Starting phenix.real_space_refine on Wed Mar 4 15:40:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fak_28959/03_2026/8fak_28959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fak_28959/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fak_28959/03_2026/8fak_28959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fak_28959/03_2026/8fak_28959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fak_28959/03_2026/8fak_28959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fak_28959/03_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-5986/lib/python3.9/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: 2.66, per 1000 atoms: 0.18 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: 1.29 Conformation dependent library (CDL) restraints added in 384.7 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: 2.46 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: 3.06 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7240 1.04 - 1.23: 133 1.23 - 1.43: 3340 1.43 - 1.62: 4500 1.62 - 1.82: 38 Bond restraints: 15251 Sorted by residual: bond pdb=" N ARG H 108 " pdb=" CA ARG H 108 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.37e-02 5.33e+03 5.68e+00 bond pdb=" C ASN H 706 " pdb=" N GLY H 707 " ideal model delta sigma weight residual 1.334 1.362 -0.028 1.32e-02 5.74e+03 4.54e+00 bond pdb=" N ALA H 110 " pdb=" CA ALA H 110 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.23e-02 6.61e+03 3.27e+00 bond pdb=" C PRO H 109 " pdb=" O PRO H 109 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.30e-02 5.92e+03 2.12e+00 bond pdb=" O3' DT Z 12 " pdb=" P DC Z 13 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.50e-02 4.44e+03 2.01e+00 ... (remaining 15246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 25143 2.10 - 4.19: 2205 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=" H4' DA J 35 " ideal model delta sigma weight residual 109.00 115.87 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C4' DA J 35 " pdb=" C3' DA J 35 " pdb=" H3' DA J 35 " ideal model delta sigma weight residual 109.00 115.42 -6.42 1.50e+00 4.44e-01 1.83e+01 angle pdb=" O4' DT J 33 " pdb=" C1' DT J 33 " pdb=" H1' DT J 33 " ideal model delta sigma weight residual 109.00 115.11 -6.11 1.50e+00 4.44e-01 1.66e+01 angle pdb=" C4' DA G 7 " pdb=" C3' DA G 7 " pdb=" H3' DA G 7 " ideal model delta sigma weight residual 109.00 115.03 -6.03 1.50e+00 4.44e-01 1.62e+01 angle pdb=" O4' DT G 13 " pdb=" C4' DT G 13 " pdb=" H4' DT G 13 " ideal model delta sigma weight residual 109.00 114.97 -5.97 1.50e+00 4.44e-01 1.58e+01 ... (remaining 27628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 6375 30.75 - 61.49: 516 61.49 - 92.24: 19 92.24 - 122.98: 0 122.98 - 153.73: 2 Dihedral angle restraints: 6912 sinusoidal: 4120 harmonic: 2792 Sorted by residual: dihedral pdb=" C4' DC J 32 " pdb=" C3' DC J 32 " pdb=" O3' DC J 32 " pdb=" P DT J 33 " ideal model delta sinusoidal sigma weight residual 220.00 66.27 153.73 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" C4' DG J 34 " pdb=" C3' DG J 34 " pdb=" O3' DG J 34 " pdb=" P DA J 35 " ideal model delta sinusoidal sigma weight residual 220.00 80.20 139.80 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA CYS A 80 " pdb=" CB CYS A 80 " pdb=" SG CYS A 80 " pdb=" SG CYS B 48 " ideal model delta sinusoidal sigma weight residual -73.00 -14.90 -58.10 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 6909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 835 0.030 - 0.060: 294 0.060 - 0.091: 55 0.091 - 0.121: 70 0.121 - 0.151: 6 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ARG H 108 " pdb=" N ARG H 108 " pdb=" C ARG H 108 " pdb=" CB ARG H 108 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE H 691 " pdb=" N ILE H 691 " pdb=" C ILE H 691 " pdb=" CB ILE H 691 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA THR H 258 " pdb=" N THR H 258 " pdb=" C THR H 258 " pdb=" CB THR H 258 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1257 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 631 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO H 632 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 632 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 632 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC Z 11 " -0.014 2.00e-02 2.50e+03 1.01e-02 2.78e+00 pdb=" N1 DC Z 11 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DC Z 11 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DC Z 11 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC Z 11 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC Z 11 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC Z 11 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC Z 11 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC Z 11 " 0.008 2.00e-02 2.50e+03 pdb=" H5 DC Z 11 " -0.018 2.00e-02 2.50e+03 pdb=" H6 