Starting phenix.real_space_refine on Fri Jul 3 14:37:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fak_28959/07_2026/8fak_28959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fak_28959/07_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_28959/07_2026/8fak_28959.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fak_28959/07_2026/8fak_28959.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fak_28959/07_2026/8fak_28959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fak_28959/07_2026/8fak_28959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fak_28959/07_2026/8fak_28959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fak_28959/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.16, per 1000 atoms: 0.14 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: 0.99 Conformation dependent library (CDL) restraints added in 271.4 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: 2.05 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: 3.07 Time building geometry restraints manager: 1.43 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: 0.430 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.000 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- 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= 0.277 Angle : 0.522 5.623 11121 Z= 0.381 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 0.51994 / 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 : 0.323 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: 0.1761 time to fit residues: 31.2190 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 : 0.364 ------------------------------------------------------------------------------- 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: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.159958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.120050 restraints weight = 37756.847| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.51 r_work: 0.3496 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8012 Z= 0.169 Angle : 0.574 6.423 11121 Z= 0.318 Chirality : 0.044 0.190 1260 Planarity : 0.005 0.043 1238 Dihedral : 21.915 155.885 1510 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.99 % Allowed : 6.82 % Favored : 92.19 % 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: 1.10 (0.31), residues: 827 helix: 2.23 (0.35), residues: 221 sheet: 1.08 (0.36), residues: 241 loop : -0.45 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 17 TYR 0.005 0.001 TYR H 88 PHE 0.009 0.001 PHE A 29 TRP 0.009 0.001 TRP H 289 HIS 0.016 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 8003) covalent geometry : angle 0.56578 / 0.32 (11107) SS BOND : bond 0.00211 / 0.11 ( 1) SS BOND : angle 3.35560 / 1.56 ( 2) hydrogen bonds : bond 0.04999 / 3.70 ( 274) hydrogen bonds : angle 4.74006 / 3.36 ( 717) metal coordination : bond 0.00668 / 0.34 ( 8) metal coordination : angle 2.73464 / 1.46 ( 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 : 0.329 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: 0.5664 (p) cc_final: 0.4554 (p) REVERT: B 89 LYS cc_start: 0.7074 (ptpp) cc_final: 0.6760 (pttp) REVERT: H 27 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8286 (mtmm) REVERT: H 321 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7782 (mm-30) outliers start: 7 outliers final: 4 residues processed: 99 average time/residue: 0.1653 time to fit residues: 22.0645 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 : 0.237 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 0.0270 chunk 75 optimal weight: 4.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 HIS ** 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 = 0.4140 r_free = 0.4140 target = 0.159656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119767 restraints weight = 37408.616| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.47 r_work: 0.3488 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8012 Z= 0.139 Angle : 0.520 7.847 11121 Z= 0.289 Chirality : 0.043 0.178 1260 Planarity : 0.004 0.043 1238 Dihedral : 21.956 156.025 1510 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.81 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: 0.97 (0.30), residues: 827 helix: 2.37 (0.36), residues: 221 sheet: 0.77 (0.36), residues: 241 loop : -0.52 (0.32), residues: 365 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 0.007 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 0.00288 / 0.14 ( 8003) covalent geometry : angle 0.51455 / 0.29 (11107) SS BOND : bond 0.00712 / 0.37 ( 1) SS BOND : angle 4.01072 / 1.88 ( 2) hydrogen bonds : bond 0.03891 / 2.82 ( 274) hydrogen bonds : angle 4.48738 / 3.15 ( 717) metal coordination : bond 0.00483 / 0.27 ( 8) metal coordination : angle 1.79358 / 0.98 ( 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 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7349 (m-80) cc_final: 0.7051 (m-80) REVERT: A 80 CYS cc_start: 0.4954 (p) cc_final: 0.3997 (p) REVERT: A 90 MET cc_start: 0.6536 (mmp) cc_final: 0.5863 (mmp) REVERT: B 89 LYS cc_start: 0.7088 (ptpp) cc_final: 0.6752 (pttp) REVERT: H 27 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8211 (mtmm) REVERT: H 321 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7781 (mm-30) outliers start: 7 outliers final: 5 residues processed: 87 average time/residue: 0.1693 time to fit residues: 20.3260 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 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: 1.