Starting phenix.real_space_refine on Wed Feb 4 15:52:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dca_46747/02_2026/9dca_46747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dca_46747/02_2026/9dca_46747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dca_46747/02_2026/9dca_46747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dca_46747/02_2026/9dca_46747.map" model { file = "/net/cci-nas-00/data/ceres_data/9dca_46747/02_2026/9dca_46747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dca_46747/02_2026/9dca_46747.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.150 sd= 0.666 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 18 5.49 5 Mg 4 5.21 5 S 54 5.16 5 C 7157 2.51 5 N 1916 2.21 5 O 2226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11376 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5588 Classifications: {'peptide': 699} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 669} Chain breaks: 2 Chain: "B" Number of atoms: 5597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5597 Classifications: {'peptide': 699} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 669} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' MG': 2, 'ATP': 2, 'TTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 94 Unusual residues: {' MG': 2, ' ZN': 1, 'ATP': 2, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10640 SG CYS B 660 78.489 51.295 72.184 1.00130.23 S ATOM 10667 SG CYS B 663 80.640 50.101 73.567 1.00133.45 S ATOM 10788 SG CYS B 678 80.318 53.443 75.346 1.00130.32 S ATOM 10809 SG CYS B 681 81.434 54.013 71.999 1.00126.10 S Time building chain proxies: 2.55, per 1000 atoms: 0.22 Number of scatterers: 11376 At special positions: 0 Unit cell: (91.52, 126.464, 118.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 54 16.00 P 18 15.00 Mg 4 11.99 O 2226 8.00 N 1916 7.00 C 7157 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: 0.93 Conformation dependent library (CDL) restraints added in 496.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 806 " pdb="ZN ZN B 806 " - pdb=" SG CYS B 678 " pdb="ZN ZN B 806 " - pdb=" SG CYS B 681 " pdb="ZN ZN B 806 " - pdb=" SG CYS B 663 " pdb="ZN ZN B 806 " - pdb=" SG CYS B 660 " Number of angles added : 6 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2614 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 51.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.680A pdb=" N THR A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 67 Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 92 through 111 Processing helix chain 'A' and resid 140 through 161 removed outlier: 3.832A pdb=" N GLN A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 215 through 231 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 242 through 262 Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 270 through 296 Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.520A pdb=" N ARG A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 376 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.658A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 467 removed outlier: 3.782A pdb=" N PHE A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 7.044A pdb=" N ALA A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 509 through 519 Processing helix chain 'A' and resid 526 through 551 Processing helix chain 'A' and resid 563 through 577 Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.863A pdb=" N GLU A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 648 removed outlier: 4.284A pdb=" N ASP A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 716 removed outlier: 3.556A pdb=" N SER A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.573A pdb=" N TYR B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 69 removed outlier: 4.035A pdb=" N GLU B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 88 removed outlier: 3.523A pdb=" N ILE B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 88 " --> pdb=" O HIS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 removed outlier: 3.663A pdb=" N ALA B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 161 removed outlier: 3.570A pdb=" N ARG B 145 " --> pdb=" O TYR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 194 through 202 removed outlier: 3.610A pdb=" N MET B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 233 Processing helix chain 'B' and resid 242 through 266 removed outlier: 3.577A pdb=" N PHE B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 270 through 294 removed outlier: 3.743A pdb=" N TYR B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 333 Processing helix chain 'B' and resid 362 through 376 Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.667A pdb=" N SER B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.771A pdb=" N PHE B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 468 No H-bonds generated for 'chain 'B' and resid 467 through 468' Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 492 through 497 removed outlier: 3.978A pdb=" N PHE B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 Processing helix chain 'B' and resid 526 through 551 Processing helix chain 'B' and resid 563 through 577 removed outlier: 3.927A pdb=" N ARG B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 634 through 644 Processing helix chain 'B' and resid 708 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 6.815A pdb=" N LYS A 16 " --> pdb=" O ILE A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 240 removed outlier: 6.880A pdb=" N THR A 307 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 347 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 309 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR A 349 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 311 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A 346 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 382 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE A 348 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 651 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N HIS A 623 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 502 through 507 Processing sheet with id=AA6, first strand: chain 'A' and resid 665 through 667 Processing sheet with id=AA7, first strand: chain 'A' and resid 670 through 671 removed outlier: 3.541A pdb=" N THR A 670 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET A 677 " --> pdb=" O THR A 670 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 17 removed outlier: 7.007A pdb=" N LYS B 16 " --> pdb=" O ILE B 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 191 through 192 removed outlier: 4.196A pdb=" N THR B 239 " --> pdb=" O CYS B 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 204 through 205 Processing sheet with id=AB3, first strand: chain 'B' and resid 502 through 507 Processing sheet with id=AB4, first strand: chain 'B' and resid 624 through 626 removed outlier: 3.762A pdb=" N ASN B 654 " --> pdb=" O CYS B 625 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 665 through 667 535 hydrogen bonds defined for protein. 1557 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: 1.72 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3465 1.33 - 1.46: 2077 1.46 - 1.58: 5975 1.58 - 1.70: 28 1.70 - 1.82: 80 Bond restraints: 11625 Sorted by residual: bond pdb=" C4' TTP B 801 " pdb=" C5' TTP B 801 " ideal model delta sigma weight residual 1.524 1.386 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" N GLY B 506 " pdb=" CA GLY B 506 " ideal model delta sigma weight residual 1.444 1.480 -0.037 1.02e-02 9.61e+03 1.28e+01 bond pdb=" C5' TTP B 801 " pdb=" O5' TTP B 801 " ideal model delta sigma weight residual 1.426 1.361 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" N VAL B 719 " pdb=" CA VAL B 719 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.88e+00 bond pdb=" N VAL B 210 " pdb=" CA VAL B 210 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.14e-02 7.69e+03 9.26e+00 ... (remaining 11620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 15558 3.46 - 6.93: 166 6.93 - 10.39: 26 10.39 - 13.86: 7 13.86 - 17.32: 8 Bond angle restraints: 15765 Sorted by residual: angle pdb=" PB ATP B 803 " pdb=" O3B ATP B 803 " pdb=" PG ATP B 803 " ideal model delta sigma weight residual 139.87 122.55 17.32 1.00e+00 1.00e+00 3.00e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 122.85 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" C5' ATP B 803 " pdb=" O5' ATP B 803 " pdb=" PA