Starting phenix.real_space_refine on Thu Aug 6 16:04:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcc_37099/08_2026/8kcc_37099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcc_37099/08_2026/8kcc_37099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kcc_37099/08_2026/8kcc_37099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcc_37099/08_2026/8kcc_37099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kcc_37099/08_2026/8kcc_37099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcc_37099/08_2026/8kcc_37099.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.055 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 P 302 5.49 5 S 34 5.16 5 Be 1 3.05 5 C 9342 2.51 5 N 2986 2.21 5 O 3603 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16271 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "C" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 719 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "I" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3053 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3097 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4088 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 487} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.34, per 1000 atoms: 0.21 Number of scatterers: 16271 At special positions: 0 Unit cell: (134.734, 100.05, 142.738, 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) S 34 16.00 P 302 15.00 F 3 9.00 O 3603 8.00 N 2986 7.00 C 9342 6.00 Be 1 4.00 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: 1.14 Conformation dependent library (CDL) restraints added in 509.1 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 65.4% alpha, 6.9% beta 60 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 35 through 47 removed outlier: 3.557A pdb=" N ILE A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 82 removed outlier: 4.416A pdb=" N VAL A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.689A pdb=" N ILE B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 82 Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'C' and resid 57 through 69 Processing helix chain 'C' and resid 75 through 104 Processing helix chain 'C' and resid 110 through 122 Processing helix chain 'C' and resid 124 through 144 Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 75 through 104 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 144 Processing helix chain 'E' and resid 42 through 58 removed outlier: 3.771A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.533A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.771A pdb=" N VAL F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.533A pdb=" N PHE F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 114 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.528A pdb=" N ILE G 29 " --> pdb=" O ILE G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 49 through 76 removed outlier: 3.732A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 48 through 76 removed outlier: 4.479A pdb=" N GLU H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.531A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 194 Processing helix chain 'K' and resid 203 through 220 Processing helix chain 'K' and resid 232 through 247 removed outlier: 3.885A pdb=" N GLN K 236 " --> pdb=" O GLY K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 272 removed outlier: 4.188A pdb=" N SER K 263 " --> pdb=" O LEU K 259 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN K 264 " --> pdb=" O SER K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 296 Processing helix chain 'K' and resid 310 through 318 Processing helix chain 'K' and resid 335 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.591A pdb=" N ARG K 347 " --> pdb=" O CYS K 343 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 380 removed outlier: 3.932A pdb=" N SER K 374 " --> pdb=" O SER K 370 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 375 " --> pdb=" O GLU K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 394 removed outlier: 3.739A pdb=" N PHE K 390 " --> pdb=" O SER K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 411 through 424 Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 467 through 472 Processing helix chain 'K' and resid 489 through 498 Processing helix chain 'K' and resid 499 through 509 removed outlier: 3.905A pdb=" N LEU K 503 " --> pdb=" O HIS K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 523 removed outlier: 4.401A pdb=" N CYS K 523 " --> pdb=" O ILE K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 540 Processing helix chain 'K' and resid 549 through 564 removed outlier: 3.599A pdb=" N LEU K 553 " --> pdb=" O TRP K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 623 through 632 removed outlier: 3.749A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 654 through 671 removed outlier: 4.001A pdb=" N LEU K 668 " --> pdb=" O SER K 664 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 669 " --> pdb=" O LYS K 665 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 711 removed outlier: 3.595A pdb=" N THR K 711 " --> pdb=" O LYS K 707 " (cutoff:3.500A) Processing helix chain 'K' and resid 714 through 723 removed outlier: 3.791A pdb=" N ASP K 723 " --> pdb=" O ASP K 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 764 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.970A pdb=" N ARG A 51 " --> pdb=" O ILE D 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 52 removed outlier: 7.245A pdb=" N ARG B 51 " --> pdb=" O ILE C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.934A pdb=" N THR B 110 " --> pdb=" O TYR G 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.144A pdb=" N ARG E 83 " --> pdb=" O VAL G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'F' and resid 83 through 84 removed outlier: 7.331A pdb=" N ARG F 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'K' and resid 224 through 225 removed outlier: 7.153A pdb=" N ILE K 224 " --> pdb=" O LEU K 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 278 through 281 removed outlier: 6.587A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N TRP K 327 " --> pdb=" O ASP K 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 278 through 281 removed outlier: 6.587A pdb=" N ILE K 279 