DC Z 11 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 630 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO H 631 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 631 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 631 " -0.022 5.00e-02 4.00e+02 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.82: 69 1.82 - 2.52: 11091 2.52 - 3.21: 43172 3.21 - 3.91: 56309 3.91 - 4.60: 87657 Nonbonded interactions: 198298 Sorted by model distance: nonbonded pdb=" HB3 HIS H 437 " pdb=" HD2 HIS H 483 " model vdw 1.129 2.270 nonbonded pdb=" HE1 HIS B 26 " pdb=" HA HIS H 483 " model vdw 1.286 2.270 nonbonded pdb=" ND1 HIS B 26 " pdb=" HD1 HIS H 483 " model vdw 1.294 2.600 nonbonded pdb=" O ASP H 17 " pdb="HO3' DC Z 13 " model vdw 1.477 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: 0.550 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.330 Find NCS groups from input model: 0.070 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8012 Z= 0.119 Angle : 0.464 5.623 11121 Z= 0.257 Chirality : 0.039 0.151 1260 Planarity : 0.004 0.055 1238 Dihedral : 19.105 153.728 3075 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00238 ( 8003) covalent geometry : angle 0.46120 (11107) SS BOND : bond 0.00273 ( 1) SS BOND : angle 2.81692 ( 2) hydrogen bonds : bond 0.16988 ( 274) hydrogen bonds : angle 5.75165 ( 717) metal coordination : bond 0.00227 ( 8) metal coordination : angle 1.01354 ( 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 : 0.381 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: 0.2008 time to fit residues: 35.3348 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: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN H 200 ASN H 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.158882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119061 restraints weight = 37628.607| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.49 r_work: 0.3476 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8012 Z= 0.163 Angle : 0.550 4.961 11121 Z= 0.301 Chirality : 0.044 0.145 1260 Planarity : 0.005 0.045 1238 Dihedral : 21.768 154.347 1510 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.14 % Allowed : 7.39 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.30), residues: 827 helix: 2.30 (0.36), residues: 221 sheet: 0.96 (0.36), residues: 240 loop : -0.46 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 44 TYR 0.006 0.001 TYR H 452 PHE 0.007 0.001 PHE H 574 TRP 0.007 0.001 TRP H 289 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8003) covalent geometry : angle 0.54581 (11107) SS BOND : bond 0.00228 ( 1) SS BOND : angle 3.32140 ( 2) hydrogen bonds : bond 0.03812 ( 274) hydrogen bonds : angle 4.37679 ( 717) metal coordination : bond 0.00671 ( 8) metal coordination : angle 1.71324 ( 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 100 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7420 (m-80) cc_final: 0.7140 (m-80) REVERT: A 80 CYS cc_start: 0.5346 (p) cc_final: 0.4573 (p) REVERT: A 89 LYS cc_start: 0.7187 (mmmm) cc_final: 0.6883 (mmmm) REVERT: A 90 MET cc_start: 0.6332 (mmp) cc_final: 0.5971 (mmt) REVERT: B 89 LYS cc_start: 0.7240 (ptpp) cc_final: 0.6869 (pttp) REVERT: H 27 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8194 (mtmm) REVERT: H 321 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7783 (mm-30) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.2085 time to fit residues: 26.3485 Evaluate side-chains 88 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 542 LEU 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: 5.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 75 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.158555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118483 restraints weight = 37317.667| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.47 r_work: 0.3470 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8012 Z= 0.123 Angle : 0.500 5.053 11121 Z= 0.274 Chirality : 0.043 0.140 1260 Planarity : 0.004 0.041 1238 Dihedral : 21.588 155.704 1510 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.99 % Allowed : 8.95 % Favored : 90.06 % 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: 0.99 (0.30), residues: 827 helix: 2.52 (0.36), residues: 221 sheet: 0.64 (0.35), residues: 247 loop : -0.50 (0.32), residues: 359 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 0.006 0.001 PHE H 617 TRP 0.007 0.001 TRP H 289 HIS 0.010 0.001 HIS H 483 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8003) covalent geometry : angle 0.49618 (11107) SS BOND : bond 0.00071 ( 1) SS BOND : angle 3.23392 ( 2) hydrogen bonds : bond 0.03237 ( 274) hydrogen bonds : angle 4.04997 ( 717) metal coordination : bond 0.00488 ( 8) metal coordination : angle 1.51619 ( 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 