ATP B 803 " ideal model delta sigma weight residual 121.27 106.25 15.02 1.00e+00 1.00e+00 2.26e+02 angle pdb=" PA ATP B 803 " pdb=" O3A ATP B 803 " pdb=" PB ATP B 803 " ideal model delta sigma weight residual 136.83 125.51 11.32 1.00e+00 1.00e+00 1.28e+02 angle pdb=" PA ATP A 802 " pdb=" O3A ATP A 802 " pdb=" PB ATP A 802 " ideal model delta sigma weight residual 136.83 125.97 10.86 1.00e+00 1.00e+00 1.18e+02 ... (remaining 15760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 6690 35.78 - 71.56: 311 71.56 - 107.34: 27 107.34 - 143.11: 4 143.11 - 178.89: 2 Dihedral angle restraints: 7034 sinusoidal: 2953 harmonic: 4081 Sorted by residual: dihedral pdb=" CD ARG B 718 " pdb=" NE ARG B 718 " pdb=" CZ ARG B 718 " pdb=" NH1 ARG B 718 " ideal model delta sinusoidal sigma weight residual 0.00 -89.69 89.69 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CD ARG B 376 " pdb=" NE ARG B 376 " pdb=" CZ ARG B 376 " pdb=" NH1 ARG B 376 " ideal model delta sinusoidal sigma weight residual 0.00 -74.93 74.93 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CD ARG B 500 " pdb=" NE ARG B 500 " pdb=" CZ ARG B 500 " pdb=" NH1 ARG B 500 " ideal model delta sinusoidal sigma weight residual 0.00 -63.80 63.80 1 1.00e+01 1.00e-02 5.36e+01 ... (remaining 7031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 1690 0.237 - 0.474: 2 0.474 - 0.711: 0 0.711 - 0.948: 0 0.948 - 1.185: 1 Chirality restraints: 1693 Sorted by residual: chirality pdb=" C4' TTP B 801 " pdb=" C3' TTP B 801 " pdb=" C5' TTP B 801 " pdb=" O4' TTP B 801 " both_signs ideal model delta sigma weight residual False -2.50 -1.31 -1.19 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA VAL B 503 " pdb=" N VAL B 503 " pdb=" C VAL B 503 " pdb=" CB VAL B 503 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PHE B 403 " pdb=" N PHE B 403 " pdb=" C PHE B 403 " pdb=" CB PHE B 403 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1690 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 718 " 1.111 9.50e-02 1.11e+02 4.98e-01 1.49e+02 pdb=" NE ARG B 718 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 718 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 718 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 718 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 376 " 1.052 9.50e-02 1.11e+02 4.72e-01 1.35e+02 pdb=" NE ARG B 376 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 376 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 376 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 376 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 500 " -1.001 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG B 500 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG B 500 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 500 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 500 " -0.025 2.00e-02 2.50e+03 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 123 2.51 - 3.11: 9028 3.11 - 3.71: 18131 3.71 - 4.30: 24088 4.30 - 4.90: 39657 Nonbonded interactions: 91027 Sorted by model distance: nonbonded pdb="MG MG A 804 " pdb=" O1B TTP B 801 " model vdw 1.915 2.170 nonbonded pdb=" O2B TTP A 805 " pdb="MG MG B 805 " model vdw 1.976 2.170 nonbonded pdb=" O1A TTP A 805 " pdb="MG MG B 805 " model vdw 1.979 2.170 nonbonded pdb=" O2G ATP A 801 " pdb="MG MG A 803 " model vdw 1.999 2.170 nonbonded pdb="MG MG A 804 " pdb=" O3G TTP B 801 " model vdw 2.027 2.170 ... (remaining 91022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 730 or resid 801 through 804)) selection = (chain 'B' and (resid 14 through 67 or resid 70 through 730 or resid 802 through \ 805)) } 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 group one per residue 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.006 0.138 11629 Z= 0.385 Angle : 1.089 36.476 15771 Z= 0.637 Chirality : 0.060 1.185 1693 Planarity : 0.026 0.498 2015 Dihedral : 19.759 178.892 4420 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 6.12 % Allowed : 30.52 % Favored : 63.36 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 10.34 % 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: -1.00 (0.22), residues: 1388 helix: 0.62 (0.21), residues: 641 sheet: -1.89 (0.52), residues: 98 loop : -1.82 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 705 TYR 0.034 0.002 TYR A 550 PHE 0.017 0.002 PHE B 496 TRP 0.056 0.002 TRP A 265 HIS 0.007 0.002 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00642 (11625) covalent geometry : angle 1.01947 (15765) hydrogen bonds : bond 0.13892 ( 535) hydrogen bonds : angle 6.67189 ( 1557) metal coordination : bond 0.03864 ( 4) metal coordination : angle 19.71718 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 512 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 55 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 85 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6747 (mm-30) REVERT: A 111 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8179 (tp40) REVERT: A 141 TYR cc_start: 0.7576 (m-10) cc_final: 0.7315 (m-10) REVERT: A 199 LEU cc_start: 0.8989 (mm) cc_final: 0.8704 (mm) REVERT: A 245 GLU cc_start: 0.8363 (tt0) cc_final: 0.7992 (mt-10) REVERT: A 282 ASP cc_start: 0.8251 (t0) cc_final: 0.7988 (t0) REVERT: A 293 GLU cc_start: 0.8521 (tp30) cc_final: 0.8306 (tp30) REVERT: A 321 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7954 (mm-30) REVERT: A 394 PHE cc_start: 0.8326 (t80) cc_final: 0.8101 (t80) REVERT: A 395 LYS cc_start: 0.8012 (pttm) cc_final: 0.7449 (pttm) REVERT: A 398 MET cc_start: 0.6559 (ptp) cc_final: 0.6312 (ptp) REVERT: A 420 MET cc_start: 0.7765 (pmm) cc_final: 0.7187 (pmm) REVERT: A 442 LYS cc_start: 0.8328 (tttt) cc_final: 0.8018 (tptm) REVERT: A 492 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.8973 (p) REVERT: A 543 CYS cc_start: 0.8231 (m) cc_final: 0.8003 (m) REVERT: A 544 GLU cc_start: 0.8248 (tt0) cc_final: 0.8017 (tm-30) REVERT: A 565 THR cc_start: 0.8030 (p) cc_final: 0.7707 (t) REVERT: A 595 ASP cc_start: 0.7836 (t0) cc_final: 0.7458 (t70) REVERT: A 625 CYS cc_start: 0.7675 (m) cc_final: 0.7071 (m) REVERT: A 638 GLU cc_start: 0.8424 (tp30) cc_final: 0.8141 (tp30) REVERT: A 661 TYR cc_start: 0.8448 (m-80) cc_final: 0.8172 (m-10) REVERT: B 51 GLU cc_start: 0.8197 (tt0) cc_final: 0.7592 (tm-30) REVERT: B 55 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 78 ILE cc_start: 0.8582 (mm) cc_final: 0.8340 (mm) REVERT: B 84 HIS cc_start: 0.6322 (t-170) cc_final: 0.5851 (m-70) REVERT: B 86 LEU cc_start: 0.8529 (pp) cc_final: 0.8218 (tt) REVERT: B 94 ILE cc_start: 0.9435 (mm) cc_final: 0.9199 (mm) REVERT: B 96 GLN cc_start: 0.5680 (tp40) cc_final: 0.4847 (tp-100) REVERT: B 97 GLU cc_start: 0.7908 (tp30) cc_final: 0.7529 (tp30) REVERT: B 115 ILE cc_start: 0.6567 (tp) cc_final: 0.6208 (mt) REVERT: B 177 HIS cc_start: 0.8248 (m-70) cc_final: 0.7948 (m-70) REVERT: B 192 LEU cc_start: 0.8909 (tt) cc_final: 0.8565 (tt) REVERT: B 199 LEU cc_start: 0.8299 (mt) cc_final: 0.8052 (mp) REVERT: B 235 TYR cc_start: 0.8354 (p90) cc_final: 0.8133 (p90) REVERT: B 252 GLU cc_start: 0.7936 (tt0) cc_final: 0.7555 (tm-30) REVERT: B 253 LEU cc_start: 0.8757 (tp) cc_final: 0.7999 (tt) REVERT: B 313 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8866 (mt) REVERT: B 319 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 330 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7472 (tpp80) REVERT: B 345 LYS cc_start: 0.8457 (tptm) cc_final: 0.7826 (tptm) REVERT: B 380 ASP cc_start: 0.7641 (m-30) cc_final: 0.7383 (m-30) REVERT: B 390 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8721 (tp) REVERT: B 395 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7065 (mtmm) REVERT: B 398 MET cc_start: 0.7968 (ttp) cc_final: 0.7412 (ttp) REVERT: B 402 SER cc_start: 0.8413 (t) cc_final: 0.7999 (p) REVERT: B 403 PHE cc_start: 0.8204 (m-80) cc_final: 0.7981 (m-80) REVERT: B 404 LEU cc_start: 0.8561 (mt) cc_final: 0.8174 (mt) REVERT: B 405 GLN cc_start: 0.8453 (pm20) cc_final: 0.8152 (pm20) REVERT: B 414 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: B 417 SER cc_start: 0.8796 (m) cc_final: 0.8292 (p) REVERT: B 451 MET cc_start: 0.8449 (mmm) cc_final: 0.8200 (mmm) REVERT: B 503 VAL cc_start: 0.8712 (t) cc_final: 0.8290 (p) REVERT: B 529 LYS cc_start: 0.9030 (tptm) cc_final: 0.8669 (tptm) REVERT: B 539 MET cc_start: 0.8461 (ttp) cc_final: 0.8220 (mtp) REVERT: B 543 CYS cc_start: 0.8932 (m) cc_final: 0.8645 (m) REVERT: B 557 TYR cc_start: 0.8657 (t80) cc_final: 0.8347 (t80) REVERT: B 558 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8318 (p) REVERT: B 590 ASN cc_start: 0.8948 (t0) cc_final: 0.8701 (t0) REVERT: B 593 HIS cc_start: 0.8279 (m170) cc_final: 0.8010 (m-70) REVERT: B 621 PHE cc_start: 0.8389 (p90) cc_final: 0.8077 (p90) REVERT: B 633 ASN cc_start: 0.8580 (t0) cc_final: 0.8363 (t0) REVERT: B 666 GLU cc_start: 0.7844 (tt0) cc_final: 0.7541 (tt0) outliers start: 74 outliers final: 28 residues processed: 548 average time/residue: 0.1069 time to fit residues: 82.2017 Evaluate side-chains 442 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 407 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 328 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 593 HIS A 633 ASN B 72 ASN B 175 HIS B 177 HIS B 201 ASN B 225 GLN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN B 632 GLN B 703 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086401 restraints weight = 24056.