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.158075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117994 restraints weight = 37191.654| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.45 r_work: 0.3462 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8012 Z= 0.156 Angle : 0.515 4.930 11121 Z= 0.287 Chirality : 0.043 0.167 1260 Planarity : 0.005 0.047 1238 Dihedral : 21.987 156.882 1510 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.99 % Allowed : 8.38 % Favored : 90.62 % 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: 0.67 (0.30), residues: 827 helix: 2.29 (0.36), residues: 221 sheet: 0.37 (0.35), residues: 241 loop : -0.63 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.008 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 8003) covalent geometry : angle 0.50976 / 0.29 (11107) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 3.47398 / 1.60 ( 2) hydrogen bonds : bond 0.03610 / 2.57 ( 274) hydrogen bonds : angle 4.26628 / 3.00 ( 717) metal coordination : bond 0.00608 / 0.34 ( 8) metal coordination : angle 1.76413 / 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 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.273 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: 0.7387 (m-80) cc_final: 0.7135 (m-80) REVERT: A 80 CYS cc_start: 0.5211 (p) cc_final: 0.4235 (p) REVERT: A 90 MET cc_start: 0.6480 (mmp) cc_final: 0.5661 (mmp) REVERT: B 89 LYS cc_start: 0.7213 (ptpp) cc_final: 0.6839 (pttp) REVERT: H 27 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8222 (mtmm) REVERT: H 321 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7777 (mm-30) REVERT: H 611 TYR cc_start: 0.7809 (m-10) cc_final: 0.7606 (m-80) outliers start: 7 outliers final: 5 residues processed: 87 average time/residue: 0.1631 time to fit residues: 19.6246 Evaluate side-chains 85 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR 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: 0.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 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: 0.6980 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.157618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117415 restraints weight = 37559.405| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.46 r_work: 0.3454 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2173 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= 0.138 Angle : 0.501 5.262 11121 Z= 0.280 Chirality : 0.043 0.170 1260 Planarity : 0.004 0.051 1238 Dihedral : 21.980 156.768 1510 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.28 % Allowed : 9.09 % Favored : 89.63 % 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: 0.57 (0.30), residues: 827 helix: 2.33 (0.36), residues: 221 sheet: 0.19 (0.35), residues: 240 loop : -0.69 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 264 TYR 0.004 0.001 TYR H 343 PHE 0.006 0.001 PHE H 617 TRP 0.008 0.001 TRP H 289 HIS 0.005 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 8003) covalent geometry : angle 0.49677 / 0.28 (11107) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 3.81344 / 1.76 ( 2) hydrogen bonds : bond 0.03398 / 2.40 ( 274) hydrogen bonds : angle 4.15103 / 2.92 ( 717) metal coordination : bond 0.00536 / 0.31 ( 8) metal coordination : angle 1.38069 / 0.78 ( 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 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7397 (m-80) cc_final: 0.7121 (m-80) REVERT: A 80 CYS cc_start: 0.5380 (p) cc_final: 0.4404 (p) REVERT: A 90 MET cc_start: 0.6529 (mmp) cc_final: 0.5873 (mmp) REVERT: B 89 LYS cc_start: 0.7209 (ptpp) cc_final: 0.6849 (pttp) REVERT: H 27 LYS cc_start: 0.8560 (mtpt) cc_final: 0.8269 (mtmm) REVERT: H 321 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7762 (mm-30) outliers start: 9 outliers final: 8 residues processed: 89 average time/residue: 0.1760 time to fit residues: 20.9862 Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 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 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: 0.8980 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 overall best weight: 2.2782 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.154850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115743 restraints weight = 36242.534| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.36 r_work: 0.3388 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2315 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= 0.155 Angle : 0.513 5.088 11121 Z= 0.285 Chirality : 0.043 0.230 1260 Planarity : 0.005 0.047 1238 Dihedral : 21.984 157.235 1510 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.28 % Allowed : 9.23 % Favored : 89.49 % 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: 0.32 (0.30), residues: 827 helix: 1.99 (0.36), residues: 232 sheet: 0.06 (0.34), residues: 240 loop : -0.85 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 264 TYR 0.005 0.001 TYR H 452 