Starting phenix.real_space_refine on Thu Jul 2 21:57:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oto_13063/07_2026/7oto_13063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oto_13063/07_2026/7oto_13063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oto_13063/07_2026/7oto_13063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oto_13063/07_2026/7oto_13063.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oto_13063/07_2026/7oto_13063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oto_13063/07_2026/7oto_13063.cif" model { file = "/net/cci-nas-00/data/ceres_data/7oto_13063/07_2026/7oto_13063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oto_13063/07_2026/7oto_13063.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6472 2.51 5 N 1841 2.21 5 O 1961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 10333 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4697 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 25, 'TRANS': 576} Chain breaks: 1 Chain: "A" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5572 Classifications: {'peptide': 711} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain breaks: 3 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.12, per 1000 atoms: 0.21 Number of scatterers: 10333 At special positions: 0 Unit cell: (112.36, 121.9, 97.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 6 15.00 Mg 2 11.99 O 1961 8.00 N 1841 7.00 C 6472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.83 Conformation dependent library (CDL) restraints added in 379.9 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 55.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.720A pdb=" N LEU B 189 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 230 through 248 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.732A pdb=" N LEU B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 Proline residue: B 340 - end of helix removed outlier: 3.655A pdb=" N GLY B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 361 through 385 Proline residue: B 376 - end of helix removed outlier: 3.811A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.578A pdb=" N GLY B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 512 through 536 Processing helix chain 'B' and resid 538 through 566 Processing helix chain 'B' and resid 585 through 592 removed outlier: 4.078A pdb=" N GLN B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 636 Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 700 through 718 Processing helix chain 'B' and resid 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' Processing helix chain 'B' and resid 734 through 739 removed outlier: 4.036A pdb=" N LYS B 738 " --> pdb=" O GLN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 780 Processing helix chain 'B' and resid 782 through 799 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.617A pdb=" N LYS A 45 " --> pdb=" O TYR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 230 through 249 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 334 through 346 Proline residue: A 340 - end of helix removed outlier: 3.532A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.622A pdb=" N ILE A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 385 Proline residue: A 376 - end of helix removed outlier: 3.525A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.642A pdb=" N GLY A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 513 through 536 Processing helix chain 'A' and resid 538 through 566 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.808A pdb=" N GLN A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.588A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.624A pdb=" N LYS A 738 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 780 Processing helix chain 'A' and resid 782 through 800 Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 138 removed outlier: 3.504A pdb=" N ARG B 154 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 178 through 181 removed outlier: 5.894A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 570 through 572 removed outlier: 3.637A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU B 582 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN B 599 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 653 through 656 removed outlier: 6.222A pdb=" N PHE B 654 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP B 693 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG B 656 " --> pdb=" O ASP B 693 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 610 " --> pdb=" O PHE B 725 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ALA B 749 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER B 761 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N LEU B 750 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET B 759 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.224A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 