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7486 (m-80) cc_final: 0.7222 (m-80) REVERT: A 80 CYS cc_start: 0.5611 (p) cc_final: 0.4457 (p) REVERT: A 89 LYS cc_start: 0.7267 (mmmm) cc_final: 0.6825 (mmmm) REVERT: A 90 MET cc_start: 0.6706 (mmp) cc_final: 0.6353 (mmt) REVERT: B 95 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7208 (mm-30) REVERT: H 27 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8255 (mtmm) REVERT: H 321 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7932 (mm-30) outliers start: 7 outliers final: 6 residues processed: 89 average time/residue: 0.2029 time to fit residues: 23.9931 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 542 LEU 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: 9.9990 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: 4.9990 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.153622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113965 restraints weight = 36249.842| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.40 r_work: 0.3372 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8012 Z= 0.157 Angle : 0.529 5.135 11121 Z= 0.289 Chirality : 0.043 0.142 1260 Planarity : 0.005 0.045 1238 Dihedral : 21.493 156.140 1510 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.14 % Allowed : 9.38 % 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: 0.55 (0.30), residues: 827 helix: 2.23 (0.36), residues: 226 sheet: 0.20 (0.35), residues: 236 loop : -0.69 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 686 TYR 0.006 0.001 TYR H 578 PHE 0.008 0.001 PHE H 617 TRP 0.007 0.001 TRP H 289 HIS 0.007 0.001 HIS H 483 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8003) covalent geometry : angle 0.52311 (11107) SS BOND : bond 0.00071 ( 1) SS BOND : angle 3.21883 ( 2) hydrogen bonds : bond 0.03462 ( 274) hydrogen bonds : angle 3.98084 ( 717) metal coordination : bond 0.00706 ( 8) metal coordination : angle 2.06990 ( 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 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7564 (m-80) cc_final: 0.7314 (m-80) REVERT: A 80 CYS cc_start: 0.5780 (p) cc_final: 0.4849 (p) REVERT: A 89 LYS cc_start: 0.7318 (mmmm) cc_final: 0.6876 (mmmm) REVERT: A 90 MET cc_start: 0.6800 (mmp) cc_final: 0.6377 (mmt) REVERT: B 90 MET cc_start: 0.8360 (ttp) cc_final: 0.8151 (ttp) REVERT: H 321 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7989 (mm-30) REVERT: H 513 ASP cc_start: 0.8281 (m-30) cc_final: 0.8071 (m-30) REVERT: H 593 GLU cc_start: 0.8256 (mp0) cc_final: 0.8035 (mp0) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 0.1895 time to fit residues: 22.9138 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 : 0.349 ------------------------------------------------------------------------------- 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 717 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 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: 5.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.151396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111816 restraints weight = 36579.131| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.40 r_work: 0.3342 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2963 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= 0.195 Angle : 0.552 5.464 11121 Z= 0.304 Chirality : 0.044 0.157 1260 Planarity : 0.005 0.047 1238 Dihedral : 21.545 157.470 1510 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.42 % Allowed : 10.80 % Favored : 87.78 % 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: 1.82 (0.35), residues: 226 sheet: -0.30 (0.33), residues: 241 loop : -1.01 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 686 TYR 0.008 0.001 TYR H 578 PHE 0.010 0.001 PHE H 502 TRP 0.009 0.001 TRP H 289 HIS 0.008 0.001 HIS H 483 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8003) covalent geometry : angle 0.54676 (11107) SS BOND : bond 0.00212 ( 1) SS BOND : angle 3.08118 ( 2) hydrogen bonds : bond 0.03845 ( 274) hydrogen bonds : angle 4.09387 ( 717) metal coordination : bond 0.00763 ( 8) metal coordination : angle 1.91265 ( 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 98 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.221 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: 0.7694 (m-80) cc_final: 0.7494 (m-80) REVERT: A 80 CYS cc_start: 0.5767 (p) cc_final: 0.4833 (p) REVERT: A 90 MET cc_start: 0.6930 (mmp) cc_final: 0.6465 (mmt) REVERT: H 51 ASP cc_start: 0.8020 (t0) cc_final: 0.7752 (t0) REVERT: H 321 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8061 (mm-30) outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.2021 time to fit residues: 24.4376 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 : 0.376 ------------------------------------------------------------------------------- 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 