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 0.00335 / 0.15 ( 8003) covalent geometry : angle 0.50846 / 0.28 (11107) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 3.58300 / 1.66 ( 2) hydrogen bonds : bond 0.03465 / 2.44 ( 274) hydrogen bonds : angle 4.10906 / 2.89 ( 717) metal coordination : bond 0.00612 / 0.34 ( 8) metal coordination : angle 1.45017 / 0.83 ( 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 91 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7518 (m-80) cc_final: 0.7255 (m-80) REVERT: A 80 CYS cc_start: 0.5665 (p) cc_final: 0.4709 (p) REVERT: A 90 MET cc_start: 0.6724 (mmp) cc_final: 0.6147 (mmp) REVERT: B 96 GLN cc_start: 0.6309 (mp-120) cc_final: 0.6046 (mp10) REVERT: H 321 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8003 (mm-30) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.1896 time to fit residues: 21.6136 Evaluate side-chains 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 257 LEU 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: 3.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.155099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116102 restraints weight = 36199.492| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.36 r_work: 0.3396 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2417 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= 0.124 Angle : 0.497 4.844 11121 Z= 0.278 Chirality : 0.042 0.171 1260 Planarity : 0.004 0.056 1238 Dihedral : 21.952 157.010 1510 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.99 % Allowed : 9.94 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.35 (0.30), residues: 827 helix: 2.07 (0.36), residues: 233 sheet: -0.01 (0.34), residues: 240 loop : -0.81 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 264 TYR 0.004 0.001 TYR H 343 PHE 0.007 0.001 PHE H 617 TRP 0.008 0.001 TRP H 289 HIS 0.005 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8003) covalent geometry : angle 0.49318 / 0.28 (11107) SS BOND : bond 0.00123 / 0.06 ( 1) SS BOND : angle 3.50242 / 1.62 ( 2) hydrogen bonds : bond 0.03210 / 2.24 ( 274) hydrogen bonds : angle 3.99353 / 2.81 ( 717) metal coordination : bond 0.00480 / 0.27 ( 8) metal coordination : angle 1.23359 / 0.69 ( 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 99 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 80 CYS cc_start: 0.5653 (p) cc_final: 0.4678 (p) REVERT: A 89 LYS cc_start: 0.7170 (mmmm) cc_final: 0.6885 (mmmm) REVERT: A 90 MET cc_start: 0.6707 (mmp) cc_final: 0.6180 (mmp) REVERT: B 95 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7021 (mm-30) REVERT: H 51 ASP cc_start: 0.8085 (t0) cc_final: 0.7768 (t0) REVERT: H 321 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8007 (mm-30) outliers start: 7 outliers final: 7 residues processed: 93 average time/residue: 0.1737 time to fit residues: 22.1122 Evaluate side-chains 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 257 LEU 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: 0.6980 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 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 = 0.4045 r_free = 0.4045 target = 0.153508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114136 restraints weight = 36410.195| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.39 r_work: 0.3368 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8012 Z= 0.180 Angle : 0.526 5.188 11121 Z= 0.292 Chirality : 0.043 0.165 1260 Planarity : 0.005 0.052 1238 Dihedral : 21.968 158.048 1510 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.14 % Allowed : 10.80 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.29), residues: 827 helix: 2.07 (0.36), residues: 226 sheet: -0.19 (0.34), residues: 240 loop : -0.93 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 44 TYR 0.006 0.001 TYR H 452 PHE 0.008 0.001 PHE H 502 TRP 0.009 0.001 TRP H 289 HIS 0.006 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 8003) covalent geometry : angle 0.52132 / 0.29 (11107) SS BOND : bond 0.00104 / 0.05 ( 1) SS BOND : angle 3.26714 / 1.52 ( 2) hydrogen bonds : bond 0.03636 / 2.53 ( 274) hydrogen bonds : angle 4.02730 / 2.85 ( 717) metal coordination : bond 0.00669 / 0.37 ( 8) metal coordination : angle 1.69818 / 1.00 ( 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 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 80 CYS cc_start: 0.5626 (p) cc_final: 0.4437 (p) REVERT: A 89 LYS cc_start: 0.7207 (mmmm) cc_final: 0.6884 (mmmm) REVERT: A 90 MET cc_start: 0.6764 (mmp) cc_final: 0.6244 (mmp) REVERT: B 96 GLN cc_start: 0.6097 (mp10) cc_final: 0.5881 (mp-120) REVERT: H 51 ASP cc_start: 0.8064 (t0) cc_final: 0.7711 (t0) REVERT: H 321 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8028 (mm-30) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.1756 time to fit residues: 20.6839 Evaluate side-chains 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 717 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 72 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** 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 = 0.4053 r_free = 0.4053 target = 0.154166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114704 restraints weight = 