112 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.325A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 572 removed outlier: 6.305A pdb=" N THR A 571 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 582 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN A 599 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 653 through 656 removed outlier: 6.136A pdb=" N PHE A 654 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASP A 693 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 656 " --> pdb=" O ASP A 693 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASN A 744 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN A 763 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A 746 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER A 761 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 748 " --> pdb=" O MET A 759 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1765 1.31 - 1.44: 2562 1.44 - 1.57: 6071 1.57 - 1.69: 10 1.69 - 1.82: 91 Bond restraints: 10499 Sorted by residual: bond pdb=" N3B ANP A1002 " pdb=" PG ANP A1002 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" N3B ANP B1002 " pdb=" PG ANP B1002 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" O3A ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sigma weight residual 1.700 1.596 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O3A ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sigma weight residual 1.700 1.600 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ILE A 66 " pdb=" CA ILE A 66 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.07e+01 ... (remaining 10494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12438 2.83 - 5.66: 1735 5.66 - 8.49: 49 8.49 - 11.32: 4 11.32 - 14.15: 1 Bond angle restraints: 14227 Sorted by residual: angle pdb=" CA GLY B 422 " pdb=" C GLY B 422 " pdb=" O GLY B 422 " ideal model delta sigma weight residual 122.45 117.11 5.34 7.20e-01 1.93e+00 5.50e+01 angle pdb=" CA PHE A 725 " pdb=" CB PHE A 725 " pdb=" CG PHE A 725 " ideal model delta sigma weight residual 113.80 120.50 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" N PRO A 25 " pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 113.40 121.99 -8.59 1.34e+00 5.57e-01 4.11e+01 angle pdb=" CA SER B 604 " pdb=" C SER B 604 " pdb=" N PRO B 605 " ideal model delta sigma weight residual 117.68 122.22 -4.54 7.10e-01 1.98e+00 4.09e+01 angle pdb=" C PRO B 231 " pdb=" CA PRO B 231 " pdb=" CB PRO B 231 " ideal model delta sigma weight residual 113.06 102.93 10.13 1.59e+00 3.96e-01 4.06e+01 ... (remaining 14222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.08: 6228 32.08 - 64.17: 166 64.17 - 96.25: 23 96.25 - 128.34: 1 128.34 - 160.42: 1 Dihedral angle restraints: 6419 sinusoidal: 2620 harmonic: 3799 Sorted by residual: dihedral pdb=" O1A ANP B1002 " pdb=" O3A ANP B1002 " pdb=" PA ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sinusoidal sigma weight residual 83.11 -77.31 160.42 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A ANP A1002 " pdb=" O3A ANP A1002 " pdb=" PA ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sinusoidal sigma weight residual 83.11 -39.51 122.62 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C GLN B 248 " pdb=" N GLN B 248 " pdb=" CA GLN B 248 " pdb=" CB GLN B 248 " ideal model delta harmonic sigma weight residual -122.60 -113.29 -9.31 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 6416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 805 0.075 - 0.149: 540 0.149 - 0.224: 215 0.224 - 0.299: 68 0.299 - 0.373: 2 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C3' ANP A1002 " pdb=" C2' ANP A1002 " pdb=" C4' ANP A1002 " pdb=" O3' ANP A1002 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1627 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 268 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C ILE B 268 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 268 " 0.017 2.00e-02 2.50e+03 pdb=" N MET B 269 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 675 " -0.011 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C THR B 675 " 0.041 2.00e-02 2.50e+03 pdb=" O THR B 675 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 676 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 213 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C LEU B 213 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 213 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B 214 " -0.014 2.00e-02 2.50e+03 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 4 2.42 - 3.04: 5531 3.04 - 3.66: 15957 3.66 - 4.28: 22989 4.28 - 4.90: 39179 Nonbonded interactions: 83660 Sorted by model distance: nonbonded pdb=" OG SER A 621 " pdb="MG MG A1001 " model vdw 1.799 2.170 nonbonded pdb=" OG SER B 621 " pdb="MG MG B1001 " model vdw 2.036 2.170 nonbonded pdb="MG MG A1001 " pdb=" O2B ANP A1002 " model vdw 2.128 2.170 nonbonded pdb="MG MG B1001 " pdb=" O1G ANP