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089471 restraints weight = 11208.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.091416 restraints weight = 6164.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092643 restraints weight = 3740.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093483 restraints weight = 2467.925| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11629 Z= 0.233 Angle : 0.719 11.439 15771 Z= 0.369 Chirality : 0.045 0.195 1693 Planarity : 0.005 0.063 2015 Dihedral : 14.621 178.003 1761 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.46 % Allowed : 28.04 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1388 helix: 1.17 (0.20), residues: 662 sheet: -1.88 (0.49), residues: 105 loop : -1.73 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 450 TYR 0.021 0.002 TYR A 76 PHE 0.024 0.002 PHE B 665 TRP 0.017 0.002 TRP A 265 HIS 0.007 0.002 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00494 (11625) covalent geometry : angle 0.70377 (15765) hydrogen bonds : bond 0.05310 ( 535) hydrogen bonds : angle 4.91160 ( 1557) metal coordination : bond 0.00736 ( 4) metal coordination : angle 7.65961 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 424 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9114 (mm) cc_final: 0.8898 (mm) REVERT: A 55 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 78 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8728 (tt) REVERT: A 85 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6776 (mm-30) REVERT: A 102 ARG cc_start: 0.8156 (ttp-170) cc_final: 0.7863 (ttp-170) REVERT: A 210 VAL cc_start: 0.8595 (m) cc_final: 0.8394 (p) REVERT: A 234 GLN cc_start: 0.8048 (pt0) cc_final: 0.7793 (pt0) REVERT: A 264 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: A 282 ASP cc_start: 0.8186 (t0) cc_final: 0.7810 (t0) REVERT: A 297 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 342 ILE cc_start: 0.9175 (pt) cc_final: 0.8828 (mt) REVERT: A 395 LYS cc_start: 0.8250 (pttm) cc_final: 0.7670 (pttm) REVERT: A 398 MET cc_start: 0.6712 (ptp) cc_final: 0.6335 (ptp) REVERT: A 420 MET cc_start: 0.7847 (pmm) cc_final: 0.7220 (pmm) REVERT: A 442 LYS cc_start: 0.8335 (tttt) cc_final: 0.7958 (tptp) REVERT: A 512 GLU cc_start: 0.7895 (mp0) cc_final: 0.7608 (mp0) REVERT: A 543 CYS cc_start: 0.8282 (m) cc_final: 0.8014 (m) REVERT: A 544 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: A 546 TRP cc_start: 0.9082 (m-10) cc_final: 0.8575 (m-10) REVERT: A 581 ASP cc_start: 0.8120 (t0) cc_final: 0.7806 (t0) REVERT: A 586 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7848 (mt-10) REVERT: A 592 PHE cc_start: 0.9072 (p90) cc_final: 0.8369 (p90) REVERT: A 595 ASP cc_start: 0.8022 (t0) cc_final: 0.7711 (t70) REVERT: A 596 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8706 (t) REVERT: A 605 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8591 (ttpt) REVERT: A 606 LEU cc_start: 0.8954 (mm) cc_final: 0.8699 (mm) REVERT: A 625 CYS cc_start: 0.7919 (m) cc_final: 0.7503 (m) REVERT: A 638 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: A 661 TYR cc_start: 0.8539 (m-80) cc_final: 0.8300 (m-10) REVERT: B 55 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 76 TYR cc_start: 0.7313 (t80) cc_final: 0.7039 (t80) REVERT: B 77 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 84 HIS cc_start: 0.6375 (t-170) cc_final: 0.5843 (m-70) REVERT: B 86 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8445 (tt) REVERT: B 97 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: B 187 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7839 (mmm) REVERT: B 199 LEU cc_start: 0.8755 (mt) cc_final: 0.8422 (mt) REVERT: B 252 GLU cc_start: 0.7984 (tt0) cc_final: 0.7612 (tm-30) REVERT: B 253 LEU cc_start: 0.8863 (tp) cc_final: 0.8496 (tt) REVERT: B 271 GLN cc_start: 0.8607 (mt0) cc_final: 0.8384 (mt0) REVERT: B 282 ASP cc_start: 0.8335 (t0) cc_final: 0.7947 (t0) REVERT: B 287 MET cc_start: 0.8030 (mmp) cc_final: 0.7337 (mmp) REVERT: B 319 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7529 (mt-10) REVERT: B 330 ARG cc_start: 0.7906 (tpp-160) cc_final: 0.7638 (tpp80) REVERT: B 345 LYS cc_start: 0.8646 (tptm) cc_final: 0.8341 (tptt) REVERT: B 377 MET cc_start: 0.7452 (mtt) cc_final: 0.7179 (mtt) REVERT: B 380 ASP cc_start: 0.7797 (m-30) cc_final: 0.7483 (m-30) REVERT: B 398 MET cc_start: 0.7719 (ttp) cc_final: 0.7083 (ttp) REVERT: B 402 SER cc_start: 0.8490 (t) cc_final: 0.7879 (p) REVERT: B 451 MET cc_start: 0.8663 (mmm) cc_final: 0.8317 (mmm) REVERT: B 529 LYS cc_start: 0.9055 (tptm) cc_final: 0.8629 (tptm) REVERT: B 539 MET cc_start: 0.8592 (ttp) cc_final: 0.8383 (mtp) REVERT: B 540 LYS cc_start: 0.9065 (tttt) cc_final: 0.8641 (tttp) REVERT: B 574 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 593 HIS cc_start: 0.8323 (m170) cc_final: 0.8073 (m-70) REVERT: B 596 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8115 (t) REVERT: B 610 LYS cc_start: 0.8372 (pttp) cc_final: 0.7676 (pttp) REVERT: B 625 CYS cc_start: 0.8210 (m) cc_final: 0.7461 (p) REVERT: B 633 ASN cc_start: 0.8694 (t0) cc_final: 0.8431 (t0) outliers start: 66 outliers final: 31 residues processed: 455 average time/residue: 0.1003 time to fit residues: 63.4248 Evaluate side-chains 443 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 401 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 78 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 271 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 680 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN B 472 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086920 restraints weight = 24055.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090036 restraints weight = 11144.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091989 restraints weight = 6079.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093254 restraints weight = 3679.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094104 restraints weight = 2415.992| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11629 Z= 0.152 Angle : 0.646 11.912 15771 Z= 0.326 Chirality : 0.043 0.186 1693 Planarity : 0.005 0.077 2015 Dihedral : 13.932 176.338 1710 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.96 % Allowed : 28.62 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1388 helix: 1.45 (0.20), residues: 662 sheet: -1.83 (0.48), residues: 105 loop : -1.59 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 401 TYR 0.026 0.002 TYR A 460 PHE 0.020 0.002 PHE A 447 TRP 0.008 0.001 TRP A 641 HIS 0.006 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00333 (11625) covalent geometry : angle 0.63132 (15765) hydrogen bonds : bond 0.04589 ( 535) hydrogen bonds : angle 4.59481 ( 1557) metal coordination : bond 0.00333 ( 4) metal coordination : angle 6.94928 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 410 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7934 (p0) REVERT: A 36 ILE cc_start: 0.9124 (mm) cc_final: 0.8904 (mm) REVERT: A 78 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8683 (tt) REVERT: A 85 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6914 (mm-30) REVERT: A 210 VAL cc_start: 0.8657 (m) cc_final: 0.8449 (p) REVERT: A 234 GLN cc_start: 0.8001 (pt0) cc_final: 0.7723 (pt0) REVERT: A 272 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 282 ASP cc_start: 0.8175 (t0) cc_final: 0.7770 (t70) REVERT: A 342 ILE cc_start: 0.9226 (pt) cc_final: 0.8826 (mt) REVERT: A 395 LYS cc_start: 0.8137 (pttm) cc_final: 0.7607 (pttm) REVERT: A 398 MET cc_start: 0.6732 (ptp) cc_final: 0.6421 (ptp) REVERT: A 420 