms: 0.13 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 270.7 milliseconds 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: 2.03 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: 2.66 Time building geometry restraints manager: 1.33 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=" C3' DC J 32 " pdb=" C2' DC J 32 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.17e+00 bond pdb=" C3' DG Z 10 " pdb=" C2' DG Z 10 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.75e+00 bond pdb=" C3' DT G 20 " pdb=" C2' DT G 20 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.43e+00 bond pdb=" C3' DA J 25 " pdb=" C2' DA J 25 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.85e+00 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 ... (remaining 15246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 25097 2.10 - 4.19: 2251 4.19 - 6.29: 281 6.29 - 8.38: 3 8.38 - 10.48: 1 Bond angle restraints: 27633 Sorted by residual: angle pdb=" O4' DA J 35 " pdb=" C4' DA J 35 " pdb=" C3' DA J 35 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT G 21 " pdb=" C4 DT G 21 " pdb=" O4 DT G 21 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT G 23 " pdb=" C4 DT G 23 " pdb=" O4 DT G 23 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT G 9 " pdb=" C4 DT G 9 " pdb=" O4 DT G 9 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT G 14 " pdb=" C4 DT G 14 " pdb=" O4 DT G 14 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.67e+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: 742 0.030 - 0.060: 341 0.060 - 0.091: 88 0.091 - 0.121: 82 0.121 - 0.151: 7 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 2.450 nonbonded pdb=" O GLN B 75 " pdb=" H GLU B 95 " model vdw 1.515 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 0.380 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: 0.060 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.003 0.033 8012 Z= 0.278 Angle : 0.524 5.623 11121 Z= 0.383 Chirality : 0.043 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (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 ARG 0.002 0.000 ARG H 509 TYR 0.003 0.000 TYR H 87 PHE 0.008 0.001 PHE H 617 TRP 0.007 0.001 TRP H 289 HIS 0.004 0.000 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.28 ( 8003) covalent geometry : angle 0.52200 / 0.38 (11107) SS BOND : bond 0.00273 / 0.14 ( 1) SS BOND : angle 2.81692 / 1.47 ( 2) hydrogen bonds : bond 0.16988 / 12.35 ( 274) hydrogen bonds : angle 5.75165 / 4.14 ( 717) metal coordination : bond 0.00227 / 0.13 ( 8) metal coordination : angle 1.01354 / 0.52 ( 12) *********************** 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 to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.254 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: 0.5336 (p) REVERT: A 90 MET cc_start: 0.6544 (mmp) cc_final: 0.6165 (mmm) REVERT: B 10 THR cc_start: 0.8218 (t) cc_final: 0.7991 (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: 0.1603 time to fit residues: 28.4946 Evaluate side-chains 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN H 200 ASN H 203 GLN H 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.159908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120041 restraints weight = 37792.642| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.50 r_work: 0.3492 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8012 Z= 0.184 Angle : 0.575 7.070 11121 Z= 0.318 Chirality : 0.044 0.195 1260 Planarity : 0.005 0.043 1238 Dihedral : 21.928 155.918 1510 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.99 % Allowed : 6.68 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.30), residues: 827 helix: 2.24 (0.35), residues: 221 sheet: 1.08 (0.36), residues: 241 loop : -0.47 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 17 TYR 0.005 0.001 TYR H 88 PHE 0.008 0.001 PHE A 29 TRP 0.009 0.001 TRP H 289 HIS 0.015 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 8003) covalent geometry : angle 0.56555 / 0.32 (11107) SS BOND : bond 0.00169 / 0.09 ( 1) SS BOND : angle 3.46433 / 1.61 ( 2) hydrogen bonds : bond 0.05009 / 3.68 ( 274) hydrogen bonds : angle 4.76767 / 3.37 ( 717) metal coordination : bond 0.00646 / 0.33 ( 8) metal coordination : angle 2.87848 / 1.50 ( 12) *********************** 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 104 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.294 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: 0.5688 (p) cc_final: 0.4579 (p) REVERT: B 89 LYS cc_start: 0.7084 (ptpp) cc_final: 0.6769 (pttp) REVERT: B 96 GLN cc_start: 0.6220 (mp-120) cc_final: 0.6018 (mp10) REVERT: H 27 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8286 (mtmm) REVERT: H 321 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7781 (mm-30) outliers start: 7 outliers final: 5 residues processed: 99 average time/residue: 0.1694 time to fit residues: 23.0388 Evaluate side-chains 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain B residue 63 THR 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 21 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 HIS ** 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 = 0.4134 r_free = 0.4134 target = 0.159112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119274 restraints weight = 37430.111| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.47 r_work: 