B1002 " model vdw 2.273 2.170 nonbonded pdb=" N ASP A 139 " pdb=" O ASP A 139 " model vdw 2.439 2.496 ... (remaining 83655 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.110 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.013 0.175 10499 Z= 0.975 Angle : 1.836 14.147 14227 Z= 1.411 Chirality : 0.110 0.373 1630 Planarity : 0.006 0.034 1852 Dihedral : 15.173 160.421 3961 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % 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: 2.59 (0.21), residues: 1301 helix: 3.35 (0.17), residues: 662 sheet: 0.72 (0.39), residues: 159 loop : -0.34 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 607 TYR 0.035 0.003 TYR A 31 PHE 0.029 0.005 PHE B 532 TRP 0.020 0.003 TRP B 202 HIS 0.010 0.002 HIS B 752 Details of bonding type rmsd/Z covalent geometry : bond 0.01297 / 0.97 (10499) covalent geometry : angle 1.83605 / 1.41 (14227) hydrogen bonds : bond 0.20863 / 14.10 ( 568) hydrogen bonds : angle 6.18931 / 4.48 ( 1641) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 THR cc_start: 0.8305 (t) cc_final: 0.8057 (m) REVERT: B 197 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7336 (mtp180) REVERT: B 198 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7546 (mtm-85) REVERT: B 201 LEU cc_start: 0.8205 (tp) cc_final: 0.7935 (mm) REVERT: B 205 GLU cc_start: 0.7437 (tt0) cc_final: 0.7155 (tt0) REVERT: B 229 ASN cc_start: 0.7428 (t0) cc_final: 0.7009 (p0) REVERT: B 323 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 355 LEU cc_start: 0.7836 (tp) cc_final: 0.7580 (tp) REVERT: B 373 GLN cc_start: 0.7608 (mt0) cc_final: 0.7377 (mm110) REVERT: B 386 ASP cc_start: 0.7722 (p0) cc_final: 0.7381 (p0) REVERT: B 402 GLU cc_start: 0.7532 (tp30) cc_final: 0.7264 (tp30) REVERT: B 535 LEU cc_start: 0.7229 (mt) cc_final: 0.6904 (mp) REVERT: B 566 ASN cc_start: 0.8095 (t0) cc_final: 0.7667 (t0) REVERT: B 640 VAL cc_start: 0.8618 (t) cc_final: 0.8350 (m) REVERT: B 656 ARG cc_start: 0.6896 (tpt90) cc_final: 0.6414 (tpt90) REVERT: B 692 MET cc_start: 0.8587 (mtp) cc_final: 0.8342 (mtt) REVERT: B 693 ASP cc_start: 0.8164 (t0) cc_final: 0.7802 (t0) REVERT: B 718 LYS cc_start: 0.8163 (mttm) cc_final: 0.7925 (ttmm) REVERT: A 52 ASP cc_start: 0.8157 (t0) cc_final: 0.7738 (t0) REVERT: A 96 ILE cc_start: 0.6907 (pt) cc_final: 0.6607 (mm) REVERT: A 122 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7628 (tp30) REVERT: A 130 ASP cc_start: 0.8327 (m-30) cc_final: 0.8018 (p0) REVERT: A 162 ASP cc_start: 0.7343 (m-30) cc_final: 0.6791 (t0) REVERT: A 166 MET cc_start: 0.7816 (tpt) cc_final: 0.7584 (tpp) REVERT: A 198 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7853 (ttm-80) REVERT: A 225 PHE cc_start: 0.7779 (m-80) cc_final: 0.7426 (m-80) REVERT: A 240 LEU cc_start: 0.8064 (tp) cc_final: 0.7734 (tp) REVERT: A 283 LEU cc_start: 0.7896 (mt) cc_final: 0.7661 (mp) REVERT: A 296 ASP cc_start: 0.7792 (t0) cc_final: 0.7486 (t0) REVERT: A 355 LEU cc_start: 0.7303 (tp) cc_final: 0.6766 (tp) REVERT: A 417 VAL cc_start: 0.7812 (t) cc_final: 0.7495 (m) REVERT: A 566 ASN cc_start: 0.8189 (t0) cc_final: 0.7639 (t0) REVERT: A 651 ASP cc_start: 0.8132 (t70) cc_final: 0.7869 (t0) REVERT: A 661 ASP cc_start: 0.7631 (t0) cc_final: 0.7427 (t0) REVERT: A 662 ASP cc_start: 0.6550 (t0) cc_final: 0.6103 (p0) REVERT: A 667 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7258 (mmm-85) REVERT: A 692 MET cc_start: 0.8278 (mtm) cc_final: 0.8015 (mtp) REVERT: A 713 GLU cc_start: 0.7284 (tt0) cc_final: 0.7077 (tt0) REVERT: A 720 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7509 (mtmm) REVERT: A 759 MET cc_start: 0.8355 (mmm) cc_final: 0.8075 (mmp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1440 time to fit residues: 66.6313 Evaluate side-chains 292 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 HIS B 734 GLN B 746 HIS A 49 GLN A 78 ASN A 254 HIS A 264 GLN A 543 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113908 restraints weight = 19439.901| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.31 r_work: 0.3340 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10499 Z= 0.143 Angle : 0.597 7.265 14227 Z= 0.315 Chirality : 0.041 0.174 1630 Planarity : 0.005 0.041 1852 Dihedral : 7.537 172.693 1455 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.58 % Allowed : 13.47 % Favored : 83.95 % 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: 2.16 (0.22), residues: 1301 helix: 2.90 (0.19), residues: 677 sheet: 0.71 (0.37), residues: 184 loop : -0.67 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 319 TYR 0.021 0.002 TYR A 31 PHE 0.017 0.002 PHE A 725 TRP 0.012 0.002 TRP A 137 HIS 0.009 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (10499) covalent geometry : angle 0.59729 / 0.32 (14227) hydrogen bonds : bond 0.05064 / 3.52 ( 568) hydrogen bonds : angle 4.62655 / 3.30 ( 1641) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LEU cc_start: 0.8478 (tp) cc_final: 0.8278 (mm) REVERT: B 229 ASN cc_start: 0.7319 (t0) cc_final: 0.6926 (p0) REVERT: B 302 MET cc_start: 0.7468 (ptm) cc_final: 0.7222 (ptt) REVERT: B 350 ARG cc_start: 0.6440 (ptt-90) cc_final: 0.5741 (ttp80) REVERT: B 354 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7652 (mtt180) REVERT: B 355 LEU cc_start: 0.8869 (tp) cc_final: 0.8573 (tp) REVERT: B 424 VAL cc_start: 0.8644 (t) cc_final: 0.8322 (p) REVERT: B 566 ASN cc_start: 0.8089 (t0) cc_final: 0.7767 (t0) REVERT: B 609 MET cc_start: 0.7608 (ttt) cc_final: 0.7350 (ttt) REVERT: B 624 MET cc_start: 0.8434 (mtp) cc_final: 0.8173 (mtp) REVERT: B 640 VAL cc_start: 0.8796 (t) cc_final: 0.8423 (m) REVERT: B 692 MET cc_start: 0.8421 (mtp) cc_final: 0.8172 (mtt) REVERT: B 693 ASP cc_start: 0.7752 (t0) cc_final: 0.7545 (t70) REVERT: B 730 PHE cc_start: 0.7827 (m-80) cc_final: 0.7627 (m-80) REVERT: A 33 MET cc_start: 0.7576 (mmm) cc_final: 0.7363 (mmt) REVERT: A 36 PHE cc_start: 0.7840 (m-10) cc_final: 0.7597 (m-10) REVERT: A 133 LEU cc_start: 0.8391 (tp) cc_final: 0.8169 (tp) REVERT: A 157 LEU cc_start: 0.8144 (tt) cc_final: 0.7656 (tp) REVERT: A 198 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8099 (ttm-80) REVERT: A 199 ARG cc_start: 0.8319 (mmm160) cc_final: 0.8041 (mmm160) REVERT: A 240 LEU cc_start: 0.8389 (tp) cc_final: 0.8024 (tp) REVERT: A 355 LEU cc_start: 0.7732 (tp) cc_final: 0.7195 (tp) REVERT: A 417 VAL cc_start: 0.7397 (t) cc_final: 0.7135 (p) REVERT: A 565 LEU cc_start: 0.8311 (mt) cc_final: 0.7810 (mt) REVERT: A 566 ASN cc_start: 0.8155 (t0) cc_final: 0.7498 (t0) REVERT: A 651 ASP cc_start: 0.8309 (t70) cc_final: 0.8100 (t0) REVERT: A 662 ASP cc_start: 0.7066 (t0) cc_final: 0.6681 (t0) REVERT: A 692 MET cc_start: 0.8111 (mtm) cc_final: 0.7824 (mtp) outliers start: 28 outliers final: 15 residues processed: 305 average time/residue: 0.1257 time to fit residues: 50.9410 Evaluate side-chains 278 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 695 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 0.0060 chunk 59 optimal weight: 8.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 602 ASN B 734 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109615 restraints weight = 19582.649| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.34 r_work: 0.3236 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10499 Z= 0.202 Angle : 0.621 8.506 14227 Z= 0.322 Chirality : 0.043 0.202 1630 Planarity : 0.005 0.079 1852 Dihedral : 7.277 163.281 1455 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.32 % Allowed : 16.79 % Favored : 79.89 % 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: 1.67 (0.22), residues: 1301 helix: 2.50 (0.19), residues: 667 sheet: 0.58 (0.38), residues: 184 loop : -0.84 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 579 TYR 0.022 0.002 TYR A 635 PHE 0.017 0.003 PHE B 334 TRP 0.014 0.002 TRP A 137 HIS 0.008 0.002 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 (10499) covalent geometry : angle 0.62134 / 0.32 (14227) hydrogen bonds : bond 0.05201 / 3.56 ( 568) hydrogen bonds : angle 4.47000 / 3.20 ( 1641) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 ASP cc_start: 0.8037 (t0) cc_final: 0.7832 (t0) REVERT: B 154 ARG cc_start: 0.7569 (ttm170) cc_final: 0.7321 (ttm170) REVERT: B 201 LEU cc_start: 0.8775 (tp) cc_final: 0.8397 (mm) REVERT: B 229 ASN cc_start: 0.7298 (t0) cc_final: 0.6865 (p0) REVERT: B 302 MET cc_start: 0.7739 (ptm) cc_final: 0.7470 (ptt) REVERT: B 354 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7626 (mtt180) REVERT: B 355 LEU cc_start: 0.8927 (tp) cc_final: 0.8652 (tp) REVERT: B 386 ASP cc_start: 0.7176 (p0) cc_final: 0.6619 (p0) REVERT: B 640 VAL cc_start: 0.8835 (t) cc_final: 0.8577 (m) REVERT: B 693 ASP cc_start: 0.7871 (t0) cc_final: 0.7629 (t0) REVERT: B 734 GLN cc_start: 0.8169 (mt0) cc_final: 0.7828 (mt0) REVERT: A 33 MET cc_start: 0.7696 (mmm) cc_final: 0.7450 (mmt) REVERT: A 182 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: A 198 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7928 (ttm-80) REVERT: A 355 LEU cc_start: 0.7819 (tp) cc_final: 0.7393 (tp) REVERT: A 417 VAL cc_start: 0.7514 (t) cc_final: 0.7265 (p) REVERT: A 566 ASN cc_start: 0.8139 (t0) cc_final: 0.7472 (t0) REVERT: A 589 GLU cc_start: 0.7881 (tt0) cc_final: 0.7554 (pt0) REVERT: A 640 VAL cc_start: 0.8750 (t) cc_final: 0.8385 (m) REVERT: A 662 ASP cc_start: 0.7127 (t0) cc_final: 0.6919 (t70) REVERT: A 692 MET cc_start: 0.8106 (mtm) cc_final: 0.7851 (mtp) outliers start: 36 outliers final: 22 residues processed: 288 average time/residue: 0.1277 time to fit residues: 48.3627 Evaluate side-chains 275 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 695 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 248 GLN A 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110035 restraints weight = 19455.428| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.36 r_work: 0.3260 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10499 