MET cc_start: 0.8018 (pmm) cc_final: 0.7258 (pmm) REVERT: A 442 LYS cc_start: 0.8264 (tttt) cc_final: 0.7863 (tptp) REVERT: A 449 GLU cc_start: 0.8438 (tp30) cc_final: 0.8232 (tp30) REVERT: A 477 TYR cc_start: 0.8354 (m-80) cc_final: 0.8023 (m-80) REVERT: A 543 CYS cc_start: 0.8223 (m) cc_final: 0.7946 (m) REVERT: A 546 TRP cc_start: 0.9066 (m-10) cc_final: 0.8595 (m-10) REVERT: A 581 ASP cc_start: 0.8288 (t0) cc_final: 0.7881 (t0) REVERT: A 586 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 595 ASP cc_start: 0.7991 (t0) cc_final: 0.7518 (t70) REVERT: A 596 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8658 (t) REVERT: A 605 LYS cc_start: 0.8807 (ttmt) cc_final: 0.8564 (ttpt) REVERT: A 606 LEU cc_start: 0.8892 (mm) cc_final: 0.8670 (mm) REVERT: A 625 CYS cc_start: 0.7986 (m) cc_final: 0.7435 (m) REVERT: A 627 TYR cc_start: 0.7840 (m-80) cc_final: 0.7592 (m-10) REVERT: A 638 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: A 651 LEU cc_start: 0.8568 (tt) cc_final: 0.8365 (tp) REVERT: A 708 VAL cc_start: 0.8840 (m) cc_final: 0.8557 (p) REVERT: A 721 HIS cc_start: 0.6469 (m170) cc_final: 0.6124 (m170) REVERT: B 55 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 77 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 84 HIS cc_start: 0.6372 (t-170) cc_final: 0.5886 (m-70) REVERT: B 86 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8460 (tt) REVERT: B 108 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 167 ASN cc_start: 0.8703 (t0) cc_final: 0.8423 (t0) REVERT: B 199 LEU cc_start: 0.8776 (mt) cc_final: 0.8441 (mt) REVERT: B 252 GLU cc_start: 0.7971 (tt0) cc_final: 0.7539 (tm-30) REVERT: B 253 LEU cc_start: 0.8845 (tp) cc_final: 0.8403 (tt) REVERT: B 282 ASP cc_start: 0.8332 (t0) cc_final: 0.7794 (t0) REVERT: B 287 MET cc_start: 0.8105 (mmp) cc_final: 0.7666 (mmp) REVERT: B 291 GLU cc_start: 0.8170 (tp30) cc_final: 0.7474 (tp30) REVERT: B 313 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8764 (mt) REVERT: B 319 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7547 (mt-10) REVERT: B 345 LYS cc_start: 0.8652 (tptm) cc_final: 0.8386 (tptt) REVERT: B 375 LYS cc_start: 0.8799 (tppp) cc_final: 0.8542 (tptt) REVERT: B 377 MET cc_start: 0.7411 (mtt) cc_final: 0.7168 (mtt) REVERT: B 380 ASP cc_start: 0.7667 (m-30) cc_final: 0.7350 (m-30) REVERT: B 398 MET cc_start: 0.7894 (ttp) cc_final: 0.7123 (ttp) REVERT: B 402 SER cc_start: 0.8475 (t) cc_final: 0.7769 (p) REVERT: B 416 ASN cc_start: 0.8793 (m-40) cc_final: 0.8563 (t0) REVERT: B 451 MET cc_start: 0.8657 (mmm) cc_final: 0.8281 (mmm) REVERT: B 529 LYS cc_start: 0.8978 (tptm) cc_final: 0.8552 (tptm) REVERT: B 540 LYS cc_start: 0.9039 (tttt) cc_final: 0.8776 (tttp) REVERT: B 573 THR cc_start: 0.8907 (t) cc_final: 0.8643 (p) REVERT: B 574 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 587 TYR cc_start: 0.8358 (p90) cc_final: 0.8142 (p90) REVERT: B 598 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8330 (mttp) REVERT: B 621 PHE cc_start: 0.8589 (p90) cc_final: 0.8251 (p90) REVERT: B 625 CYS cc_start: 0.8308 (m) cc_final: 0.7218 (p) REVERT: B 633 ASN cc_start: 0.8685 (t0) cc_final: 0.8383 (t0) REVERT: B 677 MET cc_start: 0.7631 (ptp) cc_final: 0.7420 (pmm) REVERT: B 681 CYS cc_start: 0.5968 (p) cc_final: 0.5641 (p) outliers start: 60 outliers final: 37 residues processed: 439 average time/residue: 0.1150 time to fit residues: 70.6322 Evaluate side-chains 444 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 401 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 692 VAL Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 16 optimal weight: 0.0670 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN A 632 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088339 restraints weight = 23728.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091491 restraints weight = 10956.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093451 restraints weight = 5957.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094724 restraints weight = 3593.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.095555 restraints weight = 2351.205| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11629 Z= 0.123 Angle : 0.611 9.123 15771 Z= 0.310 Chirality : 0.042 0.174 1693 Planarity : 0.004 0.041 2015 Dihedral : 13.670 173.313 1708 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.22 % Allowed : 29.78 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1388 helix: 1.59 (0.20), residues: 661 sheet: -1.68 (0.48), residues: 105 loop : -1.43 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 401 TYR 0.028 0.002 TYR A 460 PHE 0.026 0.001 PHE A 27 TRP 0.008 0.001 TRP A 522 HIS 0.005 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00260 (11625) covalent geometry : angle 0.60248 (15765) hydrogen bonds : bond 0.04123 ( 535) hydrogen bonds : angle 4.41909 ( 1557) metal coordination : bond 0.00271 ( 4) metal coordination : angle 5.24551 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 406 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9144 (mm) cc_final: 0.8924 (mm) REVERT: A 85 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6866 (mm-30) REVERT: A 175 HIS cc_start: 0.8487 (t-90) cc_final: 0.8164 (t-170) REVERT: A 204 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8446 (ttmm) REVERT: A 210 VAL cc_start: 0.8650 (m) cc_final: 0.8431 (p) REVERT: A 245 GLU cc_start: 0.8282 (tt0) cc_final: 0.7866 (mt-10) REVERT: A 272 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7130 (tm-30) REVERT: A 282 ASP cc_start: 0.8141 (t0) cc_final: 0.7752 (t70) REVERT: A 293 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: A 342 ILE cc_start: 0.9220 (pt) cc_final: 0.8792 (mt) REVERT: A 395 LYS cc_start: 0.8107 (pttm) cc_final: 0.7615 (pttm) REVERT: A 398 MET cc_start: 0.6578 (ptp) cc_final: 0.6101 (ptp) REVERT: A 420 MET cc_start: 0.8074 (pmm) cc_final: 0.7407 (pmm) REVERT: A 442 LYS cc_start: 0.8187 (tttt) cc_final: 0.7785 (tptp) REVERT: A 478 GLN cc_start: 0.8824 (pt0) cc_final: 0.8605 (pt0) REVERT: A 512 GLU cc_start: 0.7929 (mp0) cc_final: 0.7521 (mp0) REVERT: A 543 CYS cc_start: 0.8165 (m) cc_final: 0.7959 (m) REVERT: A 546 TRP cc_start: 0.9000 (m-10) cc_final: 0.8543 (m-10) REVERT: A 581 ASP cc_start: 0.8298 (t0) cc_final: 0.7906 (t0) REVERT: A 586 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7762 (mt-10) REVERT: A 587 TYR cc_start: 0.8114 (p90) cc_final: 0.7878 (p90) REVERT: A 595 ASP cc_start: 0.7972 (t0) cc_final: 0.7479 (t70) REVERT: A 596 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8562 (t) REVERT: A 606 LEU cc_start: 0.8896 (mm) cc_final: 0.8668 (mm) REVERT: A 625 CYS cc_start: 0.7964 (m) cc_final: 0.7412 (m) REVERT: A 638 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: A 651 LEU cc_start: 0.8564 (tt) cc_final: 0.8343 (tp) REVERT: A 708 VAL cc_start: 0.8842 (m) cc_final: 0.8566 (p) REVERT: B 19 LYS cc_start: 0.8579 (tptm) cc_final: 0.8242 (tptm) REVERT: B 55 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 77 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 84 HIS cc_start: 0.6337 (t-170) cc_final: 0.5845 (m-70) REVERT: B 86 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8418 (tt) REVERT: B 102 ARG cc_start: 0.7998 (tmm-80) cc_final: 0.7703 (ttt-90) REVERT: B 108 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 167 ASN cc_start: 0.8655 (t0) cc_final: 0.8440 (t0) REVERT: B 199 LEU cc_start: 0.8736 (mt) cc_final: 0.8401 (mt) REVERT: B 253 LEU cc_start: 0.8753 (tp) cc_final: 0.8458 (tt) REVERT: B 282 ASP cc_start: 0.8344 (t0) cc_final: 0.7839 (t0) REVERT: B 287 MET cc_start: 0.8028 (mmp) cc_final: 0.7695 (mmp) REVERT: B 291 GLU cc_start: 0.7997 (tp30) cc_final: 0.7694 (tp30) REVERT: B 313 LEU cc_start: 0.9037 (mm) cc_final: 0.8732 (mt) REVERT: B 319 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7439 (mt-10) REVERT: B 345 LYS cc_start: 0.8629 (tptm) cc_final: 0.8020 (tptt) REVERT: B 375 LYS cc_start: 0.8667 (tppp) cc_final: 0.8451 (tptt) REVERT: B 377 MET cc_start: 0.7338 (mtt) cc_final: 0.7112 (mtt) REVERT: B 398 MET cc_start: 0.7945 (ttp) cc_final: 0.7348 (ttp) REVERT: B 402 SER cc_start: 0.8543 (t) cc_final: 0.7941 (p) REVERT: B 403 PHE cc_start: 0.7972 (m-80) cc_final: 0.7644 (m-10) REVERT: B 451 MET cc_start: 0.8638 (mmm) cc_final: 0.8263 (mmm) REVERT: B 490 ASP cc_start: 0.8748 (t0) cc_final: 0.8545 (t70) REVERT: B 529 LYS cc_start: 0.8908 (tptm) cc_final: 0.8513 (tptm) REVERT: B 540 LYS cc_start: 0.9025 (tttt) cc_final: 0.8782 (tttp) REVERT: B 573 THR cc_start: 0.8874 (t) cc_final: 0.8612 (p) REVERT: B 574 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 589 THR cc_start: 0.8794 (m) cc_final: 0.8421 (m) REVERT: B 598 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8328 (mttt) REVERT: B 621 PHE cc_start: 0.8553 (p90) cc_final: 0.8076 (p90) REVERT: B 625 CYS cc_start: 0.8305 (m) cc_final: 0.7036 (p) REVERT: B 633 ASN cc_start: 0.8716 (t0) cc_final: 0.8379 (t0) REVERT: B 638 GLU cc_start: 0.8560 (tp30) cc_final: 0.8206 (tp30) REVERT: B 681 CYS cc_start: 0.5974 (p) cc_final: 0.5713 (p) outliers start: 51 outliers final: 31 residues processed: 429 average time/residue: 0.1145 time to fit residues: 68.8178 Evaluate side-chains 429 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 394 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 68 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 271 GLN A 472 ASN A 553 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN B 323 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088515 restraints weight = 23599.