0.3478 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8012 Z= 0.143 Angle : 0.523 6.419 11121 Z= 0.291 Chirality : 0.043 0.191 1260 Planarity : 0.005 0.043 1238 Dihedral : 21.960 155.820 1510 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.99 % Allowed : 7.81 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.30), residues: 827 helix: 2.37 (0.36), residues: 220 sheet: 0.73 (0.36), residues: 241 loop : -0.54 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 264 TYR 0.004 0.001 TYR H 452 PHE 0.006 0.001 PHE A 77 TRP 0.007 0.001 TRP H 289 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8003) covalent geometry : angle 0.51778 / 0.29 (11107) SS BOND : bond 0.00788 / 0.41 ( 1) SS BOND : angle 3.67012 / 1.70 ( 2) hydrogen bonds : bond 0.03975 / 2.89 ( 274) hydrogen bonds : angle 4.48947 / 3.16 ( 717) metal coordination : bond 0.00528 / 0.29 ( 8) metal coordination : angle 1.86679 / 1.02 ( 12) *********************** 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 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7355 (m-80) cc_final: 0.7060 (m-80) REVERT: B 89 LYS cc_start: 0.7108 (ptpp) cc_final: 0.6777 (pttp) REVERT: H 27 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8216 (mtmm) REVERT: H 321 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7804 (mm-30) REVERT: H 513 ASP cc_start: 0.7946 (m-30) cc_final: 0.7705 (m-30) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.1603 time to fit residues: 20.3543 Evaluate side-chains 91 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain H residue 644 HIS 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 77 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117946 restraints weight = 37238.553| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.45 r_work: 0.3456 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8012 Z= 0.153 Angle : 0.521 6.969 11121 Z= 0.288 Chirality : 0.043 0.180 1260 Planarity : 0.005 0.050 1238 Dihedral : 21.977 156.736 1510 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.56 % Allowed : 8.24 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.30), residues: 827 helix: 2.28 (0.36), residues: 220 sheet: 0.33 (0.35), residues: 241 loop : -0.64 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 264 TYR 0.005 0.001 TYR H 88 PHE 0.007 0.001 PHE H 502 TRP 0.008 0.001 TRP H 289 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8003) covalent geometry : angle 0.51392 / 0.29 (11107) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 4.97876 / 2.28 ( 2) hydrogen bonds : bond 0.03610 / 2.57 ( 274) hydrogen bonds : angle 4.26191 / 2.99 ( 717) metal coordination : bond 0.00601 / 0.33 ( 8) metal coordination : angle 1.77854 / 0.99 ( 12) *********************** 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 99 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7375 (m-80) cc_final: 0.7100 (m-80) REVERT: A 90 MET cc_start: 0.6738 (mmp) cc_final: 0.6051 (mmp) REVERT: B 89 LYS cc_start: 0.7149 (ptpp) cc_final: 0.6774 (pttp) REVERT: H 27 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8209 (mtmm) REVERT: H 321 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7795 (mm-30) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.1729 time to fit residues: 21.2880 Evaluate side-chains 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain H residue 644 HIS Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** 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 = 0.4089 r_free = 0.4089 target = 0.155526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115225 restraints weight = 37441.483| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.45 r_work: 0.3421 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8012 Z= 0.189 Angle : 0.543 5.570 11121 Z= 0.301 Chirality : 0.044 0.176 1260 Planarity : 0.005 0.054 1238 Dihedral : 22.015 157.392 1510 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.28 % Allowed : 9.38 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.29), residues: 827 helix: 2.05 (0.35), residues: 220 sheet: -0.13 (0.34), residues: 241 loop : -0.88 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 264 TYR 0.007 0.001 TYR H 578 PHE 0.008 0.001 PHE H 617 TRP 0.009 0.001 TRP H 289 HIS 0.007 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 8003) covalent geometry : angle 0.53621 / 0.30 (11107) SS BOND : bond 0.00565 / 0.30 ( 1) SS BOND : angle 4.09864 / 1.91 ( 2) hydrogen bonds : bond 0.03855 / 2.72 ( 274) hydrogen bonds : angle 4.25193 / 3.00 ( 717) metal coordination : bond 0.00735 / 0.41 ( 8) metal coordination : angle 2.09198 / 1.21 ( 12) *********************** 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 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7524 (m-80) cc_final: 0.7258 (m-80) REVERT: A 90 MET cc_start: 0.6828 (mmp) cc_final: 0.5745 (mmt) REVERT: H 321 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8005 (mm-30) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.1890 time to fit residues: 22.8307 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 644 HIS Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 83 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 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 = 0.153579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113991 restraints weight = 