36295.504| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.39 r_work: 0.3382 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8012 Z= 0.123 Angle : 0.508 5.460 11121 Z= 0.282 Chirality : 0.043 0.171 1260 Planarity : 0.005 0.074 1238 Dihedral : 21.927 157.260 1510 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.71 % Allowed : 11.08 % 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 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: 0.25 (0.30), residues: 827 helix: 2.19 (0.36), residues: 226 sheet: -0.19 (0.34), residues: 240 loop : -0.87 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 686 TYR 0.005 0.001 TYR H 343 PHE 0.008 0.001 PHE H 617 TRP 0.008 0.001 TRP H 289 HIS 0.005 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8003) covalent geometry : angle 0.50408 / 0.28 (11107) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 3.17540 / 1.47 ( 2) hydrogen bonds : bond 0.03230 / 2.23 ( 274) hydrogen bonds : angle 3.91829 / 2.77 ( 717) metal coordination : bond 0.00431 / 0.24 ( 8) metal coordination : angle 1.42286 / 0.83 ( 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 : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.5583 (p) cc_final: 0.4445 (p) REVERT: A 89 LYS cc_start: 0.7164 (mmmm) cc_final: 0.6909 (mmmm) REVERT: A 90 MET cc_start: 0.6727 (mmp) cc_final: 0.6293 (mmp) REVERT: B 96 GLN cc_start: 0.6071 (mp10) cc_final: 0.5855 (mp-120) REVERT: H 51 ASP cc_start: 0.8039 (t0) cc_final: 0.7685 (t0) REVERT: H 321 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8044 (mm-30) REVERT: H 593 GLU cc_start: 0.8190 (mp0) cc_final: 0.7530 (mp0) outliers start: 5 outliers final: 4 residues processed: 87 average time/residue: 0.1648 time to fit residues: 19.4643 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 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 = 0.4063 r_free = 0.4063 target = 0.154832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115349 restraints weight = 36234.396| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.39 r_work: 0.3388 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8012 Z= 0.112 Angle : 0.498 5.274 11121 Z= 0.276 Chirality : 0.042 0.170 1260 Planarity : 0.005 0.059 1238 Dihedral : 21.877 157.537 1510 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.71 % Allowed : 11.08 % 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 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: 0.35 (0.30), residues: 827 helix: 2.23 (0.36), residues: 227 sheet: -0.11 (0.34), residues: 245 loop : -0.81 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 686 TYR 0.004 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 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 8003) covalent geometry : angle 0.49429 / 0.27 (11107) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 2.92581 / 1.37 ( 2) hydrogen bonds : bond 0.03058 / 2.10 ( 274) hydrogen bonds : angle 3.82554 / 2.71 ( 717) metal coordination : bond 0.00352 / 0.19 ( 8) metal coordination : angle 1.40529 / 0.82 ( 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 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7093 (mmmm) cc_final: 0.6886 (mmmm) REVERT: B 34 ARG cc_start: 0.5647 (mmt180) cc_final: 0.5328 (mmt180) REVERT: B 96 GLN cc_start: 0.5976 (mp10) cc_final: 0.5765 (mp-120) REVERT: H 51 ASP cc_start: 0.7855 (t0) cc_final: 0.7478 (t0) REVERT: H 321 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7811 (mm-30) REVERT: H 593 GLU cc_start: 0.7914 (mp0) cc_final: 0.7239 (mp0) outliers start: 5 outliers final: 5 residues processed: 89 average time/residue: 0.1771 time to fit residues: 21.9107 Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 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 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 19 optimal weight: 10.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 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 = 0.4123 r_free = 0.4123 target = 0.158156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117896 restraints weight = 37025.284| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.46 r_work: 0.3462 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8012 Z= 0.104 Angle : 0.500 5.350 11121 Z= 0.277 Chirality : 0.042 0.173 1260 Planarity : 0.005 0.075 1238 Dihedral : 21.841 157.266 1510 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.57 % Allowed : 11.79 % Favored : 87.64 % 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: 0.45 (0.30), residues: 827 helix: 2.30 (0.36), residues: 227 sheet: -0.06 (0.35), residues: 244 loop : -0.72 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 686 TYR 0.004 0.001 TYR H 343 PHE 0.007 0.001 PHE H 617 TRP 0.007 0.001 TRP H 289 HIS 0.004 0.001 HIS H 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 8003) covalent geometry : angle 0.49630 / 0.28 (11107) SS BOND : bond 0.00270 / 0.14 ( 1) SS BOND : angle 3.17952 / 1.45 ( 2) hydrogen bonds : bond 0.02912 / 1.99 ( 274) hydrogen bonds : angle 3.76676 / 2.67 ( 717) metal coordination : bond 0.00258 / 0.14 ( 8) metal coordination : angle 1.36241 / 0.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.52 seconds wall clock time: 57 minutes 12.65 seconds (3432.65 seconds total)