Z= 0.151 Angle : 0.568 9.199 14227 Z= 0.293 Chirality : 0.040 0.142 1630 Planarity : 0.005 0.065 1852 Dihedral : 7.159 164.963 1455 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.14 % Allowed : 17.16 % Favored : 79.70 % 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: 1.65 (0.23), residues: 1301 helix: 2.54 (0.19), residues: 667 sheet: 0.42 (0.38), residues: 181 loop : -0.88 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 316 TYR 0.017 0.001 TYR A 31 PHE 0.016 0.002 PHE A 334 TRP 0.011 0.002 TRP A 137 HIS 0.005 0.001 HIS B 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (10499) covalent geometry : angle 0.56806 / 0.29 (14227) hydrogen bonds : bond 0.04381 / 3.02 ( 568) hydrogen bonds : angle 4.29969 / 3.08 ( 1641) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7703 (ttm170) cc_final: 0.7450 (ttm170) REVERT: B 201 LEU cc_start: 0.8881 (tp) cc_final: 0.8589 (mm) REVERT: B 229 ASN cc_start: 0.7327 (t0) cc_final: 0.6898 (p0) REVERT: B 302 MET cc_start: 0.7648 (ptm) cc_final: 0.7373 (ptt) REVERT: B 334 PHE cc_start: 0.7957 (m-10) cc_final: 0.7594 (m-80) REVERT: B 350 ARG cc_start: 0.6789 (ttp-110) cc_final: 0.6090 (ttp80) REVERT: B 579 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7566 (mtm180) REVERT: B 693 ASP cc_start: 0.7832 (t0) cc_final: 0.7612 (t0) REVERT: B 734 GLN cc_start: 0.8099 (mt0) cc_final: 0.7799 (mt0) REVERT: B 738 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8126 (mtmm) REVERT: A 82 LYS cc_start: 0.8449 (mttm) cc_final: 0.8125 (mttt) REVERT: A 166 MET cc_start: 0.7932 (tpp) cc_final: 0.7667 (tpp) REVERT: A 182 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7172 (pt0) REVERT: A 198 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: A 355 LEU cc_start: 0.7689 (tp) cc_final: 0.7300 (tp) REVERT: A 414 THR cc_start: 0.8135 (p) cc_final: 0.7930 (p) REVERT: A 417 VAL cc_start: 0.7569 (t) cc_final: 0.7322 (p) REVERT: A 566 ASN cc_start: 0.8151 (t0) cc_final: 0.7500 (t0) REVERT: A 589 GLU cc_start: 0.7875 (tt0) cc_final: 0.7622 (pt0) REVERT: A 692 MET cc_start: 0.8106 (mtm) cc_final: 0.7827 (mtp) outliers start: 34 outliers final: 24 residues processed: 275 average time/residue: 0.1276 time to fit residues: 46.3567 Evaluate side-chains 273 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110708 restraints weight = 19737.178| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.37 r_work: 0.3241 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10499 Z= 0.178 Angle : 0.582 10.147 14227 Z= 0.300 Chirality : 0.041 0.147 1630 Planarity : 0.005 0.073 1852 Dihedral : 7.125 163.638 1455 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 3.41 % Allowed : 17.99 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.51 (0.23), residues: 1301 helix: 2.43 (0.19), residues: 662 sheet: 0.36 (0.38), residues: 181 loop : -0.92 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 667 TYR 0.018 0.002 TYR A 31 PHE 0.029 0.002 PHE A 36 TRP 0.013 0.002 TRP A 137 HIS 0.006 0.002 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (10499) covalent geometry : angle 0.58185 / 0.30 (14227) hydrogen bonds : bond 0.04563 / 3.14 ( 568) hydrogen bonds : angle 4.30881 / 3.09 ( 1641) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7463 (ttm170) REVERT: B 205 GLU cc_start: 0.7063 (mp0) cc_final: 0.6740 (mp0) REVERT: B 229 ASN cc_start: 0.7411 (t0) cc_final: 0.6903 (p0) REVERT: B 302 MET cc_start: 0.7702 (ptm) cc_final: 0.7427 (ptt) REVERT: B 334 PHE cc_start: 0.7969 (m-10) cc_final: 0.7618 (m-80) REVERT: B 350 ARG cc_start: 0.6896 (ttp-110) cc_final: 0.6507 (ttp80) REVERT: B 373 GLN cc_start: 0.7920 (mm110) cc_final: 0.7586 (mm-40) REVERT: B 579 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7559 (mtm180) REVERT: B 640 VAL cc_start: 0.8699 (t) cc_final: 0.8470 (m) REVERT: B 667 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7544 (mtm-85) REVERT: B 693 ASP cc_start: 0.7847 (t0) cc_final: 0.7601 (t0) REVERT: B 738 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8119 (mtmm) REVERT: A 82 LYS cc_start: 0.8469 (mttm) cc_final: 0.8171 (mttt) REVERT: A 166 MET cc_start: 0.7958 (tpp) cc_final: 0.7686 (tpp) REVERT: A 182 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7132 (pt0) REVERT: A 198 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: A 355 LEU cc_start: 0.7685 (tp) cc_final: 0.7304 (tp) REVERT: A 412 ILE cc_start: 0.8184 (pt) cc_final: 0.7967 (pt) REVERT: A 417 VAL cc_start: 0.7582 (t) cc_final: 0.7350 (p) REVERT: A 566 ASN cc_start: 0.8125 (t0) cc_final: 0.7525 (t0) REVERT: A 589 GLU cc_start: 0.7896 (tt0) cc_final: 0.7663 (pt0) REVERT: A 692 MET cc_start: 0.8122 (mtm) cc_final: 0.7863 (mtp) outliers start: 37 outliers final: 26 residues processed: 278 average time/residue: 0.1309 time to fit residues: 48.0251 Evaluate side-chains 276 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 129 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 