36313.227| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.40 r_work: 0.3371 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8012 Z= 0.157 Angle : 0.520 5.586 11121 Z= 0.289 Chirality : 0.043 0.213 1260 Planarity : 0.005 0.048 1238 Dihedral : 21.996 157.174 1510 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.42 % Allowed : 10.09 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.29), residues: 827 helix: 1.94 (0.35), residues: 226 sheet: -0.22 (0.34), residues: 241 loop : -1.03 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 264 TYR 0.005 0.001 TYR H 578 PHE 0.007 0.001 PHE H 617 TRP 0.009 0.001 TRP H 289 HIS 0.005 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 8003) covalent geometry : angle 0.51495 / 0.29 (11107) SS BOND : bond 0.00221 / 0.12 ( 1) SS BOND : angle 3.95284 / 1.80 ( 2) hydrogen bonds : bond 0.03620 / 2.54 ( 274) hydrogen bonds : angle 4.15540 / 2.93 ( 717) metal coordination : bond 0.00662 / 0.36 ( 8) metal coordination : angle 1.68452 / 0.98 ( 12) *********************** 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 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7421 (m-80) cc_final: 0.7150 (m-80) REVERT: A 90 MET cc_start: 0.6638 (mmp) cc_final: 0.5500 (mmt) REVERT: B 34 ARG cc_start: 0.5585 (mmt180) cc_final: 0.5230 (mmt180) REVERT: H 51 ASP cc_start: 0.7920 (t0) cc_final: 0.7597 (t0) REVERT: H 321 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7835 (mm-30) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.1731 time to fit residues: 21.7818 Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain H residue 644 HIS 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 61 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 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 = 0.4044 r_free = 0.4044 target = 0.153393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113923 restraints weight = 36175.154| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.38 r_work: 0.3370 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8012 Z= 0.151 Angle : 0.516 5.241 11121 Z= 0.287 Chirality : 0.043 0.181 1260 Planarity : 0.005 0.055 1238 Dihedral : 21.962 157.380 1510 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.14 % Allowed : 10.23 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.29), residues: 827 helix: 1.81 (0.35), residues: 232 sheet: -0.25 (0.34), residues: 246 loop : -1.03 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 264 TYR 0.005 0.001 TYR H 578 PHE 0.008 0.001 PHE H 617 TRP 0.009 0.001 TRP H 289 HIS 0.005 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8003) covalent geometry : angle 0.51112 / 0.29 (11107) SS BOND : bond 0.00398 / 0.21 ( 1) SS BOND : angle 3.70841 / 1.69 ( 2) hydrogen bonds : bond 0.03492 / 2.43 ( 274) hydrogen bonds : angle 4.08310 / 2.88 ( 717) metal coordination : bond 0.00574 / 0.32 ( 8) metal coordination : angle 1.61700 / 0.94 ( 12) *********************** 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 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7529 (m-80) cc_final: 0.7271 (m-80) REVERT: A 90 MET cc_start: 0.6866 (mmp) cc_final: 0.5728 (mmt) REVERT: B 28 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7451 (mm-40) REVERT: B 34 ARG cc_start: 0.5571 (mmt180) cc_final: 0.5228 (mmt180) REVERT: H 51 ASP cc_start: 0.8048 (t0) cc_final: 0.7703 (t0) REVERT: H 321 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8067 (mm-30) REVERT: H 593 GLU cc_start: 0.8213 (mp0) cc_final: 0.7708 (mp0) outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 0.1620 time to fit residues: 20.3898 Evaluate side-chains 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 644 HIS Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.154239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114885 restraints weight = 36423.948| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.39 r_work: 0.3384 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8012 Z= 0.113 Angle : 0.495 5.026 11121 Z= 0.276 Chirality : 0.042 0.185 1260 Planarity : 0.004 0.057 1238 Dihedral : 21.895 156.978 1510 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.85 % Allowed : 10.65 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.30), residues: 827 helix: 2.18 (0.36), residues: 226 sheet: -0.18 (0.34), residues: 245 loop : -0.94 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 264 TYR 0.005 0.001 TYR H 343 PHE 0.007 0.001 PHE H 617 TRP 0.008 0.001 TRP H 289 HIS 0.004 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8003) covalent geometry : angle 0.49180 / 0.27 (11107) SS BOND : bond 0.00321 / 0.17 ( 1) SS BOND : angle 3.36403 / 1.53 ( 2) hydrogen bonds : bond 0.03150 / 2.17 ( 274) hydrogen bonds : angle 3.95219 / 2.79 ( 717) metal coordination : bond 0.00424 / 0.23 ( 8) metal coordination : angle 1.29641 / 0.74 ( 12) *********************** 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 98 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6827 (mmp) cc_final: 0.5634 (mmt) REVERT: B 28 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7429 (mm-40) REVERT: B 34 ARG cc_start: 0.5542 (mmt180) cc_final: 0.5203 (mmt180) REVERT: H 51 ASP cc_start: 0.7991 (t0) cc_final: 0.7633 (t0) REVERT: H 321 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8058 (mm-30) REVERT: H 593 GLU cc_start: 0.8156 (mp0) cc_final: 0.7501 (mp0) outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 0.1737 time to fit residues: 22.2814 Evaluate side-chains 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.153496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114095 restraints weight = 36411.348| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.39 r_work: 0.3371 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8012 Z= 0.139 Angle : 0.505 5.038 11121 Z= 0.281 Chirality : 0.042 0.181 1260 Planarity : 0.005 0.055 1238 Dihedral : 21.888 157.726 1510 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.71 % Allowed : 11.36 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.30), residues: 827 helix: 2.12 (0.36), residues: 226 sheet: -0.26 (0.34), residues: 246 loop : -0.96 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 264 TYR 0.004 0.001 TYR H 452 PHE 0.006 0.001 PHE H 617 TRP 0.009 0.001 TRP H 289 HIS 0.004 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8003) covalent geometry : angle 0.50077 / 0.28 (11107) SS BOND : bond 0.00713 / 0.38 ( 1) SS BOND : angle 3.33021 / 1.51 ( 2) hydrogen bonds : bond 0.03342 / 2.30 ( 274) hydrogen bonds : angle 3.91490 / 2.77 ( 717) metal coordination : bond 0.00497 / 0.28 ( 8) metal coordination : angle 1.51511 / 0.88 ( 12) *********************** 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 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6851 (mmp) cc_final: 0.5735 (mmt) REVERT: B 28 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7441 (mm-40) REVERT: H 51 ASP cc_start: 0.8047 (t0) cc_final: 0.7687 (t0) REVERT: H 321 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8056 (mm-30) REVERT: H 593 GLU cc_start: 0.8171 (mp0) cc_final: 0.7694 (mp0) outliers start: 5 outliers final: 5 residues processed: 88 average time/residue: 0.1844 time to fit residues: 22.4088 Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain H residue 422 ILE 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 22 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 84 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.153729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114450 restraints weight = 36314.477| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.38 r_work: 0.3374 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8012 Z= 0.123 Angle : 0.502 4.968 11121 Z= 0.279 Chirality : 0.043 0.184 1260 Planarity : 0.005 0.059 1238 Dihedral : 21.863 157.407 1510 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.71 % Allowed : 11.93 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.30), residues: 827 helix: 2.30 (0.36), residues: 220 sheet: -0.25 (0.34), residues: 245 loop : -0.78 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 264 TYR 0.005 0.001 TYR H 343 PHE 0.007 0.001 PHE H 617 TRP 0.008 0.001 TRP H 289 HIS 0.004 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8003) covalent geometry : angle 0.49867 / 0.28 (11107) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 2.85021 / 1.30 ( 2) hydrogen bonds : bond 0.03231 / 2.21 ( 274) hydrogen bonds : angle 3.86637 / 2.74 ( 717) metal coordination : bond 0.00458 / 0.25 ( 8) metal coordination : angle 1.40607 / 0.81 ( 12) ********************** 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 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6859 (mmp) cc_final: 0.5749 (mmt) REVERT: B 28 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7430 (mm-40) REVERT: B 34 ARG cc_start: 0.5598 (mmt180) cc_final: 0.5299 (mmt180) REVERT: H 51 ASP cc_start: 0.7993 (t0) cc_final: 0.7627 (t0) REVERT: H 321 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8045 (mm-30) REVERT: H 513 ASP cc_start: 0.8237 (m-30) cc_final: 0.8022 (m-30) REVERT: H 593 GLU cc_start: 0.8158 (mp0) cc_final: 0.7679 (mp0) outliers start: 5 outliers final: 4 residues processed: 88 average time/residue: 0.1913 time to fit residues: 23.4208 Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 91 VAL 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: 10.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 0.0970 chunk 32 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.154779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114399 restraints weight = 37209.048| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.44 r_work: 0.3415 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8012 Z= 0.165 Angle : 0.522 5.252 11121 Z= 0.290 Chirality : 0.043 0.179 1260 Planarity : 0.005 0.054 1238 Dihedral : 21.890 158.309 1510 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.57 % Allowed : 11.93 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.29), residues: 827 helix: 1.97 (0.36), residues: 226 sheet: -0.40 (0.34), residues: 243 loop : -1.04 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 264 TYR 0.006 0.001 TYR H 578 PHE 0.007 0.001 PHE H 502 TRP 0.009 0.001 TRP H 289 HIS 0.005 0.001 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 8003) covalent geometry : angle 0.51763 / 0.29 (11107) SS BOND : bond 0.00198 / 0.10 ( 1) SS BOND : angle 2.85121 / 1.30 ( 2) hydrogen bonds : bond 0.03563 / 2.47 ( 274) hydrogen bonds : angle 3.92919 / 2.79 ( 717) metal coordination : bond 0.00661 / 0.36 ( 8) metal coordination : angle 1.75695 / 1.03 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3392.16 seconds wall clock time: 58 minutes 7.33 seconds (3487.33 seconds total)