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU K 360 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE K 332 " --> pdb=" O LEU K 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 567 through 570 removed outlier: 6.036A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER K 599 " --> pdb=" O CYS K 568 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE K 570 " --> pdb=" O SER K 599 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL K 543 " --> pdb=" O PHE K 596 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU K 598 " --> pdb=" O VAL K 543 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE K 545 " --> pdb=" O LEU K 598 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.61 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: 2974 1.33 - 1.45: 5348 1.45 - 1.57: 8200 1.57 - 1.69: 602 1.69 - 1.82: 57 Bond restraints: 17181 Sorted by residual: bond pdb=" C1' ADP K 801 " pdb=" C2' ADP K 801 " ideal model delta sigma weight residual 1.524 1.307 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C1' ADP K 801 " pdb=" O4' ADP K 801 " ideal model delta sigma weight residual 1.426 1.628 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C4' ADP K 801 " pdb=" O4' ADP K 801 " ideal model delta sigma weight residual 1.426 1.277 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C4 ADP K 801 " pdb=" C5 ADP K 801 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" F2 BEF K 802 " pdb="BE BEF K 802 " ideal model delta sigma weight residual 1.476 1.366 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 17176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 24326 2.55 - 5.11: 128 5.11 - 7.66: 11 7.66 - 10.21: 3 10.21 - 12.77: 9 Bond angle restraints: 24477 Sorted by residual: angle pdb=" N ARG H 17 " pdb=" CA ARG H 17 " pdb=" C ARG H 17 " ideal model delta sigma weight residual 109.52 96.75 12.77 1.55e+00 4.16e-01 6.79e+01 angle pdb=" N HIS H 18 " pdb=" CA HIS H 18 " pdb=" C HIS H 18 " ideal model delta sigma weight residual 110.24 99.80 10.44 1.47e+00 4.63e-01 5.05e+01 angle pdb=" N ARG H 19 " pdb=" CA ARG H 19 " pdb=" C ARG H 19 " ideal model delta sigma weight residual 109.85 119.37 -9.52 1.58e+00 4.01e-01 3.63e+01 angle pdb=" O4' DG J 55 " pdb=" C4' DG J 55 " pdb=" C3' DG J 55 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" N3 DT I 41 " pdb=" C4 DT I 41 " pdb=" O4 DT I 41 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 24472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.24: 7879 30.24 - 60.49: 1632 60.49 - 90.73: 56 90.73 - 120.98: 1 120.98 - 151.22: 3 Dihedral angle restraints: 9571 sinusoidal: 5912 harmonic: 3659 Sorted by residual: dihedral pdb=" C4' ADP K 801 " pdb=" C5' ADP K 801 " pdb=" O5' ADP K 801 " pdb=" PA ADP K 801 " ideal model delta sinusoidal sigma weight residual 180.00 77.08 102.92 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" CA GLN K 366 " pdb=" C GLN K 366 " pdb=" N ASN K 367 " pdb=" CA ASN K 367 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 68.78 151.22 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 9568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2141 0.046 - 0.092: 539 0.092 - 0.139: 88 0.139 - 0.185: 4 0.185 - 0.231: 4 Chirality restraints: 2776 Sorted by residual: chirality pdb=" CA ARG H 19 " pdb=" N ARG H 19 " pdb=" C ARG H 19 " pdb=" CB ARG H 19 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ARG H 17 " pdb=" N ARG H 17 " pdb=" C ARG H 17 " pdb=" CB ARG H 17 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASP H 24 " pdb=" N ASP H 24 " pdb=" C ASP H 24 " pdb=" CB ASP H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2773 not shown) Planarity restraints: 2050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN K 652 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" CD GLN K 652 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN K 652 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN K 652 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " -0.021 2.00e-02 2.50e+03 9.24e-03 2.56e+00 pdb=" N9 DG I 131 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 131 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 131 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 131 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 131 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 94 " -0.017 2.00e-02 2.50e+03 8.97e-03 2.21e+00 pdb=" N9 DA I 94 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 94 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 94 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 94 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA I 94 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 94 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 94 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 94 " 0.000 2.00e-02 2.50e+03 ... (remaining 2047 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1295 2.74 - 3.28: 15815 3.28 - 3.82: 31079 3.82 - 4.36: 35745 4.36 - 4.90: 53697 Nonbonded interactions: 137631 Sorted by model distance: nonbonded pdb=" OG SER K 386 " pdb=" OD1 ASP K 388 " model vdw 2.199 3.040 nonbonded pdb=" O LEU C 93 " pdb=" OG SER C 97 " model vdw 2.218 3.040 nonbonded pdb=" O LEU D 93 " pdb=" OG SER D 97 " model vdw 2.219 3.040 nonbonded pdb=" O2 DT I 60 " pdb=" N2 DG J 92 " model vdw 2.221 3.120 nonbonded pdb=" O2 DT I 49 " pdb=" N2 DG J 103 " model vdw 2.225 3.120 ... (remaining 137626 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' selection = (chain 'B' and resid 24 through 125) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 23 through 102) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.900 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 0.217 17181 Z= 0.450 Angle : 0.682 12.768 24477 Z= 0.562 Chirality : 0.041 0.231 2776 Planarity : 0.003 0.032 2050 Dihedral : 25.142 151.222 7207 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.20 % Allowed : 1.75 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.22), residues: 1244 helix: 0.77 (0.17), residues: 798 sheet: -1.70 (0.56), residues: 66 loop : -1.34 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 17 TYR 0.008 0.001 TYR B 66 PHE 0.012 0.001 PHE K 459 TRP 0.004 0.001 TRP K 212 HIS 0.010 0.001 HIS K 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.45 (17181) covalent geometry : angle 0.68225 / 0.56 (24477) hydrogen bonds : bond 0.17466 / 11.65 ( 735) hydrogen bonds : angle 6.49654 / 4.69 ( 2045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 279 time to evaluate : 0.325 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 29 LYS cc_start: 0.9468 (tttt) cc_final: 0.8939 (tttm) REVERT: A 70 GLU cc_start: 0.8277 (tp30) cc_final: 0.7851 (tp30) REVERT: A 99 ASP cc_start: 0.8687 (t70) cc_final: 0.8168 (t0) REVERT: A 101 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8562 (mm-30) REVERT: B 26 LYS cc_start: 0.9205 (mttt) cc_final: 0.8865 (mtmm) REVERT: B 47 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8229 (mtp180) REVERT: B 70 GLU cc_start: 0.8309 (tp30) cc_final: 0.7896 (tp30) REVERT: B 73 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7875 (tp30) REVERT: B 81 ASP cc_start: 0.8988 (m-30) cc_final: 0.8756 (m-30) REVERT: B 99 ASP cc_start: 0.8610 (t0) cc_final: 0.8200 (t0) REVERT: C 52 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8803 (tppt) REVERT: C 71 ASP cc_start: 0.8704 (p0) cc_final: 0.8341 (p0) REVERT: C 88 ASP cc_start: 0.8141 (t0) cc_final: 0.7867 (t0) REVERT: C 113 GLU cc_start: 0.8409 (mp0) cc_final: 0.8092 (mp0) REVERT: D 52 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8366 (mttt) REVERT: D 79 MET cc_start: 0.8647 (tpp) cc_final: 0.8361 (tpp) REVERT: D 84 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9357 (m) REVERT: D 88 ASP cc_start: 0.8536 (t0) cc_final: 0.8011 (t0) REVERT: D 96 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7963 (mm-30) REVERT: D 113 GLU cc_start: 0.8135 (mp0) cc_final: 0.7753 (mp0) REVERT: F 50 GLU cc_start: 0.8957 (tt0) cc_final: 0.8652 (tt0) REVERT: F 125 GLN cc_start: 0.9172 (mt0) cc_final: 0.8957 (mt0) REVERT: G 59 LYS cc_start: 0.8429 (tttt) cc_final: 0.8194 (tttm) REVERT: G 100 PHE cc_start: 0.8254 (m-80) cc_final: 0.7840 (m-80) REVERT: H 26 ILE cc_start: 0.9300 (tp) cc_final: 0.9071 (tp) REVERT: H 59 LYS cc_start: 0.8829 (tttt) cc_final: 0.8546 (tttp) REVERT: H 79 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8603 (mmtm) REVERT: H 98 TYR cc_start: 0.8434 (m-10) cc_final: 0.8169 (m-10) REVERT: K 284 ASP cc_start: 0.8369 (t70) cc_final: 0.8100 (t0) REVERT: K 296 MET cc_start: 0.8463 (ppp) cc_final: 0.8089 (ppp) REVERT: K 354 MET cc_start: 0.8710 (pmm) cc_final: 0.8320 (pmm) REVERT: K 452 MET cc_start: 0.7928 (ttp) cc_final: 0.7394 (ttm) REVERT: K 556 MET cc_start: 0.9437 (mtm) cc_final: 0.8582 (ptm) REVERT: K 622 TRP cc_start: 0.8534 (m100) cc_final: 0.7690 (m100) REVERT: K 631 MET cc_start: 0.9234 (ptm) cc_final: 0.8820 (ptp) REVERT: K 758 MET cc_start: 0.5691 (tpt) cc_final: 0.5039 (tpp) outliers start: 13 outliers final: 3 residues processed: 288 average time/residue: 0.1331 time to fit residues: 54.5536 Evaluate side-chains 205 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain H residue 17 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 GLN C 69 HIS D 69 HIS D 115 GLN E 39 HIS E 113 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 GLN K 282 HIS K 336 HIS ** K 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 455 HIS K 462 HIS ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 710 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.089552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057619 restraints weight = 55951.398| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.00 r_work: 0.2822 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.136 17181 Z= 0.488 Angle : 0.970 9.748 24477 Z= 0.505 Chirality : 0.058 0.343 2776 Planarity : 0.007 0.066 2050 Dihedral : 29.806 151.599 4689 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.51 % Allowed : 12.73 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.23), residues: 1244 helix: 1.53 (0.18), residues: 807 sheet: -1.73 (0.59), residues: 68 loop : -1.15 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 112 TYR 0.025 0.003 TYR K 513 PHE 0.020 0.003 PHE B 34 TRP 0.017 0.003 TRP K 373 HIS 0.012 0.003 HIS G 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01028 / 0.49 (17181) covalent geometry : angle 0.97030 / 0.51 (24477) hydrogen bonds : bond 0.09879 / 7.02 ( 735) hydrogen bonds : angle 4.64504 / 3.40 ( 2045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8962 (tp30) cc_final: 0.8537 (tp30) REVERT: B 47 ARG cc_start: 0.9159 (ttm110) cc_final: 0.8847 (mtm110) REVERT: B 70 GLU cc_start: 0.9117 (tp30) cc_final: 0.8826 (tp30) REVERT: B 73 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8492 (tp30) REVERT: B 99 ASP cc_start: 0.8704 (t0) cc_final: 0.8283 (t0) REVERT: B 101 GLU cc_start: 0.8418 (pm20) cc_final: 0.8146 (pm20) REVERT: C 52 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8803 (tppt) REVERT: C 88 ASP cc_start: 0.9080 (t0) cc_final: 0.8864 (t0) REVERT: C 91 GLU cc_start: 0.8853 (tt0) cc_final: 0.8506 (tp30) REVERT: C 96 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8279 (mm-30) REVERT: C 113 GLU cc_start: 0.8948 (mp0) cc_final: 0.8301 (mp0) REVERT: D 55 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8046 (mm-30) REVERT: D 79 MET cc_start: 0.9086 (tpp) cc_final: 0.8823 (tpp) REVERT: D 88 ASP cc_start: 0.9078 (t0) cc_final: 0.8487 (t0) REVERT: D 91 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8646 (tm-30) REVERT: D 113 GLU cc_start: 0.8733 (mp0) cc_final: 0.7981 (mp0) REVERT: E 54 TYR cc_start: 0.9010 (m-80) cc_final: 0.8620 (m-80) REVERT: E 134 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7824 (mmm160) REVERT: F 50 GLU cc_start: 0.9160 (tt0) cc_final: 0.8780 (tt0) REVERT: F 53 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8970 (ttpp) REVERT: F 54 TYR cc_start: 0.9304 (m-80) cc_final: 0.8943 (m-80) REVERT: G 59 LYS cc_start: 0.8983 (tttt) cc_final: 0.8700 (tttm) REVERT: H 16 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8603 (mmtm) REVERT: H 27 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8814 (mm-40) REVERT: H 59 LYS cc_start: 0.9298 (tttt) cc_final: 0.8970 (tttp) REVERT: H 79 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8811 (mmtp) REVERT: K 284 ASP cc_start: 0.8586 (t70) cc_final: 0.8338 (t70) REVERT: K 296 MET cc_start: 0.8567 (ppp) cc_final: 0.8265 (ppp) REVERT: K 354 MET cc_start: 0.8901 (pmm) cc_final: 0.8505 (pmm) REVERT: K 452 MET cc_start: 0.8433 (ttp) cc_final: 0.7923 (ttm) REVERT: K 454 ASP cc_start: 0.9401 (p0) cc_final: 0.9064 (t0) REVERT: K 502 LEU cc_start: 0.8574 (tp) cc_final: 0.8243 (tp) REVERT: K 556 MET cc_start: 0.9425 (mtm) cc_final: 0.8517 (ptp) REVERT: K 631 MET cc_start: 0.9396 (ptm) cc_final: 0.8923 (ptp) outliers start: 38 outliers final: 24 residues processed: 205 average time/residue: 0.1220 time to fit residues: 36.7256 Evaluate side-chains 192 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 616 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 50.