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091610 restraints weight = 10900.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093563 restraints weight = 5931.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094815 restraints weight = 3581.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095590 restraints weight = 2354.785| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11629 Z= 0.118 Angle : 0.604 8.231 15771 Z= 0.306 Chirality : 0.041 0.167 1693 Planarity : 0.004 0.043 2015 Dihedral : 13.648 174.865 1708 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.05 % Allowed : 30.93 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.23), residues: 1388 helix: 1.65 (0.20), residues: 665 sheet: -1.36 (0.50), residues: 97 loop : -1.41 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 145 TYR 0.024 0.002 TYR A 557 PHE 0.019 0.001 PHE A 27 TRP 0.007 0.001 TRP B 641 HIS 0.005 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00259 (11625) covalent geometry : angle 0.59650 (15765) hydrogen bonds : bond 0.03929 ( 535) hydrogen bonds : angle 4.34605 ( 1557) metal coordination : bond 0.00190 ( 4) metal coordination : angle 4.78452 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7925 (p0) REVERT: A 36 ILE cc_start: 0.9168 (mm) cc_final: 0.8940 (mm) REVERT: A 85 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6850 (mm-30) REVERT: A 175 HIS cc_start: 0.8498 (t-90) cc_final: 0.8147 (t-170) REVERT: A 190 CYS cc_start: 0.8156 (p) cc_final: 0.7804 (m) REVERT: A 204 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8430 (ttmm) REVERT: A 210 VAL cc_start: 0.8686 (m) cc_final: 0.8447 (p) REVERT: A 245 GLU cc_start: 0.8297 (tt0) cc_final: 0.7868 (mt-10) REVERT: A 282 ASP cc_start: 0.8105 (t0) cc_final: 0.7709 (t70) REVERT: A 287 MET cc_start: 0.8895 (mmt) cc_final: 0.8662 (mmt) REVERT: A 293 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: A 339 ARG cc_start: 0.8671 (ttm170) cc_final: 0.8358 (ttm110) REVERT: A 342 ILE cc_start: 0.9219 (pt) cc_final: 0.8836 (mt) REVERT: A 345 LYS cc_start: 0.8406 (tttp) cc_final: 0.8073 (tptt) REVERT: A 395 LYS cc_start: 0.8086 (pttm) cc_final: 0.7571 (pttm) REVERT: A 420 MET cc_start: 0.8147 (pmm) cc_final: 0.7445 (pmm) REVERT: A 442 LYS cc_start: 0.8159 (tttt) cc_final: 0.7773 (tptp) REVERT: A 512 GLU cc_start: 0.7981 (mp0) cc_final: 0.7659 (mp0) REVERT: A 543 CYS cc_start: 0.8185 (m) cc_final: 0.7929 (m) REVERT: A 546 TRP cc_start: 0.8991 (m-10) cc_final: 0.8488 (m-10) REVERT: A 557 TYR cc_start: 0.7725 (t80) cc_final: 0.7434 (t80) REVERT: A 581 ASP cc_start: 0.8335 (t0) cc_final: 0.7920 (t0) REVERT: A 585 LYS cc_start: 0.9006 (pttp) cc_final: 0.8783 (pttm) REVERT: A 586 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 587 TYR cc_start: 0.8080 (p90) cc_final: 0.7633 (p90) REVERT: A 595 ASP cc_start: 0.7962 (t0) cc_final: 0.7481 (t70) REVERT: A 596 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8484 (t) REVERT: A 625 CYS cc_start: 0.8106 (m) cc_final: 0.7605 (m) REVERT: A 638 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: A 651 LEU cc_start: 0.8583 (tt) cc_final: 0.8317 (tp) REVERT: A 694 ARG cc_start: 0.8030 (ttm170) cc_final: 0.7017 (ttt180) REVERT: A 708 VAL cc_start: 0.8818 (m) cc_final: 0.8547 (p) REVERT: B 19 LYS cc_start: 0.8613 (tptm) cc_final: 0.8213 (tptm) REVERT: B 77 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 84 HIS cc_start: 0.6525 (t-170) cc_final: 0.6028 (m-70) REVERT: B 86 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8469 (tt) REVERT: B 102 ARG cc_start: 0.7989 (tmm-80) cc_final: 0.7714 (ttt-90) REVERT: B 108 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8236 (mm-30) REVERT: B 167 ASN cc_start: 0.8694 (t0) cc_final: 0.8449 (t0) REVERT: B 253 LEU cc_start: 0.8709 (tp) cc_final: 0.8493 (tt) REVERT: B 282 ASP cc_start: 0.8369 (t0) cc_final: 0.7796 (t0) REVERT: B 287 MET cc_start: 0.8050 (mmp) cc_final: 0.7779 (mmp) REVERT: B 291 GLU cc_start: 0.8074 (tp30) cc_final: 0.7760 (tp30) REVERT: B 313 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8715 (mt) REVERT: B 319 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7453 (mt-10) REVERT: B 345 LYS cc_start: 0.8643 (tptm) cc_final: 0.8387 (tptt) REVERT: B 377 MET cc_start: 0.7385 (mtt) cc_final: 0.7175 (mtt) REVERT: B 391 THR cc_start: 0.8744 (m) cc_final: 0.8502 (p) REVERT: B 398 MET cc_start: 0.7906 (ttp) cc_final: 0.7334 (ttp) REVERT: B 402 SER cc_start: 0.8526 (t) cc_final: 0.7898 (p) REVERT: B 403 PHE cc_start: 0.8039 (m-80) cc_final: 0.7798 (m-10) REVERT: B 451 MET cc_start: 0.8608 (mmm) cc_final: 0.8378 (mmt) REVERT: B 505 LEU cc_start: 0.8833 (tt) cc_final: 0.8447 (tt) REVERT: B 529 LYS cc_start: 0.8898 (tptm) cc_final: 0.8513 (tptm) REVERT: B 540 LYS cc_start: 0.9028 (tttt) cc_final: 0.8778 (tttp) REVERT: B 573 THR cc_start: 0.8829 (t) cc_final: 0.8610 (p) REVERT: B 574 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 589 THR cc_start: 0.8780 (m) cc_final: 0.8431 (m) REVERT: B 598 LYS cc_start: 0.8679 (mtmm) cc_final: 0.8297 (mttt) REVERT: B 621 PHE cc_start: 0.8566 (p90) cc_final: 0.8083 (p90) REVERT: B 625 CYS cc_start: 0.8299 (m) cc_final: 0.7000 (p) REVERT: B 633 ASN cc_start: 0.8703 (t0) cc_final: 0.8385 (t0) REVERT: B 638 GLU cc_start: 0.8579 (tp30) cc_final: 0.8253 (tp30) REVERT: B 674 ARG cc_start: 0.7736 (tmm160) cc_final: 0.7506 (tmt170) REVERT: B 681 CYS cc_start: 0.6061 (p) cc_final: 0.5746 (p) outliers start: 49 outliers final: 31 residues processed: 421 average time/residue: 0.1179 time to fit residues: 69.4852 Evaluate side-chains 428 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 391 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 478 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089535 restraints weight = 23754.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092642 restraints weight = 10934.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094586 restraints weight = 5937.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095851 restraints weight = 3561.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096655 restraints weight = 2320.728| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11629 Z= 0.116 Angle : 0.605 9.208 15771 Z= 0.305 Chirality : 0.041 0.171 1693 Planarity : 0.004 0.046 2015 Dihedral : 13.555 174.828 1706 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.14 % Allowed : 31.93 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1388 helix: 1.67 (0.20), residues: 665 sheet: -1.34 (0.49), residues: 97 loop : -1.41 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 711 TYR 0.022 0.002 TYR A 557 PHE 0.019 0.001 PHE B 394 TRP 0.007 0.001 TRP B 546 HIS 0.006 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00255 (11625) covalent geometry : angle 0.59660 (15765) hydrogen bonds : bond 0.03841 ( 535) hydrogen bonds : angle 4.32326 ( 1557) metal coordination : bond 0.00269 ( 4) metal coordination : angle 5.11467 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 388 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9175 (mm) cc_final: 0.8948 (mm) REVERT: A 85 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6856 (mm-30) REVERT: A 204 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8424 (ttmm) REVERT: A 210 VAL cc_start: 0.8680 (m) cc_final: 0.8448 (p) REVERT: A 245 GLU cc_start: 0.8293 (tt0) cc_final: 0.7865 (mt-10) REVERT: A 276 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7603 (ttm-80) REVERT: A 282 ASP cc_start: 