254 HIS A 344 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112393 restraints weight = 19855.159| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.38 r_work: 0.3250 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10499 Z= 0.135 Angle : 0.544 7.825 14227 Z= 0.281 Chirality : 0.039 0.136 1630 Planarity : 0.005 0.066 1852 Dihedral : 7.045 163.813 1455 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.69 % Favored : 98.23 % Rotamer: Outliers : 3.23 % Allowed : 18.36 % Favored : 78.41 % 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: 1.64 (0.23), residues: 1301 helix: 2.56 (0.19), residues: 664 sheet: 0.20 (0.37), residues: 197 loop : -0.83 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 220 TYR 0.017 0.001 TYR A 31 PHE 0.028 0.002 PHE A 334 TRP 0.011 0.001 TRP A 137 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (10499) covalent geometry : angle 0.54409 / 0.28 (14227) hydrogen bonds : bond 0.04040 / 2.80 ( 568) hydrogen bonds : angle 4.18295 / 3.00 ( 1641) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7737 (ttm170) cc_final: 0.7477 (ttm170) REVERT: B 201 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8640 (tt) REVERT: B 205 GLU cc_start: 0.7043 (mp0) cc_final: 0.6758 (mp0) REVERT: B 229 ASN cc_start: 0.7392 (t0) cc_final: 0.6993 (p0) REVERT: B 302 MET cc_start: 0.7629 (ptm) cc_final: 0.7342 (ptt) REVERT: B 334 PHE cc_start: 0.7955 (m-10) cc_final: 0.7595 (m-80) REVERT: B 350 ARG cc_start: 0.6867 (ttp-110) cc_final: 0.6312 (ttp80) REVERT: B 354 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7393 (mtt180) REVERT: B 566 ASN cc_start: 0.8179 (t0) cc_final: 0.7834 (t0) REVERT: B 579 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7498 (mtm180) REVERT: B 640 VAL cc_start: 0.8736 (t) cc_final: 0.8500 (m) REVERT: B 667 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7501 (mtm-85) REVERT: B 693 ASP cc_start: 0.7851 (t0) cc_final: 0.7590 (t0) REVERT: A 82 LYS cc_start: 0.8402 (mttm) cc_final: 0.8101 (mtmt) REVERT: A 166 MET cc_start: 0.7965 (tpp) cc_final: 0.7719 (tpp) REVERT: A 198 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8128 (ttm-80) REVERT: A 355 LEU cc_start: 0.7609 (tp) cc_final: 0.7241 (tp) REVERT: A 417 VAL cc_start: 0.7614 (t) cc_final: 0.7376 (p) REVERT: A 566 ASN cc_start: 0.8118 (t0) cc_final: 0.7627 (t0) REVERT: A 692 MET cc_start: 0.8117 (mtm) cc_final: 0.7835 (mtp) outliers start: 35 outliers final: 25 residues processed: 285 average time/residue: 0.1371 time to fit residues: 51.4291 Evaluate side-chains 288 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 261 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 84 optimal weight: 0.0770 chunk 83 optimal weight: 0.4980 chunk 87 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 212 GLN A 74 HIS A 248 GLN A 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112091 restraints weight = 19558.875| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.36 r_work: 0.3264 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10499 Z= 0.144 Angle : 0.569 8.035 14227 Z= 0.292 Chirality : 0.039 0.135 1630 Planarity : 0.005 0.070 1852 Dihedral : 7.019 163.359 1455 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.84 % Favored : 98.08 % Rotamer: Outliers : 3.60 % Allowed : 18.63 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.62 (0.23), residues: 1301 helix: 2.56 (0.20), residues: 659 sheet: 0.23 (0.37), residues: 197 loop : -0.85 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 667 TYR 0.017 0.001 TYR A 31 PHE 0.026 0.002 PHE A 334 TRP 0.011 0.001 TRP A 137 HIS 0.006 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (10499) covalent geometry : angle 0.56869 / 0.29 (14227) hydrogen bonds : bond 0.04028 / 2.80 ( 568) hydrogen bonds : angle 4.17398 / 3.00 ( 1641) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7501 (ttm170) REVERT: B 205 GLU cc_start: 0.7052 (mp0) cc_final: 0.6779 (mp0) REVERT: B 229 ASN cc_start: 0.7331 (t0) cc_final: 0.7002 (p0) REVERT: B 302 MET cc_start: 0.7658 (ptm) cc_final: 0.7386 (ptt) REVERT: B 350 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6203 (ttp80) REVERT: B 354 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7434 (mtt180) REVERT: B 373 GLN cc_start: 0.7923 (mm110) cc_final: 0.7563 (mm-40) REVERT: B 579 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7467 (mtm180) REVERT: B 640 VAL cc_start: 0.8744 (t) cc_final: 0.8488 (m) REVERT: B 667 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7471 (mtm-85) REVERT: B 693 ASP cc_start: 0.7867 (t0) cc_final: 0.7614 (t0) REVERT: A 82 LYS cc_start: 0.8387 (mttm) cc_final: 0.8112 (mtmt) REVERT: A 166 MET cc_start: 0.7954 (tpp) cc_final: 0.7753 (tpp) REVERT: A 198 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8091 (ttm-80) REVERT: A 199 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8148 (mmm160) REVERT: A 355 LEU cc_start: 0.7616 (tp) cc_final: 0.7258 (tp) REVERT: A 417 VAL