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 39 HIS F 93 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 HIS K 351 HIS K 455 HIS ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.091861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.060347 restraints weight = 55060.179| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.96 r_work: 0.2896 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17181 Z= 0.150 Angle : 0.595 6.869 24477 Z= 0.338 Chirality : 0.042 0.354 2776 Planarity : 0.004 0.061 2050 Dihedral : 29.593 151.771 4683 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.94 % Allowed : 14.21 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1244 helix: 2.20 (0.18), residues: 805 sheet: -1.59 (0.56), residues: 68 loop : -0.92 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 47 TYR 0.013 0.001 TYR B 48 PHE 0.010 0.001 PHE H 61 TRP 0.018 0.001 TRP K 373 HIS 0.012 0.001 HIS F 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (17181) covalent geometry : angle 0.59461 / 0.34 (24477) hydrogen bonds : bond 0.05890 / 4.18 ( 735) hydrogen bonds : angle 3.75317 / 2.73 ( 2045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8853 (tp30) cc_final: 0.8466 (tp30) REVERT: A 73 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8584 (tm-30) REVERT: A 99 ASP cc_start: 0.8918 (t0) cc_final: 0.8616 (t0) REVERT: A 101 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8667 (mm-30) REVERT: B 73 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8649 (tp30) REVERT: B 99 ASP cc_start: 0.8689 (t0) cc_final: 0.8162 (t0) REVERT: B 101 GLU cc_start: 0.8366 (pm20) cc_final: 0.8136 (pm20) REVERT: C 52 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8771 (tppt) REVERT: C 88 ASP cc_start: 0.9034 (t0) cc_final: 0.8751 (t0) REVERT: C 91 GLU cc_start: 0.8768 (tt0) cc_final: 0.8431 (tp30) REVERT: C 96 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8219 (mm-30) REVERT: D 57 TYR cc_start: 0.9314 (m-80) cc_final: 0.9112 (m-80) REVERT: D 79 MET cc_start: 0.8896 (tpp) cc_final: 0.8539 (tpp) REVERT: D 88 ASP cc_start: 0.9028 (t0) cc_final: 0.8397 (t0) REVERT: D 91 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8570 (tm-30) REVERT: D 113 GLU cc_start: 0.8730 (mp0) cc_final: 0.7967 (mp0) REVERT: D 125 GLU cc_start: 0.8269 (tp30) cc_final: 0.8049 (tp30) REVERT: E 50 GLU cc_start: 0.8564 (tt0) cc_final: 0.7882 (tt0) REVERT: E 54 TYR cc_start: 0.9002 (m-80) cc_final: 0.8694 (m-80) REVERT: G 59 LYS cc_start: 0.8930 (tttt) cc_final: 0.8683 (tttm) REVERT: G 100 PHE cc_start: 0.8767 (m-80) cc_final: 0.8438 (m-80) REVERT: H 16 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8386 (mmtm) REVERT: H 27 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8731 (mm-40) REVERT: H 59 LYS cc_start: 0.9217 (tttt) cc_final: 0.8988 (ttpp) REVERT: H 79 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8751 (mmtp) REVERT: K 194 CYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7187 (p) REVERT: K 284 ASP cc_start: 0.8598 (t70) cc_final: 0.8295 (t70) REVERT: K 296 MET cc_start: 0.8787 (ppp) cc_final: 0.8481 (ppp) REVERT: K 354 MET cc_start: 0.9067 (pmm) cc_final: 0.8520 (pmm) REVERT: K 452 MET cc_start: 0.8290 (ttp) cc_final: 0.7546 (ttm) REVERT: K 454 ASP cc_start: 0.9420 (p0) cc_final: 0.9101 (t0) REVERT: K 556 MET cc_start: 0.9420 (mtm) cc_final: 0.8534 (ptp) REVERT: K 622 TRP cc_start: 0.8983 (m100) cc_final: 0.7415 (m100) REVERT: K 758 MET cc_start: 0.5075 (tpp) cc_final: 0.4402 (mmm) outliers start: 21 outliers final: 12 residues processed: 215 average time/residue: 0.1143 time to fit residues: 36.8261 Evaluate side-chains 198 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 97 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 49 optimal weight: 0.0970 chunk 91 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 68 GLN F 113 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 644 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.092122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060913 restraints weight = 55865.398| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.87 r_work: 0.2922 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 17181 Z= 0.133 Angle : 0.567 7.336 24477 Z= 0.322 Chirality : 0.040 0.364 2776 Planarity : 0.004 0.051 2050 Dihedral : 29.425 152.827 4682 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 15.13 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.24), residues: 1244 helix: 2.42 (0.18), residues: 805 sheet: -1.32 (0.55), residues: 68 loop : -0.81 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 47 TYR 0.012 0.001 TYR B 66 PHE 0.016 0.001 PHE E 41 TRP 0.017 0.001 TRP K 373 HIS 0.005 0.001 HIS K 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (17181) covalent geometry : angle 0.56653 / 0.32 (24477) hydrogen bonds : bond 0.05087 / 3.59 ( 735) hydrogen bonds : angle 3.50647 / 2.54 ( 2045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8840 (tp30) cc_final: 0.8402 (tp30) REVERT: A 73 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 83 LYS cc_start: 0.9379 (mptt) cc_final: 0.9087 (mppt) REVERT: A 99 ASP cc_start: 0.8949 (t0) cc_final: 0.8262 (t0) REVERT: B 47 ARG cc_start: 0.9136 (ptm160) cc_final: 0.8771 (mtm110) REVERT: B 73 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8635 (tp30) REVERT: B 99 ASP cc_start: 0.8663 (t0) cc_final: 0.8093 (t0) REVERT: B 101 GLU cc_start: 0.8405 (pm20) cc_final: 0.8033 (pm20) REVERT: C 88 ASP cc_start: 0.8887 (t0) cc_final: 0.8578 (t0) REVERT: C 91 GLU cc_start: 0.8735 (tt0) cc_final: 0.8456 (tp30) REVERT: C 96 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D 55 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7204 (mm-30) REVERT: D 79 MET cc_start: 0.8873 (tpp) cc_final: 0.8554 (tpp) REVERT: D 88 ASP cc_start: 0.9018 (t0) cc_final: 0.8381 (t0) REVERT: D 91 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8564 (tm-30) REVERT: D 113 GLU cc_start: 0.8761 (mp0) cc_final: 0.7964 (mp0) REVERT: D 125 GLU cc_start: 0.8251 (tp30) cc_final: 0.8014 (tp30) REVERT: E 50 GLU cc_start: 0.8556 (tt0) cc_final: 0.7877 (tt0) REVERT: E 54 TYR cc_start: 0.9009 (m-80) cc_final: 0.8703 (m-80) REVERT: E 115 LYS cc_start: 0.9374 (mttm) cc_final: 0.9161 (mmtt) REVERT: E 134 ARG cc_start: 0.8172 (mmm160) cc_final: 0.7750 (mmm160) REVERT: F 50 GLU cc_start: 0.9227 (tt0) cc_final: 0.9024 (tt0) REVERT: G 59 LYS cc_start: 0.8855 (tttt) cc_final: 0.8607 (tttm) REVERT: G 100 PHE cc_start: 0.8829 (m-80) cc_final: 0.8517 (m-80) REVERT: H 59 LYS cc_start: 0.9184 (tttt) cc_final: 0.8957 (ttpp) REVERT: H 79 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8796 (mmtp) REVERT: K 284 ASP cc_start: 0.8589 (t70) cc_final: 0.8225 (t70) REVERT: K 296 MET cc_start: 0.8828 (ppp) cc_final: 0.8464 (ppp) REVERT: K 354 MET cc_start: 0.8954 (pmm) cc_final: 0.8547 (pmm) REVERT: K 452 MET cc_start: 0.8173 (ttp) cc_final: 0.7303 (ttm) REVERT: K 556 MET cc_start: 0.9385 (mtm) cc_final: 0.8513 (ptp) REVERT: K 622 TRP cc_start: 0.8984 (m100) cc_final: 0.7388 (m100) REVERT: K 626 MET cc_start: 0.9077 (tpp) cc_final: 0.8792 (tpp) REVERT: K 758 MET cc_start: 0.5005 (tpp) cc_final: 0.4436 (tpt) outliers start: 20 outliers final: 15 residues processed: 209 average time/residue: 0.1117 time to fit residues: 34.9397 Evaluate side-chains 205 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 17 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 68 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 ASN K 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.089277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.057981 restraints weight = 55453.644| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.83 r_work: 0.2844 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17181 Z= 0.222 Angle : 0.642 7.686 24477 Z= 0.352 Chirality : 0.042 0.364 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.610 156.000 4678 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.58 % Allowed : 16.33 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.24), residues: 1244 helix: 2.53 (0.18), residues: 804 sheet: -1.55 (0.53), residues: 78 loop : -0.79 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 38 TYR 0.017 0.002 TYR B 48 PHE 0.013 0.001 PHE K 390 TRP 0.015 0.002 TRP K 373 HIS 0.029 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (17181) covalent geometry : angle 0.64202 / 0.35 (24477) hydrogen bonds : bond 0.05744 / 4.05 ( 735) hydrogen bonds : angle 3.71762 / 2.72 ( 2045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8913 (tp30) cc_final: 0.8437 (tp30) REVERT: A 73 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8766 (tm-30) REVERT: A 81 ASP cc_start: 0.9012 (m-30) cc_final: 0.8526 (t0) REVERT: A 83 LYS cc_start: 0.9397 (mptt) cc_final: 0.9168 (mppt) REVERT: A 99 ASP cc_start: 0.8973 (t0) cc_final: 0.8308 (t0) REVERT: A 123 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8758 (m) REVERT: B 70 GLU cc_start: 0.9021 (tp30) cc_final: 0.8801 (tp30) REVERT: B 73 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8729 (tp30) REVERT: B 99 ASP cc_start: 0.8742 (t0) cc_final: 0.8367 (t0) REVERT: B 101 GLU cc_start: 0.8295 (pm20) cc_final: 0.7864 (pm20) REVERT: C 88 ASP cc_start: 0.9057 (t0) cc_final: 0.8779 (t0) REVERT: C 91 GLU cc_start: 0.8830 (tt0) cc_final: 0.8557 (tp30) REVERT: C 96 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8323 (mm-30) REVERT: C 113 GLU cc_start: 0.8822 (mp0) cc_final: 0.8120 (mp0) REVERT: C 125 GLU cc_start: 0.8372 (tp30) cc_final: 0.8035 (tp30) REVERT: C 129 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8735 (m-70) REVERT: D 55 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8295 (mm-30) REVERT: D 88 ASP cc_start: 0.9057 (t0) cc_final: 0.8436 (t0) REVERT: D 91 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8596 (tm-30) REVERT: D 113 GLU cc_start: 0.8666 (mp0) cc_final: 0.7890 (mp0) REVERT: D 125 GLU cc_start: 0.8406 (tp30) cc_final: 0.8163 (tp30) REVERT: E 50 GLU cc_start: 0.8625 (tt0) cc_final: 0.7955 (tt0) REVERT: E 134 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7658 (mmm160) REVERT: F 50 GLU cc_start: 0.9196 (tt0) cc_final: 0.8980 (tt0) REVERT: G 59 LYS cc_start: 0.8933 (tttt) cc_final: 0.8682 (tttm) REVERT: G 100 PHE cc_start: 0.8879 (m-80) cc_final: 0.8582 (m-80) REVERT: H 59 LYS cc_start: 0.9196 (tttt) cc_final: 0.8967 (ttpp) REVERT: H 79 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8825 (mmtp) REVERT: K 296 MET cc_start: 0.8708 (ppp) cc_final: 0.8156 (ppp) REVERT: K 354 MET cc_start: 0.8871 (pmm) cc_final: 0.8379 (pmm) REVERT: K 373 TRP cc_start: 0.9275 (t60) cc_final: 0.8598 (t60) REVERT: K 452 MET cc_start: 0.8239 (ttp) cc_final: 0.7401 (ttm) REVERT: K 454 ASP cc_start: 0.9398 (p0) cc_final: 0.8999 (t0) REVERT: K 556 MET cc_start: 0.9371 (mtm) cc_final: 0.8406 (ptp) REVERT: K 626 MET cc_start: 0.9065 (tpp) cc_final: 0.8657 (tpp) REVERT: K 758 MET cc_start: 0.5056 (tpp) cc_final: 0.4506 (mmm) outliers start: 28 outliers final: 22 residues processed: 204 average time/residue: 0.1106 time to fit residues: 33.7306 Evaluate side-chains 203 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 552 LEU Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS E 68 GLN H 25 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** 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 = 0.3823 r_free = 0.3823 target = 0.086767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055732 restraints weight = 56600.031| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.86 r_work: 0.2795 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17181 Z= 0.256 Angle : 0.666 14.538 24477 Z= 0.365 Chirality : 0.043 0.363 2776 Planarity : 0.005 0.083 2050 Dihedral : 29.795 158.216 4678 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.86 % Allowed : 16.97 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.24), residues: 1244 helix: 2.49 (0.18), residues: 807 sheet: -1.53 (0.53), residues: 78 loop : -0.66 