0.8086 (t0) cc_final: 0.7702 (t70) REVERT: A 293 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 342 ILE cc_start: 0.9218 (pt) cc_final: 0.8872 (mt) REVERT: A 345 LYS cc_start: 0.8425 (tttp) cc_final: 0.8216 (tptt) REVERT: A 395 LYS cc_start: 0.8079 (pttm) cc_final: 0.7671 (pttm) REVERT: A 398 MET cc_start: 0.6107 (ptp) cc_final: 0.5896 (ptp) REVERT: A 420 MET cc_start: 0.8151 (pmm) cc_final: 0.7522 (pmm) REVERT: A 442 LYS cc_start: 0.8137 (tttt) cc_final: 0.7745 (tptp) REVERT: A 533 LEU cc_start: 0.8888 (mp) cc_final: 0.8467 (mp) REVERT: A 543 CYS cc_start: 0.8155 (m) cc_final: 0.7910 (m) REVERT: A 546 TRP cc_start: 0.8993 (m-10) cc_final: 0.8499 (m-10) REVERT: A 581 ASP cc_start: 0.8330 (t0) cc_final: 0.7910 (t0) REVERT: A 586 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 587 TYR cc_start: 0.8070 (p90) cc_final: 0.7827 (p90) REVERT: A 595 ASP cc_start: 0.7949 (t0) cc_final: 0.7451 (t70) REVERT: A 596 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8427 (t) REVERT: A 625 CYS cc_start: 0.8049 (m) cc_final: 0.7613 (m) REVERT: A 638 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: A 651 LEU cc_start: 0.8607 (tt) cc_final: 0.8344 (tp) REVERT: A 694 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7469 (ttt180) REVERT: A 708 VAL cc_start: 0.8789 (m) cc_final: 0.8539 (p) REVERT: B 19 LYS cc_start: 0.8639 (tptm) cc_final: 0.8235 (tptm) REVERT: B 77 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 84 HIS cc_start: 0.6528 (t-170) cc_final: 0.6015 (m-70) REVERT: B 86 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (tt) REVERT: B 108 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8259 (mm-30) REVERT: B 167 ASN cc_start: 0.8688 (t0) cc_final: 0.8433 (t0) REVERT: B 173 ASP cc_start: 0.7394 (t70) cc_final: 0.7166 (t70) REVERT: B 199 LEU cc_start: 0.8609 (mt) cc_final: 0.8235 (mt) REVERT: B 253 LEU cc_start: 0.8676 (tp) cc_final: 0.8376 (tt) REVERT: B 282 ASP cc_start: 0.8347 (t0) cc_final: 0.7789 (t0) REVERT: B 287 MET cc_start: 0.8041 (mmp) cc_final: 0.7765 (mmp) REVERT: B 291 GLU cc_start: 0.8096 (tp30) cc_final: 0.7786 (tp30) REVERT: B 311 PHE cc_start: 0.8107 (p90) cc_final: 0.7870 (p90) REVERT: B 313 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8716 (mt) REVERT: B 319 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7425 (mt-10) REVERT: B 345 LYS cc_start: 0.8602 (tptm) cc_final: 0.8367 (tptt) REVERT: B 377 MET cc_start: 0.7351 (mtt) cc_final: 0.7139 (mtt) REVERT: B 398 MET cc_start: 0.7899 (ttp) cc_final: 0.7377 (ttp) REVERT: B 402 SER cc_start: 0.8529 (t) cc_final: 0.7900 (p) REVERT: B 403 PHE cc_start: 0.8058 (m-80) cc_final: 0.7818 (m-10) REVERT: B 529 LYS cc_start: 0.8891 (tptm) cc_final: 0.8066 (tptm) REVERT: B 533 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7525 (mm) REVERT: B 544 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8395 (tt0) REVERT: B 573 THR cc_start: 0.8835 (t) cc_final: 0.8629 (p) REVERT: B 574 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 589 THR cc_start: 0.8806 (m) cc_final: 0.8418 (m) REVERT: B 598 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8327 (mttt) REVERT: B 621 PHE cc_start: 0.8541 (p90) cc_final: 0.8065 (p90) REVERT: B 633 ASN cc_start: 0.8661 (t0) cc_final: 0.8379 (t0) REVERT: B 638 GLU cc_start: 0.8579 (tp30) cc_final: 0.8215 (tp30) REVERT: B 674 ARG cc_start: 0.7700 (tmm160) cc_final: 0.7346 (tmt170) REVERT: B 681 CYS cc_start: 0.5995 (p) cc_final: 0.5793 (p) outliers start: 50 outliers final: 33 residues processed: 412 average time/residue: 0.1189 time to fit residues: 68.2325 Evaluate side-chains 425 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 386 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 134 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 478 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** B 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087698 restraints weight = 23885.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.090724 restraints weight = 10893.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092624 restraints weight = 5866.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093851 restraints weight = 3507.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094653 restraints weight = 2284.811| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11629 Z= 0.139 Angle : 0.616 9.145 15771 Z= 0.311 Chirality : 0.042 0.158 1693 Planarity : 0.004 0.046 2015 Dihedral : 13.348 173.881 1706 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.47 % Allowed : 33.09 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1388 helix: 1.62 (0.20), residues: 668 sheet: -1.22 (0.50), residues: 97 loop : -1.39 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 145 TYR 0.024 0.002 TYR A 507 PHE 0.018 0.001 PHE B 394 TRP 0.009 0.001 TRP B 641 HIS 0.007 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00313 (11625) covalent geometry : angle 0.60824 (15765) hydrogen bonds : bond 0.03970 ( 535) hydrogen bonds : angle 4.29859 ( 1557) metal coordination : bond 0.00345 ( 4) metal coordination : angle 5.08989 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 401 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9205 (mm) cc_final: 0.8974 (mm) REVERT: A 85 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6919 (mm-30) REVERT: A 204 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8828 (ttmt) REVERT: A 210 VAL cc_start: 0.8699 (m) cc_final: 0.8443 (p) REVERT: A 245 GLU cc_start: 0.8324 (tt0) cc_final: 0.7883 (mt-10) REVERT: A 276 ARG cc_start: 0.8152 (mmt90) cc_final: 0.7606 (ttm-80) REVERT: A 282 ASP cc_start: 0.8096 (t0) cc_final: 0.7726 (t70) REVERT: A 293 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: A 342 ILE cc_start: 0.9227 (pt) cc_final: 0.8885 (mt) REVERT: A 395 LYS cc_start: 0.8108 (pttm) cc_final: 0.7596 (pttm) REVERT: A 398 MET cc_start: 0.6228 (ptp) cc_final: 0.6023 (ptp) REVERT: A 420 MET cc_start: 0.8211 (pmm) cc_final: 0.7609 (pmm) REVERT: A 442 LYS cc_start: 0.8182 (tttt) cc_final: 0.7761 (tptp) REVERT: A 512 GLU cc_start: 0.7964 (mp0) cc_final: 0.7718 (mp0) REVERT: A 539 MET cc_start: 0.8524 (mtp) cc_final: 0.8131 (mtp) REVERT: A 543 CYS cc_start: 0.8218 (m) cc_final: 0.7924 (m) REVERT: A 546 TRP cc_start: 0.9039 (m-10) cc_final: 0.8378 (m-10) REVERT: A 581 ASP cc_start: 0.8356 (t0) cc_final: 0.7960 (t0) REVERT: A 586 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 587 TYR cc_start: 0.8175 (p90) cc_final: 0.7886 (p90) REVERT: A 595 ASP cc_start: 0.7998 (t0) cc_final: 0.7504 (t70) REVERT: A 596 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8479 (t) REVERT: A 625 CYS cc_start: 0.8079 (m) cc_final: 0.7672 (m) REVERT: A 638 GLU cc_start: 0.8486 (tp30) cc_final: 0.8258 (tp30) REVERT: A 651 LEU cc_start: 0.8625 (tt) cc_final: 0.8381 (tp) REVERT: A 708 VAL cc_start: 0.8783 (m) cc_final: 0.8529 (p) REVERT: B 19 LYS cc_start: 0.8733 (tptm) cc_final: 0.8460 (tptm) REVERT: B 77 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 84 HIS cc_start: 0.6538 (t-170) cc_final: 0.6015 (m-70) REVERT: B 86 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 167 ASN cc_start: 0.8724 (t0) cc_final: 0.8488 (t0) REVERT: B 173 ASP cc_start: 0.7399 (t70) cc_final: 0.7172 (t70) REVERT: B 282 ASP cc_start: 0.8374 (t0) cc_final: 0.7813 (t0) REVERT: B 287 MET cc_start: 0.8140 (mmp) cc_final: 0.7810 (mmp) REVERT: B 291 GLU cc_start: 0.8144 (tp30) cc_final: 0.7887 (tp30) REVERT: B 311 PHE cc_start: 0.8222 (p90) cc_final: 0.7961 (p90) REVERT: B 313 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8728 (mt) REVERT: B 319 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 345 LYS cc_start: 0.8607 (tptm) cc_final: 0.8358 (tptt) REVERT: B 402 SER cc_start: 0.8544 (t) cc_final: 0.7922 (p) REVERT: B 403 PHE cc_start: 0.8161 (m-80) cc_final: 0.7822 (m-10) REVERT: B 422 LEU cc_start: 0.8854 (mp) cc_final: 0.8612 (mm) REVERT: B 529 LYS cc_start: 0.8913 (tptm) cc_final: 0.8111 (tptm) REVERT: B 533 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7537 (mm) REVERT: B 544 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8398 (tt0) REVERT: B 573 THR cc_start: 0.8842 (t) cc_final: 0.8636 (p) REVERT: B 574 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 589 THR cc_start: 0.8800 (m) cc_final: 0.8449 (m) REVERT: B 598 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8349 (mttt) REVERT: B 621 PHE cc_start: 0.8581 (p90) cc_final: 0.8075 (p90) REVERT: B 633 ASN cc_start: 0.8661 (t0) cc_final: 0.8332 (t0) REVERT: B 638 GLU cc_start: 0.8576 (tp30) cc_final: 0.8239 (tp30) REVERT: B 674 ARG cc_start: 0.7779 (tmm160) cc_final: 0.7396 (tmt170) outliers start: 42 outliers final: 31 residues processed: 423 average time/residue: 0.1143 time to fit residues: 68.2010 Evaluate side-chains 425 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 389 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 109 optimal weight: 0.0970 chunk 44 optimal weight: 0.0570 chunk 57 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.090036 restraints weight = 23608.