628 MET 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: 10.0000 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.152363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112928 restraints weight = 36130.645| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.39 r_work: 0.3357 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8012 Z= 0.145 Angle : 0.520 5.034 11121 Z= 0.285 Chirality : 0.043 0.148 1260 Planarity : 0.005 0.050 1238 Dihedral : 21.429 156.920 1510 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.99 % Allowed : 11.22 % Favored : 87.78 % 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: 1.94 (0.36), residues: 226 sheet: -0.35 (0.33), residues: 249 loop : -0.99 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 686 TYR 0.004 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 483 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8003) covalent geometry : angle 0.51630 (11107) SS BOND : bond 0.00131 ( 1) SS BOND : angle 3.01978 ( 2) hydrogen bonds : bond 0.03331 ( 274) hydrogen bonds : angle 3.94025 ( 717) metal coordination : bond 0.00529 ( 8) metal coordination : angle 1.50268 ( 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 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.5740 (p) cc_final: 0.4849 (p) REVERT: A 90 MET cc_start: 0.6751 (mmp) cc_final: 0.6247 (mmt) REVERT: H 51 ASP cc_start: 0.8001 (t0) cc_final: 0.7654 (t0) REVERT: H 254 GLU cc_start: 0.8655 (pm20) cc_final: 0.8109 (pt0) REVERT: H 321 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8034 (mm-30) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1954 time to fit residues: 23.7251 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 : 0.277 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 257 LEU 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: 4.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.154390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114305 restraints weight = 36930.618| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.44 r_work: 0.3411 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8012 Z= 0.146 Angle : 0.518 5.158 11121 Z= 0.284 Chirality : 0.043 0.143 1260 Planarity : 0.005 0.053 1238 Dihedral : 21.374 157.227 1510 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.14 % Allowed : 11.51 % 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: -0.08 (0.29), residues: 827 helix: 1.97 (0.36), residues: 226 sheet: -0.48 (0.33), residues: 251 loop : -1.04 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 686 TYR 0.005 0.001 TYR H 452 PHE 0.007 0.001 PHE H 502 TRP 0.009 0.001 TRP H 289 HIS 0.004 0.001 HIS H 483 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8003) covalent geometry : angle 0.51431 (11107) SS BOND : bond 0.00157 ( 1) SS BOND : angle 2.84623 ( 2) hydrogen bonds : bond 0.03363 ( 274) hydrogen bonds : angle 3.92374 ( 717) metal coordination : bond 0.00570 ( 8) metal coordination : angle 1.48154 ( 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 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7291 (mmmm) cc_final: 0.6784 (mmmm) REVERT: A 90 MET cc_start: 0.6757 (mmp) cc_final: 0.6386 (mmt) REVERT: H 51 ASP cc_start: 0.7973 (t0) cc_final: 0.7628 (t0) REVERT: H 321 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8035 (mm-30) outliers start: 8 outliers final: 7 residues processed: 89 average time/residue: 0.2042 time to fit residues: 24.2882 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 : 0.369 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.154598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114730 restraints weight = 37325.022| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.45 r_work: 0.3418 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8012 Z= 0.133 Angle : 0.514 5.023 11121 Z= 0.282 Chirality : 0.043 0.142 1260 Planarity : 0.005 0.058 1238 Dihedral : 21.334 158.291 1510 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.71 % Allowed : 11.79 % 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: -0.02 (0.30), residues: 827 helix: 2.03 (0.36), residues: 226 sheet: -0.46 (0.33), residues: 252 loop : -0.99 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 686 TYR 0.004 0.001 TYR H 452 PHE 0.007 0.001 PHE H 502 TRP 0.008 0.001 TRP H 289 HIS 0.004 0.001 HIS H 483 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8003) covalent geometry : angle 0.51070 (11107) SS BOND : bond 0.00135 ( 1) SS BOND : angle 2.84043 ( 2) hydrogen bonds : bond 0.03193 ( 274) hydrogen bonds : angle 3.85109 ( 717) metal coordination : bond 0.00489 ( 8) metal coordination : angle 1.32718 ( 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: 5 poor density : 88 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7236 (mmmm) cc_final: 0.6735 (mmmm) REVERT: A 90 MET cc_start: 0.6703 (mmp) cc_final: 0.6328 (mmt) REVERT: H 51 ASP cc_start: 0.8003 (t0) cc_final: 0.7657 (t0) REVERT: H 321 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7938 (mm-30) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.1964 time to fit residues: 23.7682 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 : 0.268 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain A residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114945 restraints weight = 37335.040| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.45 r_work: 0.3423 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8012 Z= 0.126 Angle : 0.507 4.961 11121 Z= 0.279 Chirality : 0.043 0.139 1260 Planarity : 0.005 0.063 1238 Dihedral : 21.259 159.526 1510 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.99 % Allowed : 11.93 % Favored : 87.07 % 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: 0.03 (0.30), residues: 827 helix: 2.15 (0.36), residues: 225 sheet: -0.47 (0.33), residues: 252 loop : -0.98 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 686 TYR 0.004 0.001 TYR H 452 PHE 0.006 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 covalent geometry : bond 0.00291 ( 8003) covalent geometry : angle 0.50491 (11107) SS BOND : bond 0.00111 ( 1) SS BOND : angle 2.69893 ( 2) hydrogen bonds : bond 0.03120 ( 274) hydrogen bonds : angle 3.77188 ( 717) metal coordination : bond 0.00482 ( 8) metal coordination : angle 1.21368 ( 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 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7259 (mmmm) cc_final: 0.6727 (mmmm) REVERT: A 90 MET cc_start: 0.6676 (mmp) cc_final: 0.6313 (mmt) REVERT: H 51 ASP cc_start: 0.8022 (t0) cc_final: 0.7675 (t0) REVERT: H 230 LYS cc_start: 0.8756 (mttm) cc_final: 0.8313 (mttp) REVERT: H 321 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8089 (mm-30) REVERT: H 593 GLU cc_start: 0.8252 (mp0) cc_final: 0.7740 (mp0) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.2069 time to fit residues: 24.9512 Evaluate side-chains 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.153145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113273 restraints weight = 37177.736| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.44 r_work: 0.3399 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8012 Z= 0.173 Angle : 0.539 5.372 11121 Z= 0.297 Chirality : 0.044 0.142 1260 Planarity : 0.005 0.067 1238 Dihedral : 21.293 158.907 1510 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.85 % Allowed : 11.79 % 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: -0.22 (0.29), residues: 827 helix: 1.86 (0.36), residues: 226 sheet: -0.62 (0.34), residues: 242 loop : -1.07 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 686 TYR 0.006 0.001 TYR H 578 PHE 0.009 0.001 PHE H 502 TRP 0.010 0.001 TRP H 289 HIS 0.005 0.001 HIS H 460 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8003) covalent geometry : angle 0.53513 (11107) SS BOND : bond 0.00255 ( 1) SS BOND : angle 2.72288 ( 2) hydrogen bonds : bond 0.03640 ( 274) hydrogen bonds : angle 3.95105 ( 717) metal coordination : bond 0.00729 ( 8) metal coordination : angle 1.70993 ( 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 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7243 (mmmm) cc_final: 0.6722 (mmmm) REVERT: A 90 MET cc_start: 0.6882 (mmp) cc_final: 0.6484 (mmt) REVERT: H 51 ASP cc_start: 0.7995 (t0) cc_final: 0.7642 (t0) REVERT: H 321 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7956 (mm-30) outliers start: 6 outliers final: 5 residues processed: 89 average time/residue: 0.2097 time to fit residues: 24.6517 Evaluate side-chains 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.155507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.115795 restraints weight = 37007.402| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.44 r_work: 0.3435 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8012 Z= 0.106 Angle : 0.503 4.675 11121 Z= 0.276 Chirality : 0.042 0.140 1260 Planarity : 0.005 0.070 1238 Dihedral : 21.177 161.090 1510 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.43 % Allowed : 12.93 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.24 (0.36), residues: 226 sheet: -0.41 (0.34), residues: 252 loop : -0.94 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 686 TYR 0.004 0.001 TYR H 452 PHE 0.006 0.001 PHE H 97 TRP 0.008 0.001 TRP H 289 HIS 0.004 0.001 HIS H 483 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8003) covalent geometry : angle 0.50045 (11107) SS BOND : bond 0.00040 ( 1) SS BOND : angle 2.61630 ( 2) hydrogen bonds : bond 0.02833 ( 274) hydrogen bonds : angle 3.68857 ( 717) metal coordination : bond 0.00332 ( 8) metal coordination : angle 1.10625 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4107.42 seconds wall clock time: 70 minutes 4.90 seconds (4204.90 seconds total)