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 47 TYR 0.021 0.002 TYR B 48 PHE 0.011 0.002 PHE F 67 TRP 0.017 0.002 TRP K 373 HIS 0.032 0.002 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.26 (17181) covalent geometry : angle 0.66559 / 0.36 (24477) hydrogen bonds : bond 0.05934 / 4.20 ( 735) hydrogen bonds : angle 3.79832 / 2.77 ( 2045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8912 (tp30) cc_final: 0.8468 (tp30) REVERT: A 73 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8779 (tm-30) REVERT: A 81 ASP cc_start: 0.9033 (m-30) cc_final: 0.8711 (t0) REVERT: A 99 ASP cc_start: 0.9008 (t0) cc_final: 0.8299 (t0) REVERT: A 125 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7695 (mt) REVERT: B 73 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8723 (tp30) REVERT: B 99 ASP cc_start: 0.8802 (t0) cc_final: 0.8494 (t0) REVERT: B 101 GLU cc_start: 0.8284 (pm20) cc_final: 0.7871 (pm20) REVERT: C 88 ASP cc_start: 0.9045 (t0) cc_final: 0.8767 (t0) REVERT: C 91 GLU cc_start: 0.8847 (tt0) cc_final: 0.8571 (tp30) REVERT: C 96 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8323 (mm-30) REVERT: C 113 GLU cc_start: 0.8817 (mp0) cc_final: 0.8041 (mp0) REVERT: C 125 GLU cc_start: 0.8484 (tp30) cc_final: 0.8268 (tp30) REVERT: C 129 HIS cc_start: 0.9148 (OUTLIER) cc_final: 0.8905 (m-70) REVERT: D 55 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8620 (mm-30) REVERT: D 88 ASP cc_start: 0.9077 (t0) cc_final: 0.8574 (t0) REVERT: D 91 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8586 (tm-30) REVERT: D 125 GLU cc_start: 0.8423 (tp30) cc_final: 0.8146 (tp30) REVERT: E 50 GLU cc_start: 0.8541 (tt0) cc_final: 0.7681 (tt0) REVERT: E 54 TYR cc_start: 0.9059 (m-80) cc_final: 0.8505 (m-80) REVERT: E 115 LYS cc_start: 0.9431 (mttm) cc_final: 0.9180 (mmtt) REVERT: E 134 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7739 (mmm160) REVERT: F 50 GLU cc_start: 0.9277 (tt0) cc_final: 0.8995 (tt0) REVERT: G 59 LYS cc_start: 0.8947 (tttt) cc_final: 0.8669 (tttm) REVERT: G 100 PHE cc_start: 0.8926 (m-80) cc_final: 0.8695 (m-80) REVERT: H 24 ASP cc_start: 0.8811 (t0) cc_final: 0.8105 (p0) REVERT: H 79 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8903 (mmtm) REVERT: H 98 TYR cc_start: 0.9137 (OUTLIER) cc_final: 0.8362 (m-10) REVERT: K 296 MET cc_start: 0.8980 (ppp) cc_final: 0.8647 (ppp) REVERT: K 354 MET cc_start: 0.8927 (pmm) cc_final: 0.8280 (pmm) REVERT: K 452 MET cc_start: 0.8302 (ttp) cc_final: 0.7637 (ttm) REVERT: K 502 LEU cc_start: 0.8180 (tp) cc_final: 0.7972 (tp) REVERT: K 626 MET cc_start: 0.9112 (tpp) cc_final: 0.8856 (tpp) REVERT: K 758 MET cc_start: 0.5065 (tpp) cc_final: 0.4280 (tpt) outliers start: 31 outliers final: 22 residues processed: 203 average time/residue: 0.1139 time to fit residues: 34.8162 Evaluate side-chains 199 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 552 LEU Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 97 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 87 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 ASN ** K 506 GLN ** 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 = 0.3837 r_free = 0.3837 target = 0.087556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056319 restraints weight = 55861.548| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.86 r_work: 0.2825 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17181 Z= 0.162 Angle : 0.600 11.707 24477 Z= 0.335 Chirality : 0.041 0.366 2776 Planarity : 0.004 0.050 2050 Dihedral : 29.739 159.571 4678 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.21 % Allowed : 17.99 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.24), residues: 1244 helix: 2.61 (0.18), residues: 804 sheet: -1.54 (0.52), residues: 78 loop : -0.55 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 47 TYR 0.021 0.001 TYR B 48 PHE 0.012 0.001 PHE F 67 TRP 0.018 0.001 TRP K 373 HIS 0.031 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (17181) covalent geometry : angle 0.60036 / 0.33 (24477) hydrogen bonds : bond 0.05041 / 3.53 ( 735) hydrogen bonds : angle 3.53529 / 2.56 ( 2045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8877 (tp30) cc_final: 0.8424 (tp30) REVERT: A 73 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8728 (tm-30) REVERT: A 81 ASP cc_start: 0.9025 (m-30) cc_final: 0.8569 (t0) REVERT: A 83 LYS cc_start: 0.9431 (mptt) cc_final: 0.9108 (mppt) REVERT: A 99 ASP cc_start: 0.9005 (t0) cc_final: 0.8286 (t0) REVERT: B 28 MET cc_start: 0.8704 (ppp) cc_final: 0.8479 (ppp) REVERT: B 73 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8693 (tp30) REVERT: B 99 ASP cc_start: 0.8837 (t0) cc_final: 0.8413 (t0) REVERT: B 101 GLU cc_start: 0.8284 (pm20) cc_final: 0.7893 (pm20) REVERT: C 88 ASP cc_start: 0.9010 (t0) cc_final: 0.8725 (t0) REVERT: C 91 GLU cc_start: 0.8818 (tt0) cc_final: 0.8570 (tp30) REVERT: C 96 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8327 (mm-30) REVERT: C 113 GLU cc_start: 0.8861 (mp0) cc_final: 0.8087 (mp0) REVERT: C 125 GLU cc_start: 0.8382 (tp30) cc_final: 0.8107 (tp30) REVERT: C 129 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8741 (m-70) REVERT: D 55 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8499 (mm-30) REVERT: D 88 ASP cc_start: 0.9063 (t0) cc_final: 0.8443 (t0) REVERT: D 91 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8557 (tm-30) REVERT: D 113 GLU cc_start: 0.8488 (mp0) cc_final: 0.7781 (mp0) REVERT: D 125 GLU cc_start: 0.8357 (tp30) cc_final: 0.8109 (tp30) REVERT: E 50 GLU cc_start: 0.8558 (tt0) cc_final: 0.7824 (tt0) REVERT: E 115 LYS cc_start: 0.9420 (mttm) cc_final: 0.9173 (mmtt) REVERT: E 134 ARG cc_start: 0.8209 (mmm160) cc_final: 0.7730 (mmm160) REVERT: F 50 GLU cc_start: 0.9257 (tt0) cc_final: 0.8962 (tt0) REVERT: G 59 LYS cc_start: 0.8926 (tttt) cc_final: 0.8666 (tttm) REVERT: G 100 PHE cc_start: 0.8975 (m-80) cc_final: 0.8754 (m-80) REVERT: H 24 ASP cc_start: 0.8857 (t0) cc_final: 0.8202 (p0) REVERT: H 79 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8916 (mmtm) REVERT: K 296 MET cc_start: 0.9039 (ppp) cc_final: 0.8647 (ppp) REVERT: K 354 MET cc_start: 0.8855 (pmm) cc_final: 0.8314 (pmm) REVERT: K 373 TRP cc_start: 0.9244 (t60) cc_final: 0.8616 (t60) REVERT: K 452 MET cc_start: 0.8243 (ttp) cc_final: 0.7616 (ttm) REVERT: K 502 LEU