cc_start: 0.7657 (t) cc_final: 0.7436 (p) REVERT: A 566 ASN cc_start: 0.8094 (t0) cc_final: 0.7512 (t0) REVERT: A 692 MET cc_start: 0.8117 (mtm) cc_final: 0.7848 (mtp) outliers start: 39 outliers final: 29 residues processed: 285 average time/residue: 0.1371 time to fit residues: 51.4244 Evaluate side-chains 295 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 37 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112655 restraints weight = 19665.878| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.37 r_work: 0.3266 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10499 Z= 0.137 Angle : 0.560 7.479 14227 Z= 0.288 Chirality : 0.039 0.133 1630 Planarity : 0.005 0.061 1852 Dihedral : 6.979 162.806 1455 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.69 % Favored : 98.23 % Rotamer: Outliers : 3.04 % Allowed : 19.28 % Favored : 77.68 % 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: 1.64 (0.23), residues: 1301 helix: 2.60 (0.20), residues: 659 sheet: 0.21 (0.37), residues: 197 loop : -0.85 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 220 TYR 0.017 0.001 TYR A 31 PHE 0.012 0.001 PHE A 725 TRP 0.011 0.001 TRP A 137 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10499) covalent geometry : angle 0.56010 / 0.29 (14227) hydrogen bonds : bond 0.03913 / 2.71 ( 568) hydrogen bonds : angle 4.13438 / 2.98 ( 1641) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: B 139 ASP cc_start: 0.8042 (t0) cc_final: 0.7686 (t0) REVERT: B 154 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7483 (ttm170) REVERT: B 205 GLU cc_start: 0.6964 (mp0) cc_final: 0.6709 (mp0) REVERT: B 229 ASN cc_start: 0.7230 (t0) cc_final: 0.6881 (p0) REVERT: B 302 MET cc_start: 0.7558 (ptm) cc_final: 0.7269 (ptt) REVERT: B 334 PHE cc_start: 0.7966 (m-10) cc_final: 0.7617 (m-80) REVERT: B 350 ARG cc_start: 0.6920 (ttp-110) cc_final: 0.6149 (ttp80) REVERT: B 354 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7443 (mtt180) REVERT: B 373 GLN cc_start: 0.7899 (mm110) cc_final: 0.7553 (mm-40) REVERT: B 393 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7690 (mp) REVERT: B 579 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7477 (mtm180) REVERT: B 640 VAL cc_start: 0.8736 (t) cc_final: 0.8473 (m) REVERT: B 667 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7476 (mtm-85) REVERT: B 738 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8121 (mtmm) REVERT: A 33 MET cc_start: 0.7635 (mmm) cc_final: 0.7297 (mmt) REVERT: A 82 LYS cc_start: 0.8402 (mttm) cc_final: 0.8156 (mtmt) REVERT: A 198 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: A 199 ARG cc_start: 0.8402 (mmm160) cc_final: 0.8120 (mmm160) REVERT: A 355 LEU cc_start: 0.7603 (tp) cc_final: 0.7246 (tp) REVERT: A 417 VAL cc_start: 0.7720 (t) cc_final: 0.7518 (p) REVERT: A 566 ASN cc_start: 0.8076 (t0) cc_final: 0.7504 (t0) REVERT: A 692 MET cc_start: 0.8126 (mtm) cc_final: 0.7858 (mtp) outliers start: 33 outliers final: 28 residues processed: 285 average time/residue: 0.1346 time to fit residues: 50.3025 Evaluate side-chains 295 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 59 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 744 ASN A 74 HIS A 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113776 restraints weight = 19514.316| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.49 r_work: 0.3240 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10499 Z= 0.167 Angle : 0.603 8.232 14227 Z= 0.310 Chirality : 0.040 0.134 1630 Planarity : 0.005 0.064 1852 Dihedral : 7.023 161.894 1455 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.23 % Favored : 97.69 % Rotamer: Outliers : 2.86 % Allowed : 20.11 % Favored : 77.03 % 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: 1.50 (0.23), residues: 1301 helix: 2.48 (0.20), residues: 659 sheet: 0.16 (0.37), residues: 196 loop : -0.93 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 198 TYR 0.034 0.002 TYR B 180 PHE 0.028 0.002 PHE A 36 TRP 0.014 0.002 TRP A 137 HIS 0.007 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (10499) covalent geometry : angle 0.60328 / 0.31 (14227) hydrogen bonds : bond 0.04191 / 2.89 ( 568) hydrogen bonds : angle 4.18645 / 3.02 ( 1641) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 ASP cc_start: 0.7933 (t0) cc_final: 0.7726 (t0) REVERT: B 154 ARG cc_start: 0.7783 (ttm170) cc_final: 0.7511 (ttm170) REVERT: B 205 GLU cc_start: 0.7079 (mp0) cc_final: 0.6783 (mp0) REVERT: B 229 ASN cc_start: 0.7290 (t0) cc_final: 0.6914 (p0) REVERT: B 302 MET cc_start: 0.7640 (ptm) cc_final: 0.7366 (ptt) REVERT: B 350 ARG cc_start: 0.6865 (ttp-110) cc_final: 0.6163 (ttp80) REVERT: B 354 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7398 (mtt180) REVERT: B 373 GLN cc_start: 0.7904 (mm110) cc_final: 0.7585 (mm-40) REVERT: B 393 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7676 (mp) REVERT: B 579 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7406 (mtm180) REVERT: B 640 VAL cc_start: 0.8731 (t) cc_final: 0.8472 (m) REVERT: B 656 ARG cc_start: 0.7490 (tpt90) cc_final: 0.6957 (tpt90) REVERT: B 667 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: B 738 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8185 (mtmm) REVERT: A 82 LYS cc_start: 0.8410 (mttm) cc_final: 0.8185 (mtmt) REVERT: A 198 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8071 (ttm-80) REVERT: A 199 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8150 (mmm160) REVERT: A 355 LEU cc_start: 0.7606 (tp) cc_final: 0.7261 (tp) REVERT: A 566 ASN cc_start: 0.8089 (t0) cc_final: 0.7480 (t0) REVERT: A 692 MET cc_start: 0.8161 (mtm) cc_final: 0.7905 (mtp) outliers start: 31 outliers final: 25 residues processed: 280 average time/residue: 0.1342 time to fit residues: 49.5781 Evaluate side-chains 284 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 0.0040 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 102 optimal weight: 0.0020 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 744 ASN A 74 HIS A 254 HIS A 590 GLN A 717 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111827 restraints weight = 19431.950| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.33 r_work: 0.3266 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10499 Z= 0.129 Angle : 0.581 7.879 14227 Z= 0.298 Chirality : 0.039 0.141 1630 Planarity : 0.004 0.049 1852 Dihedral : 6.968 161.641 1455 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.92 % Favored : 98.00 % Rotamer: Outliers : 2.58 % Allowed : 20.66 % Favored : 76.75 % 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: 1.62 (0.23), residues: 1301 helix: 2.60 (0.20), residues: 660 sheet: 0.16 (0.37), residues: 196 loop : -0.89 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 220 TYR 0.016 0.001 TYR A 31 PHE 0.023 0.001 PHE B 143 TRP 0.011 0.001 TRP A 137 HIS 0.008 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10499) covalent geometry : angle 0.58077 / 0.30 (14227) hydrogen bonds : bond 0.03757 / 2.61 ( 568) hydrogen bonds : angle 4.10635 / 2.95 ( 1641) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7494 (ttm170) REVERT: B 182 GLU cc_start: 0.7198 (tp30) cc_final: 0.6985 (mm-30) REVERT: B 205 GLU cc_start: 0.7038 (mp0) cc_final: 0.6734 (mp0) REVERT: B 229 ASN cc_start: 0.7195 (t0) cc_final: 0.6690 (p0) REVERT: B 302 MET cc_start: 0.7485 (ptm) cc_final: 0.7203 (ptt) REVERT: B 350 ARG cc_start: 0.6744 (ttp-110) cc_final: 0.6368 (ttp80) REVERT: B 373 GLN cc_start: 0.7864 (mm110) cc_final: 0.7542 (mm-40) REVERT: B 393 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7649 (mp) REVERT: B 566 ASN cc_start: 0.8200 (t0) cc_final: 0.7834 (t0) REVERT: B 579 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7400 (mtm180) REVERT: B 640 VAL cc_start: 0.8714 (t) cc_final: 0.8460 (m) REVERT: B 656 ARG cc_start: 0.7438 (tpt90) cc_final: 0.6906 (tpt90) REVERT: B 667 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7414 (mtm-85) REVERT: B 738 LYS cc_start: 0.8347 (mtmm) cc_final: 0.8136 (mtmm) REVERT: A 33 MET cc_start: 0.7641 (mmm) cc_final: 0.7287 (mmt) REVERT: A 198 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: A 199 ARG cc_start: 0.8462 (mmm160) cc_final: 0.8183 (mmm160) REVERT: A 219 THR cc_start: 0.8625 (m) cc_final: 0.8309 (p) REVERT: A 355 LEU cc_start: 0.7552 (tp) cc_final: 0.7202 (tp) REVERT: A 566 ASN cc_start: 0.7998 (t0) cc_final: 0.7502 (t0) REVERT: A 692 MET cc_start: 0.8122 (mtm) cc_final: 0.7861 (mtp) outliers start: 28 outliers final: 24 residues processed: 273 average time/residue: 0.1333 time to fit residues: 47.9653 Evaluate side-chains 286 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 107 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 744 ASN A 254 HIS A 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114440 restraints weight = 19610.289| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.50 r_work: 0.3233 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10499 Z= 0.150 Angle : 0.594 8.570 14227 Z= 0.304 Chirality : 0.040 0.144 1630 Planarity : 0.005 0.047 1852 Dihedral : 6.967 160.975 1455 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.85 % Rotamer: Outliers : 2.68 % Allowed : 20.85 % Favored : 76.48 % 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: 1.57 (0.23), residues: 1301 helix: 2.55 (0.20), residues: 660 sheet: 0.13 (0.37), residues: 196 loop : -0.90 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 220 TYR 0.017 0.002 TYR B 180 PHE 0.029 0.002 PHE B 143 TRP 0.012 0.002 TRP A 137 HIS 0.008 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (10499) covalent geometry : angle 0.59440 / 0.30 (14227) hydrogen bonds : bond 0.03941 / 2.73 ( 568) hydrogen bonds : angle 4.12710 / 2.97 ( 1641) =============================================================================== Job complete usr+sys time: 2327.46 seconds wall clock time: 40 minutes 39.61 seconds (2439.61 seconds total)