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093182 restraints weight = 10944.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095158 restraints weight = 5935.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096432 restraints weight = 3565.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097270 restraints weight = 2312.571| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11629 Z= 0.117 Angle : 0.619 9.729 15771 Z= 0.309 Chirality : 0.041 0.154 1693 Planarity : 0.004 0.049 2015 Dihedral : 13.186 174.900 1706 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.31 % Allowed : 34.00 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1388 helix: 1.67 (0.20), residues: 669 sheet: -1.12 (0.51), residues: 97 loop : -1.36 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 145 TYR 0.025 0.002 TYR A 507 PHE 0.025 0.001 PHE B 394 TRP 0.010 0.001 TRP B 546 HIS 0.005 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00256 (11625) covalent geometry : angle 0.60793 (15765) hydrogen bonds : bond 0.03766 ( 535) hydrogen bonds : angle 4.23708 ( 1557) metal coordination : bond 0.01066 ( 4) metal coordination : angle 5.89852 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 398 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9181 (mm) cc_final: 0.8945 (mm) REVERT: A 81 ILE cc_start: 0.8410 (mm) cc_final: 0.7709 (mm) REVERT: A 85 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6891 (mm-30) REVERT: A 204 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8813 (ttmt) REVERT: A 210 VAL cc_start: 0.8675 (m) cc_final: 0.8413 (p) REVERT: A 234 GLN cc_start: 0.7678 (pt0) cc_final: 0.7337 (pt0) REVERT: A 245 GLU cc_start: 0.8300 (tt0) cc_final: 0.7864 (mt-10) REVERT: A 276 ARG cc_start: 0.8127 (mmt90) cc_final: 0.7642 (ttm-80) REVERT: A 282 ASP cc_start: 0.8079 (t0) cc_final: 0.7709 (t70) REVERT: A 293 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: A 342 ILE cc_start: 0.9236 (pt) cc_final: 0.8915 (mt) REVERT: A 395 LYS cc_start: 0.8110 (pttm) cc_final: 0.7627 (pttm) REVERT: A 398 MET cc_start: 0.6100 (ptp) cc_final: 0.5898 (ptp) REVERT: A 420 MET cc_start: 0.8161 (pmm) cc_final: 0.7458 (pmm) REVERT: A 442 LYS cc_start: 0.8099 (tttt) cc_final: 0.7706 (tptp) REVERT: A 512 GLU cc_start: 0.7952 (mp0) cc_final: 0.7619 (mp0) REVERT: A 533 LEU cc_start: 0.8830 (mp) cc_final: 0.8474 (mp) REVERT: A 539 MET cc_start: 0.8514 (mtp) cc_final: 0.8167 (mtp) REVERT: A 543 CYS cc_start: 0.8161 (m) cc_final: 0.7877 (m) REVERT: A 546 TRP cc_start: 0.8984 (m-10) cc_final: 0.8270 (m-10) REVERT: A 581 ASP cc_start: 0.8336 (t0) cc_final: 0.7945 (t0) REVERT: A 585 LYS cc_start: 0.9009 (pttp) cc_final: 0.8718 (pttm) REVERT: A 586 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 595 ASP cc_start: 0.7931 (t0) cc_final: 0.7485 (t70) REVERT: A 596 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8461 (t) REVERT: A 625 CYS cc_start: 0.8238 (m) cc_final: 0.7902 (m) REVERT: A 638 GLU cc_start: 0.8455 (tp30) cc_final: 0.8248 (tp30) REVERT: A 651 LEU cc_start: 0.8628 (tt) cc_final: 0.8358 (tp) REVERT: A 694 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7631 (ttm-80) REVERT: A 708 VAL cc_start: 0.8766 (m) cc_final: 0.8516 (p) REVERT: B 19 LYS cc_start: 0.8781 (tptm) cc_final: 0.8511 (tptm) REVERT: B 77 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 84 HIS cc_start: 0.6385 (t-170) cc_final: 0.5872 (m-70) REVERT: B 102 ARG cc_start: 0.8099 (tmm-80) cc_final: 0.7699 (ttt-90) REVERT: B 167 ASN cc_start: 0.8712 (t0) cc_final: 0.8447 (t0) REVERT: B 282 ASP cc_start: 0.8342 (t0) cc_final: 0.7778 (t0) REVERT: B 287 MET cc_start: 0.8109 (mmp) cc_final: 0.7861 (mmp) REVERT: B 291 GLU cc_start: 0.8120 (tp30) cc_final: 0.7883 (tp30) REVERT: B 311 PHE cc_start: 0.8113 (p90) cc_final: 0.7878 (p90) REVERT: B 313 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8795 (mt) REVERT: B 319 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7404 (mt-10) REVERT: B 345 LYS cc_start: 0.8532 (tptm) cc_final: 0.8237 (tptt) REVERT: B 398 MET cc_start: 0.7945 (ttp) cc_final: 0.7329 (ttp) REVERT: B 402 SER cc_start: 0.8510 (t) cc_final: 0.7849 (p) REVERT: B 403 PHE cc_start: 0.8055 (m-80) cc_final: 0.7831 (m-10) REVERT: B 451 MET cc_start: 0.8518 (mmm) cc_final: 0.8236 (mmm) REVERT: B 529 LYS cc_start: 0.8873 (tptm) cc_final: 0.8390 (tptp) REVERT: B 544 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8387 (tt0) REVERT: B 574 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 589 THR cc_start: 0.8782 (m) cc_final: 0.8453 (m) REVERT: B 598 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8404 (mttp) REVERT: B 621 PHE cc_start: 0.8523 (p90) cc_final: 0.8059 (p90) REVERT: B 633 ASN cc_start: 0.8611 (t0) cc_final: 0.8402 (t0) REVERT: B 638 GLU cc_start: 0.8580 (tp30) cc_final: 0.8232 (tp30) REVERT: B 674 ARG cc_start: 0.7764 (tmm160) cc_final: 0.7433 (tmt170) outliers start: 40 outliers final: 27 residues processed: 418 average time/residue: 0.1225 time to fit residues: 71.2804 Evaluate side-chains 412 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 382 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 99 optimal weight: 0.0050 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087358 restraints weight = 23745.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090368 restraints weight = 10905.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092256 restraints weight = 5904.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093490 restraints weight = 3539.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094299 restraints weight = 2309.861| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11629 Z= 0.149 Angle : 0.643 12.076 15771 Z= 0.321 Chirality : 0.042 0.164 1693 Planarity : 0.004 0.051 2015 Dihedral : 13.083 173.895 1704 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.98 % Allowed : 34.74 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.23), residues: 1388 helix: 1.66 (0.20), residues: 669 sheet: -1.12 (0.51), residues: 97 loop : -1.37 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 145 TYR 0.028 0.002 TYR B 557 PHE 0.019 0.002 PHE A 482 TRP 0.021 0.001 TRP B 546 HIS 0.007 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00336 (11625) covalent geometry : angle 0.63122 (15765) hydrogen bonds : bond 0.04042 ( 535) hydrogen bonds : angle 4.26518 ( 1557) metal coordination : bond 0.00606 ( 4) metal coordination : angle 6.41297 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 398 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9225 (mm) cc_final: 0.9010 (mm) REVERT: A 81 ILE cc_start: 0.8449 (mm) cc_final: 0.7721 (tp) REVERT: A 85 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6740 (mm-30) REVERT: A 204 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8806 (ttmt) REVERT: A 210 VAL cc_start: 0.8690 (m) cc_final: 0.8438 (p) REVERT: A 234 GLN cc_start: 0.7754 (pt0) cc_final: 0.7336 (pt0) REVERT: A 276 ARG cc_start: 0.8136 (mmt90) cc_final: 0.7646 (ttm-80) REVERT: A 282 ASP cc_start: 0.8100 (t0) cc_final: 0.7732 (t70) REVERT: A 342 ILE cc_start: 0.9248 (pt) cc_final: 0.8943 (mt) REVERT: A 395 LYS cc_start: 0.8099 (pttm) cc_final: 0.7720 (pttm) REVERT: A 398 MET cc_start: 0.6281 (ptp) cc_final: 0.6075 (ptp) REVERT: A 420 MET cc_start: 0.8031 (pmm) cc_final: 0.7674 (pmm) REVERT: A 442 LYS cc_start: 0.8155 (tttt) cc_final: 0.7739 (tptp) REVERT: A 512 GLU cc_start: 0.8044 (mp0) cc_final: 0.7583 (mp0) REVERT: A 533 LEU cc_start: 0.8839 (mp) cc_final: 0.8584 (mp) REVERT: A 539 MET cc_start: 0.8546 (mtp) cc_final: 0.8171 (mtp) REVERT: A 543 CYS cc_start: 0.8240 (m) cc_final: 0.7949 (m) REVERT: A 546 TRP cc_start: 0.9060 (m-10) cc_final: 0.8422 (m-10) REVERT: A 579 VAL cc_start: 0.8588 (t) cc_final: 0.8356 (p) REVERT: A 581 ASP cc_start: 0.8386 (t0) cc_final: 0.7956 (t0) REVERT: A 586 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 587 TYR cc_start: 0.8256 (p90) cc_final: 0.7963 (p90) REVERT: A 595 ASP cc_start: 0.7978 (t0) cc_final: 0.7488 (t70) REVERT: A 596 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8603 (t) REVERT: A 625 CYS cc_start: 0.8221 (m) cc_final: 0.7910 (m) REVERT: A 651 LEU cc_start: 0.8633 (tt) cc_final: 0.8391 (tp) REVERT: A 708 VAL cc_start: 0.8769 (m) cc_final: 0.8516 (p) REVERT: B 77 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 84 HIS cc_start: 0.6412 (t-170) cc_final: 0.5878 (m-70) REVERT: B 167 ASN cc_start: 0.8749 (t0) cc_final: 0.8524 (t0) REVERT: B 173 ASP cc_start: 0.7946 (t70) cc_final: 0.7387 (t0) REVERT: B 282 ASP cc_start: 0.8384 (t0) cc_final: 0.7811 (t0) REVERT: B 287 MET cc_start: 0.8254 (mmp) cc_final: 0.7978 (mmp) REVERT: B 313 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8802 (mt) REVERT: B 319 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7434 (mt-10) REVERT: B 345 LYS cc_start: 0.8613 (tptm) cc_final: 0.8235 (tptt) REVERT: B 383 SER cc_start: 0.8563 (t) cc_final: 0.8167 (p) REVERT: B 402 SER cc_start: 0.8511 (t) cc_final: 0.7931 (p) REVERT: B 403 PHE cc_start: 0.8196 (m-80) cc_final: 0.7873 (m-10) REVERT: B 420 MET cc_start: 0.7541 (pmm) cc_final: 0.6967 (pmm) REVERT: B 451 MET cc_start: 0.8535 (mmm) cc_final: 0.8250 (mmm) REVERT: B 529 LYS cc_start: 0.8938 (tptm) cc_final: 0.8613 (tptp) REVERT: B 544 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8410 (tt0) REVERT: B 557 TYR cc_start: 0.8365 (t80) cc_final: 0.7907 (t80) REVERT: B 574 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 589 THR cc_start: 0.8813 (m) cc_final: 0.8480 (m) REVERT: B 595 ASP cc_start: 0.8635 (t0) cc_final: 0.7475 (t0) REVERT: B 598 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8582 (mttp) REVERT: B 621 PHE cc_start: 0.8580 (p90) cc_final: 0.8054 (p90) REVERT: B 633 ASN cc_start: 0.8592 (t0) cc_final: 0.8332 (t0) REVERT: B 638 GLU cc_start: 0.8610 (tp30) cc_final: 0.8243 (tp30) REVERT: B 670 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8946 (p) REVERT: B 674 ARG cc_start: 0.7816 (tmm160) cc_final: 0.7544 (tmt170) outliers start: 36 outliers final: 31 residues processed: 418 average time/residue: 0.0970 time to fit residues: 57.5004 Evaluate side-chains 423 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 389 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088012 restraints weight = 23838.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.091101 restraints weight = 11058.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093041 restraints weight = 6018.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094283 restraints weight = 3611.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095125 restraints weight = 2356.005| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11629 Z= 0.144 Angle : 0.649 8.926 15771 Z= 0.328 Chirality : 0.043 0.176 1693 Planarity : 0.004 0.052 2015 Dihedral : 13.021 173.161 1704 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.98 % Allowed : 35.07 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.23), residues: 1388 helix: 1.67 (0.20), residues: 668 sheet: -1.15 (0.50), residues: 97 loop : -1.38 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 145 TYR 0.029 0.002 TYR A 378 PHE 0.022 0.001 PHE A 482 TRP 0.034 0.002 TRP B 546 HIS 0.006 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00326 (11625) covalent geometry : angle 0.63788 (15765) hydrogen bonds : bond 0.04063 ( 535) hydrogen bonds : angle 4.28704 ( 1557) metal coordination : bond 0.00532 ( 4) metal coordination : angle 6.15376 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 386 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9237 (mm) cc_final: 0.9028 (mm) REVERT: A 81 ILE cc_start: 0.8451 (mm) cc_final: 0.7735 (tp) REVERT: A 85 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6753 (mm-30) REVERT: A 204 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8808 (ttmt) REVERT: A 210 VAL cc_start: 0.8719 (m) cc_final: 0.8445 (p) REVERT: A 234 GLN cc_start: 0.7742 (pt0) cc_final: 0.7349 (pt0) REVERT: A 276 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7621 (ttm-80) REVERT: A 282 ASP cc_start: 0.8087 (t0) cc_final: 0.7733 (t70) REVERT: A 293 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: A 342 ILE cc_start: 0.9272 (pt) cc_final: 0.8978 (mt) REVERT: A 395 LYS cc_start: 0.8083 (pttm) cc_final: 0.7682 (pttm) REVERT: A 420 MET cc_start: 0.8016 (pmm) cc_final: 0.7671 (pmm) REVERT: A 442 LYS cc_start: 0.8119 (tttt) cc_final: 0.7703 (tptp) REVERT: A 451 MET cc_start: 0.8136 (tpp) cc_final: 0.7930 (mmm) REVERT: A 512 GLU cc_start: 0.8012 (mp0) cc_final: 0.7738 (mp0) REVERT: A 539 MET cc_start: 0.8512 (mtp) cc_final: 0.8186 (mtp) REVERT: A 543 CYS cc_start: 0.8220 (m) cc_final: 0.7945 (m) REVERT: A 546 TRP cc_start: 0.9054 (m-10) cc_final: 0.8401 (m-10) REVERT: A 579 VAL cc_start: 0.8600 (t) cc_final: 0.8374 (p) REVERT: A 581 ASP cc_start: 0.8377 (t0) cc_final: 0.7931 (t0) REVERT: A 586 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 595 ASP cc_start: 0.7941 (t0) cc_final: 0.7475 (t70) REVERT: A 596 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8530 (t) REVERT: A 708 VAL cc_start: 0.8753 (m) cc_final: 0.8503 (p) REVERT: B 77 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 84 HIS cc_start: 0.6080 (t-170) cc_final: 0.5567 (m-70) REVERT: B 167 ASN cc_start: 0.8783 (t0) cc_final: 0.8534 (t0) REVERT: B 282 ASP cc_start: 0.8356 (t0) cc_final: 0.7777 (t0) REVERT: B 313 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8778 (mt) REVERT: B 319 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 345 LYS cc_start: 0.8639 (tptm) cc_final: 0.8267 (tptt) REVERT: B 383 SER cc_start: 0.8569 (t) cc_final: 0.8140 (p) REVERT: B 398 MET cc_start: 0.7893 (ttp) cc_final: 0.7196 (ttp) REVERT: B 402 SER cc_start: 0.8510 (t) cc_final: 0.7835 (p) REVERT: B 420 MET cc_start: 0.7419 (pmm) cc_final: 0.6887 (pmm) REVERT: B 451 MET cc_start: 0.8451 (mmm) cc_final: 0.8235 (mmt) REVERT: B 529 LYS cc_start: 0.8909 (tptm) cc_final: 0.8571 (tptp) REVERT: B 544 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8367 (tt0) REVERT: B 557 TYR cc_start: 0.8359 (t80) cc_final: 0.7896 (t80) REVERT: B 574 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8046 (tm-30) REVERT: B 589 THR cc_start: 0.8817 (m) cc_final: 0.8484 (m) REVERT: B 595 ASP cc_start: 0.8650 (t0) cc_final: 0.7484 (t0) REVERT: B 598 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8566 (mttp) REVERT: B 633 ASN cc_start: 0.8555 (t0) cc_final: 0.8240 (t0) REVERT: B 638 GLU cc_start: 0.8559 (tp30) cc_final: 0.8218 (tp30) REVERT: B 654 ASN cc_start: 0.8330 (m-40) cc_final: 0.8067 (m-40) REVERT: B 670 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8954 (p) REVERT: B 674 ARG cc_start: 0.7804 (tmm160) cc_final: 0.7545 (tmt170) outliers start: 36 outliers final: 30 residues processed: 405 average time/residue: 0.0951 time to fit residues: 54.7702 Evaluate side-chains 410 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 376 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 692 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 105 optimal weight: 0.0000 chunk 50 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 478 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086009 restraints weight = 24062.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089084 restraints weight = 11158.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091018 restraints weight = 6054.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.092199 restraints weight = 3629.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093002 restraints weight = 2391.900| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11629 Z= 0.182 Angle : 0.689 12.697 15771 Z= 0.350 Chirality : 0.044 0.182 1693 Planarity : 0.005 0.055 2015 Dihedral : 12.995 170.532 1704 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.06 % Allowed : 35.65 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.23), residues: 1388 helix: 1.58 (0.20), residues: 664 sheet: -1.35 (0.47), residues: 107 loop : -1.37 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 450 TYR 0.026 0.002 TYR A 507 PHE 0.015 0.002 PHE B 394 TRP 0.043 0.002 TRP B 546 HIS 0.007 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00410 (11625) covalent geometry : angle 0.67685 (15765) hydrogen bonds : bond 0.04459 ( 535) hydrogen bonds : angle 4.40978 ( 1557) metal coordination : bond 0.00651 ( 4) metal coordination : angle 6.76141 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.39 seconds wall clock time: 36 minutes 21.15 seconds (2181.15 seconds total)