cc_start: 0.8250 (tp) cc_final: 0.8025 (tp) REVERT: K 626 MET cc_start: 0.9092 (tpp) cc_final: 0.8588 (tpp) REVERT: K 758 MET cc_start: 0.4947 (tpp) cc_final: 0.4252 (tpt) outliers start: 24 outliers final: 16 residues processed: 210 average time/residue: 0.1164 time to fit residues: 36.5192 Evaluate side-chains 200 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 102 optimal weight: 40.0000 chunk 39 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 HIS F 68 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** 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 = 0.3834 r_free = 0.3834 target = 0.087527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.056597 restraints weight = 55244.550| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.84 r_work: 0.2825 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17181 Z= 0.170 Angle : 0.602 11.674 24477 Z= 0.333 Chirality : 0.040 0.368 2776 Planarity : 0.004 0.055 2050 Dihedral : 29.719 160.469 4678 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.94 % Allowed : 18.82 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.24), residues: 1244 helix: 2.61 (0.18), residues: 804 sheet: -1.54 (0.51), residues: 78 loop : -0.50 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 112 TYR 0.010 0.001 TYR B 66 PHE 0.011 0.001 PHE F 67 TRP 0.016 0.001 TRP K 373 HIS 0.026 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (17181) covalent geometry : angle 0.60248 / 0.33 (24477) hydrogen bonds : bond 0.04945 / 3.45 ( 735) hydrogen bonds : angle 3.52147 / 2.55 ( 2045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9135 (mttp) cc_final: 0.8763 (mttp) REVERT: A 70 GLU cc_start: 0.8898 (tp30) cc_final: 0.8452 (tp30) REVERT: A 73 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8722 (tm-30) REVERT: A 81 ASP cc_start: 0.9037 (m-30) cc_final: 0.8726 (t0) REVERT: A 99 ASP cc_start: 0.9006 (t0) cc_final: 0.8320 (t0) REVERT: B 41 ARG cc_start: 0.9599 (ttp-170) cc_final: 0.9373 (ttp80) REVERT: B 73 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8680 (tp30) REVERT: B 99 ASP cc_start: 0.8826 (t0) cc_final: 0.8406 (t0) REVERT: B 101 GLU cc_start: 0.8354 (pm20) cc_final: 0.7911 (pm20) REVERT: C 88 ASP cc_start: 0.9026 (t0) cc_final: 0.8743 (t0) REVERT: C 91 GLU cc_start: 0.8821 (tt0) cc_final: 0.8557 (tp30) REVERT: C 96 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8371 (mm-30) REVERT: C 113 GLU cc_start: 0.8845 (mp0) cc_final: 0.8039 (mp0) REVERT: C 125 GLU cc_start: 0.8394 (tp30) cc_final: 0.8137 (tp30) REVERT: C 129 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.8812 (m-70) REVERT: D 55 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8481 (mm-30) REVERT: D 88 ASP cc_start: 0.9072 (t0) cc_final: 0.8447 (t0) REVERT: D 91 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8578 (tm-30) REVERT: D 113 GLU cc_start: 0.8649 (mp0) cc_final: 0.7784 (mp0) REVERT: D 125 GLU cc_start: 0.8404 (tp30) cc_final: 0.8107 (tp30) REVERT: E 50 GLU cc_start: 0.8470 (tt0) cc_final: 0.7802 (tt0) REVERT: E 115 LYS cc_start: 0.9423 (mttm) cc_final: 0.9182 (mmtt) REVERT: E 134 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7737 (mmm160) REVERT: F 50 GLU cc_start: 0.9267 (tt0) cc_final: 0.8968 (tt0) REVERT: G 59 LYS cc_start: 0.8880 (tttt) cc_final: 0.8623 (tttm) REVERT: H 79 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8826 (mmtp) REVERT: K 296 MET cc_start: 0.9033 (ppp) cc_final: 0.8389 (ppp) REVERT: K 354 MET cc_start: 0.8875 (pmm) cc_final: 0.8230 (pmm) REVERT: K 373 TRP cc_start: 0.9250 (t60) cc_final: 0.8641 (t60) REVERT: K 452 MET cc_start: 0.8176 (ttp) cc_final: 0.7574 (ttm) REVERT: K 626 MET cc_start: 0.9097 (tpp) cc_final: 0.8581 (tpp) REVERT: K 758 MET cc_start: 0.4902 (tpp) cc_final: 0.4180 (tpt) outliers start: 21 outliers final: 19 residues processed: 200 average time/residue: 0.1139 time to fit residues: 34.2569 Evaluate side-chains 202 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 HIS F 68 GLN H 18 HIS ** K 190 GLN ** 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 = 0.3834 r_free = 0.3834 target = 0.087498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056571 restraints weight = 55257.321| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.86 r_work: 0.2826 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17181 Z= 0.173 Angle : 0.608 11.925 24477 Z= 0.335 Chirality : 0.040 0.368 2776 Planarity : 0.004 0.049 2050 Dihedral : 29.730 161.925 4678 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.03 % Allowed : 19.19 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.24), residues: 1244 helix: 2.60 (0.18), residues: 804 sheet: -1.49 (0.51), residues: 78 loop : -0.46 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 47 TYR 0.014 0.001 TYR B 48 PHE 0.010 0.001 PHE F 67 TRP 0.015 0.001 TRP K 373 HIS 0.027 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (17181) covalent geometry : angle 0.60776 / 0.33 (24477) hydrogen bonds : bond 0.04868 / 3.37 ( 735) hydrogen bonds : angle 3.51359 / 2.54 ( 2045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9077 (mttp) cc_final: 0.8850 (mttp) REVERT: A 28 MET cc_start: 0.9409 (tmm) cc_final: 0.9146 (ppp) REVERT: A 29 LYS cc_start: 0.9590 (tttm) cc_final: 0.9359 (tppp) REVERT: A 70 GLU cc_start: 0.8887 (tp30) cc_final: 0.8428 (tp30) REVERT: A 73 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8710 (tm-30) REVERT: A 81 ASP cc_start: 0.9032 (m-30) cc_final: 0.8586 (t0) REVERT: A 83 LYS cc_start: 0.9401 (mptt) cc_final: 0.9108 (mppt) REVERT: A 99 ASP cc_start: 0.8989 (t0) cc_final: 0.8331 (t0) REVERT: B 28 MET cc_start: 0.8683 (ppp) cc_final: 0.8464 (ppp) REVERT: B 73 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8644 (tp30) REVERT: B 99 ASP cc_start: 0.8772 (t0) cc_final: 0.8023 (t0) REVERT: C 88 ASP cc_start: 0.9021 (t0) cc_final: 0.8734 (t0) REVERT: C 91 GLU cc_start: 0.8817 (tt0) cc_final: 0.8557 (tp30) REVERT: C 96 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8370 (mm-30) REVERT: C 113 GLU cc_start: 0.8894 (mp0) cc_final: 0.8039 (mp0) REVERT: C 125 GLU cc_start: 0.8371 (tp30) cc_final: 0.8117 (tp30) REVERT: C 129 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.8787 (m-70) REVERT: D 55 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8455 (mm-30) REVERT: D 88 ASP cc_start: 0.9072 (t0) cc_final: 0.8449 (t0) REVERT: D 91 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8578 (tm-30) REVERT: D 113 GLU cc_start: 0.8536 (mp0) cc_final: 0.7814 (mp0) REVERT: D 125 GLU cc_start: 0.8388 (tp30) cc_final: 0.8093 (tp30) REVERT: E 50 GLU cc_start: 0.8495 (tt0) cc_final: 0.7851 (tt0) REVERT: E 115 LYS cc_start: 0.9419 (mttm) cc_final: 0.9163 (mptt) REVERT: E 134 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7767 (mmm160) REVERT: F 50 GLU cc_start: 0.9276 (tt0) cc_final: 0.8974 (tt0) REVERT: G 59 LYS cc_start: 0.8881 (tttt) cc_final: 0.8646 (tttm) REVERT: H 79 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8832 (mmtp) REVERT: K 296 MET cc_start: 0.9040 (ppp) cc_final: 0.8785 (ppp) REVERT: K 354 MET cc_start: 0.8879 (pmm) cc_final: 0.8197 (pmm) REVERT: K 373 TRP cc_start: 0.9246 (t60) cc_final: 0.8646 (t60) REVERT: K 452 MET cc_start: 0.8161 (ttp) cc_final: 0.7575 (ttm) REVERT: K 626 MET cc_start: 0.9097 (tpp) cc_final: 0.8576 (tpp) REVERT: K 758 MET cc_start: 0.4861 (tpp) cc_final: 0.4141 (tpt) outliers start: 22 outliers final: 21 residues processed: 199 average time/residue: 0.1295 time to fit residues: 38.3652 Evaluate side-chains 202 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 116 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 HIS G 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** 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 = 0.3847 r_free = 0.3847 target = 0.088120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.057416 restraints weight = 54813.056| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.82 r_work: 0.2858 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17181 Z= 0.134 Angle : 0.583 11.323 24477 Z= 0.326 Chirality : 0.039 0.368 2776 Planarity : 0.004 0.043 2050 Dihedral : 29.634 162.833 4678 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.75 % Allowed : 19.65 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.24), residues: 1244 helix: 2.62 (0.18), residues: 804 sheet: -1.44 (0.50), residues: 78 loop : -0.44 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 47 TYR 0.012 0.001 TYR C 57 PHE 0.009 0.001 PHE E 67 TRP 0.015 0.001 TRP K 373 HIS 0.025 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (17181) covalent geometry : angle 0.58292 / 0.33 (24477) hydrogen bonds : bond 0.04513 / 3.11 ( 735) hydrogen bonds : angle 3.38284 / 2.44 ( 2045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.9417 (tmm) cc_final: 0.9190 (tmm) REVERT: A 29 LYS cc_start: 0.9605 (tttm) cc_final: 0.9199 (tptm) REVERT: A 70 GLU cc_start: 0.8861 (tp30) cc_final: 0.8421 (tp30) REVERT: A 73 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8695 (tm-30) REVERT: A 81 ASP cc_start: 0.9015 (m-30) cc_final: 0.8557 (t0) REVERT: A 83 LYS cc_start: 0.9392 (mptt) cc_final: 0.9089 (mppt) REVERT: A 99 ASP cc_start: 0.8987 (t0) cc_final: 0.8340 (t0) REVERT: B 28 MET cc_start: 0.8661 (ppp) cc_final: 0.8436 (ppp) REVERT: B 73 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8631 (tp30) REVERT: B 99 ASP cc_start: 0.8624 (t0) cc_final: 0.8066 (t0) REVERT: B 101 GLU cc_start: 0.8399 (pm20) cc_final: 0.7627 (pm20) REVERT: C 88 ASP cc_start: 0.9003 (t0) cc_final: 0.8711 (t0) REVERT: C 91 GLU cc_start: 0.8806 (tt0) cc_final: 0.8526 (tp30) REVERT: C 96 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8351 (mm-30) REVERT: C 113 GLU cc_start: 0.8855 (mp0) cc_final: 0.8023 (mp0) REVERT: C 125 GLU cc_start: 0.8325 (tp30) cc_final: 0.8076 (tp30) REVERT: C 129 HIS cc_start: 0.9145 (OUTLIER) cc_final: 0.8758 (m-70) REVERT: D 55 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8471 (mm-30) REVERT: D 88 ASP cc_start: 0.9055 (t0) cc_final: 0.8428 (t0) REVERT: D 91 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8544 (tm-30) REVERT: D 96 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: D 113 GLU cc_start: 0.8611 (mp0) cc_final: 0.7755 (mp0) REVERT: D 125 GLU cc_start: 0.8367 (tp30) cc_final: 0.8110 (tp30) REVERT: E 50 GLU cc_start: 0.8595 (tt0) cc_final: 0.7970 (tt0) REVERT: E 115 LYS cc_start: 0.9409 (mttm) cc_final: 0.9163 (mptt) REVERT: E 134 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7926 (mmm160) REVERT: F 50 GLU cc_start: 0.9249 (tt0) cc_final: 0.8980 (tt0) REVERT: G 59 LYS cc_start: 0.8883 (tttt) cc_final: 0.8646 (tttm) REVERT: H 79 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8922 (mmtm) REVERT: K 296 MET cc_start: 0.9090 (ppp) cc_final: 0.8398 (ppp) REVERT: K 354 MET cc_start: 0.8782 (pmm) cc_final: 0.8091 (pmm) REVERT: K 373 TRP cc_start: 0.9228 (t60) cc_final: 0.8654 (t60) REVERT: K 452 MET cc_start: 0.8090 (ttp) cc_final: 0.7444 (ttm) REVERT: K 626 MET cc_start: 0.9089 (tpp) cc_final: 0.8553 (tpp) REVERT: K 758 MET cc_start: 0.4872 (tpp) cc_final: 0.4147 (tpt) outliers start: 19 outliers final: 16 residues processed: 203 average time/residue: 0.1247 time to fit residues: 38.0523 Evaluate side-chains 207 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 49 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 HIS G 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 539 ASN ** 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 = 0.3838 r_free = 0.3838 target = 0.087608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.056632 restraints weight = 54985.944| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.81 r_work: 0.2833 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17181 Z= 0.167 Angle : 0.607 11.207 24477 Z= 0.334 Chirality : 0.040 0.368 2776 Planarity : 0.004 0.042 2050 Dihedral : 29.676 164.144 4678 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.03 % Allowed : 19.65 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.24), residues: 1244 helix: 2.65 (0.18), residues: 804 sheet: -1.43 (0.51), residues: 78 loop : -0.40 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 47 TYR 0.012 0.001 TYR B 48 PHE 0.010 0.001 PHE F 67 TRP 0.014 0.001 TRP K 373 HIS 0.026 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (17181) covalent geometry : angle 0.60742 / 0.33 (24477) hydrogen bonds : bond 0.04707 / 3.24 ( 735) hydrogen bonds : angle 3.43671 / 2.48 ( 2045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.88 seconds wall clock time: 70 minutes 19.17 seconds (4219.17 seconds total)