Starting phenix.real_space_refine on Fri Jul 3 20:33:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcc_37099/07_2026/8kcc_37099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcc_37099/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kcc_37099/07_2026/8kcc_37099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcc_37099/07_2026/8kcc_37099.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcc_37099/07_2026/8kcc_37099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcc_37099/07_2026/8kcc_37099.cif" } 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-dev-6108/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: 3.24, per 1000 atoms: 0.20 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: 1.35 Conformation dependent library (CDL) restraints added in 450.6 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: 1.96 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: 3.98 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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: 24327 2.55 - 5.11: 127 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: 1.340 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.290 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:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- 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 : 0.678 12.768 24477 Z= 0.558 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 0.67792 / 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 : 0.496 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: 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 84 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7770 (mmmt) 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: 0.8561 (mm-30) REVERT: B 26 LYS cc_start: 0.9205 (mttt) cc_final: 0.8962 (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 79 MET cc_start: 0.8647 (tpp) cc_final: 0.8363 (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: 0.9070 (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 631 MET cc_start: 0.9234 (ptm) cc_final: 0.8820 (ptp) REVERT: K 758 MET cc_start: 0.5691 (tpt) cc_final: 0.5036 (tpp) outliers start: 13 outliers final: 3 residues processed: 288 average time/residue: 0.1449 time to fit residues: 59.5489 Evaluate side-chains 205 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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: 8.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN K 236 GLN K 282 HIS K 295 HIS K 336 HIS ** K 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 462 HIS K 506 GLN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.088980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.057164 restraints weight = 56075.534| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.01 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.190 17181 Z= 0.515 Angle : 0.992 9.694 24477 Z= 0.519 Chirality : 0.057 0.323 2776 Planarity : 0.008 0.071 2050 Dihedral : 29.923 152.943 4685 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.69 % Allowed : 12.82 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1244 helix: 1.35 (0.17), residues: 807 sheet: -1.88 (0.55), residues: 78 loop : -1.18 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.029 0.003 TYR K 513 PHE 0.018 0.003 PHE B 34 TRP 0.016 0.003 TRP K 373 HIS 0.011 0.003 HIS G 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01079 / 0.52 (17181) covalent geometry : angle 0.99183 / 0.52 (24477) hydrogen bonds : bond 0.10190 / 7.23 ( 735) hydrogen bonds : angle 4.71972 / 3.46 ( 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 212 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8587 (ttp-170) REVERT: A 70 GLU cc_start: 0.8684 (tp30) cc_final: 0.8269 (tp30) REVERT: A 81 ASP cc_start: 0.8908 (m-30) cc_final: 0.8596 (t0) REVERT: A 101 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8779 (mm-30) REVERT: B 48 TYR cc_start: 0.9586 (m-80) cc_final: 0.9182 (m-80) REVERT: B 70 GLU cc_start: 0.8683 (tp30) cc_final: 0.8348 (tp30) REVERT: B 73 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8162 (tp30) REVERT: B 99 ASP cc_start: 0.8618 (t0) cc_final: 0.8214 (t0) REVERT: C 52 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8840 (tppt) REVERT: C 88 ASP cc_start: 0.8815 (t0) cc_final: 0.8576 (t0) REVERT: C 91 GLU cc_start: 0.8413 (tt0) cc_final: 0.8167 (tp30) REVERT: C 96 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7824 (mm-30) REVERT: C 113 GLU cc_start: 0.8663 (mp0) cc_final: 0.7945 (mp0) REVERT: D 55 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8053 (mm-30) REVERT: D 79 MET cc_start: 0.8816 (tpp) cc_final: 0.8500 (tpp) REVERT: D 88 ASP cc_start: 0.8865 (t0) cc_final: 0.8228 (t0) REVERT: D 91 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8232 (tm-30) REVERT: D 113 GLU cc_start: 0.8394 (mp0) cc_final: 0.7532 (mp0) REVERT: F 50 GLU cc_start: 0.9082 (tt0) cc_final: 0.8784 (tt0) REVERT: F 53 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8902 (ttpp) REVERT: F 54 TYR cc_start: 0.9218 (m-80) cc_final: 0.8862 (m-80) REVERT: G 59 LYS cc_start: 0.8700 (tttt) cc_final: 0.8325 (tttm) REVERT: H 27 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8779 (mm-40) REVERT: H 59 LYS cc_start: 0.9114 (tttt) cc_final: 0.8753 (tttp) REVERT: H 79 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8663 (mmtp) REVERT: K 284 ASP cc_start: 0.8402 (t70) cc_final: 0.8154 (t70) REVERT: K 296 MET cc_start: 0.8515 (ppp) cc_final: 0.8229 (ppp) REVERT: K 354 MET cc_start: 0.8953 (pmm) cc_final: 0.8533 (pmm) REVERT: K 452 MET cc_start: 0.8056 (ttp) cc_final: 0.7648 (ttm) REVERT: K 454 ASP cc_start: 0.9376 (p0) cc_final: 0.9038 (t0) REVERT: K 556 MET cc_start: 0.9427 (mtm) cc_final: 0.8577 (ptp) REVERT: K 631 MET cc_start: 0.9353 (ptm) cc_final: 0.8871 (ptp) outliers start: 40 outliers final: 24 residues processed: 202 average time/residue: 0.1318 time to fit residues: 39.2353 Evaluate side-chains 190 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 86 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: 9.9990 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 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 295 HIS K 336 HIS K 351 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 = 0.3894 r_free = 0.3894 target = 0.091672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.060164 restraints weight = 55272.613| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.94 r_work: 0.2897 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17181 Z= 0.146 Angle : 0.595 7.254 24477 Z= 0.340 Chirality : 0.042 0.326 2776 Planarity : 0.004 0.054 2050 Dihedral : 29.676 152.728 4683 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.57 % Allowed : 15.22 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1244 helix: 2.14 (0.18), residues: 805 sheet: -1.57 (0.55), residues: 68 loop : -0.95 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 47 TYR 0.015 0.001 TYR C 60 PHE 0.016 0.001 PHE H 100 TRP 0.018 0.001 TRP K 373 HIS 0.008 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (17181) covalent geometry : angle 0.59463 / 0.34 (24477) hydrogen bonds : bond 0.05830 / 4.13 ( 735) hydrogen bonds : angle 3.73598 / 2.72 ( 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 222 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8863 (ttp80) cc_final: 0.8581 (ttp-170) REVERT: A 50 GLN cc_start: 0.8490 (mp10) cc_final: 0.8251 (mp10) REVERT: A 70 GLU cc_start: 0.8838 (tp30) cc_final: 0.8471 (tp30) REVERT: A 73 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 81 ASP cc_start: 0.8986 (m-30) cc_final: 0.8621 (t0) REVERT: B 47 ARG cc_start: 0.9130 (ttm-80) cc_final: 0.8902 (mtm110) REVERT: B 73 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8633 (tp30) REVERT: B 99 ASP cc_start: 0.8700 (t0) cc_final: 0.8156 (t0) REVERT: B 101 GLU cc_start: 0.8366 (pm20) cc_final: 0.8132 (pm20) REVERT: C 52 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8771 (tppt) REVERT: C 55 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 88 ASP cc_start: 0.9024 (t0) cc_final: 0.8738 (t0) REVERT: C 91 GLU cc_start: 0.8741 (tt0) cc_final: 0.8494 (tp30) REVERT: C 96 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 57 TYR cc_start: 0.9302 (m-80) cc_final: 0.9097 (m-80) REVERT: D 79 MET cc_start: 0.8877 (tpp) cc_final: 0.8527 (tpp) REVERT: D 88 ASP cc_start: 0.9024 (t0) cc_final: 0.8394 (t0) REVERT: D 91 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8575 (tm-30) REVERT: D 113 GLU cc_start: 0.8723 (mp0) cc_final: 0.7967 (mp0) REVERT: E 50 GLU cc_start: 0.8563 (tt0) cc_final: 0.7919 (tt0) REVERT: E 106 ASP cc_start: 0.8796 (m-30) cc_final: 0.8592 (m-30) REVERT: E 115 LYS cc_start: 0.9388 (mttm) cc_final: 0.9183 (mmtt) REVERT: E 134 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7585 (mmm160) REVERT: F 50 GLU cc_start: 0.9087 (tt0) cc_final: 0.8874 (tt0) REVERT: G 59 LYS cc_start: 0.8927 (tttt) cc_final: 0.8677 (tttm) REVERT: G 100 PHE cc_start: 0.8805 (m-80) cc_final: 0.8584 (m-80) REVERT: H 27 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8734 (mm-40) REVERT: H 59 LYS cc_start: 0.9202 (tttt) cc_final: 0.8974 (ttpp) REVERT: H 79 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8756 (mmtp) REVERT: K 194 CYS cc_start: 0.8064 (m) cc_final: 0.7185 (p) REVERT: K 284 ASP cc_start: 0.8590 (t70) cc_final: 0.8275 (t70) REVERT: K 296 MET cc_start: 0.8732 (ppp) cc_final: 0.8412 (ppp) REVERT: K 354 MET cc_start: 0.9077 (pmm) cc_final: 0.8514 (pmm) REVERT: K 452 MET cc_start: 0.8279 (ttp) cc_final: 0.7539 (ttm) REVERT: K 454 ASP cc_start: 0.9395 (p0) cc_final: 0.9087 (t0) REVERT: K 622 TRP cc_start: 0.8995 (m100) cc_final: 0.7358 (m100) REVERT: K 758 MET cc_start: 0.5044 (tpp) cc_final: 0.4358 (mmm) outliers start: 17 outliers final: 13 residues processed: 218 average time/residue: 0.1345 time to fit residues: 43.2171 Evaluate side-chains 199 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 86 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 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: 0.5980 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 HIS F 68 GLN H 25 ASN ** K 190 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.090107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058516 restraints weight = 55502.161| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.86 r_work: 0.2860 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17181 Z= 0.193 Angle : 0.603 6.960 24477 Z= 0.338 Chirality : 0.041 0.336 2776 Planarity : 0.004 0.046 2050 Dihedral : 29.675 155.222 4682 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.31 % Allowed : 16.42 % Favored : 81.27 % 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: 1.94 (0.24), residues: 1244 helix: 2.44 (0.18), residues: 805 sheet: -1.32 (0.56), residues: 68 loop : -0.85 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 38 TYR 0.019 0.002 TYR B 48 PHE 0.018 0.001 PHE E 41 TRP 0.018 0.001 TRP K 373 HIS 0.005 0.001 HIS K 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (17181) covalent geometry : angle 0.60263 / 0.34 (24477) hydrogen bonds : bond 0.05826 / 4.14 ( 735) hydrogen bonds : angle 3.68974 / 2.68 ( 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 214 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8900 (mttp) REVERT: A 47 ARG cc_start: 0.8891 (ttp80) cc_final: 0.8572 (ttp-170) REVERT: A 70 GLU cc_start: 0.8901 (tp30) cc_final: 0.8454 (tp30) REVERT: A 73 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8742 (tm-30) REVERT: A 81 ASP cc_start: 0.9027 (m-30) cc_final: 0.8495 (t0) REVERT: A 83 LYS cc_start: 0.9384 (mptt) cc_final: 0.9050 (mppt) REVERT: A 99 ASP cc_start: 0.8894 (t0) cc_final: 0.8420 (t0) REVERT: B 73 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8367 (tp30) REVERT: B 99 ASP cc_start: 0.8700 (t0) cc_final: 0.8186 (t0) REVERT: C 88 ASP cc_start: 0.9050 (t0) cc_final: 0.8762 (t0) REVERT: C 91 GLU cc_start: 0.8806 (tt0) cc_final: 0.8574 (tp30) REVERT: C 96 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8317 (mm-30) REVERT: C 113 GLU cc_start: 0.8817 (mp0) cc_final: 0.8143 (mp0) REVERT: C 125 GLU cc_start: 0.8340 (tp30) cc_final: 0.8040 (tp30) REVERT: C 129 HIS cc_start: 0.9188 (OUTLIER) cc_final: 0.8783 (m-70) REVERT: D 57 TYR cc_start: 0.9353 (m-80) cc_final: 0.9135 (m-80) REVERT: D 79 MET cc_start: 0.8898 (tpp) cc_final: 0.8547 (tpp) REVERT: D 88 ASP cc_start: 0.9039 (t0) cc_final: 0.8420 (t0) REVERT: D 91 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8602 (tm-30) REVERT: D 113 GLU cc_start: 0.8784 (mp0) cc_final: 0.8022 (mp0) REVERT: E 50 GLU cc_start: 0.8580 (tt0) cc_final: 0.7943 (tt0) REVERT: G 59 LYS cc_start: 0.8940 (tttt) cc_final: 0.8688 (tttm) REVERT: G 100 PHE cc_start: 0.8848 (m-80) cc_final: 0.8628 (m-80) REVERT: H 27 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8727 (mm-40) REVERT: H 59 LYS cc_start: 0.9198 (tttt) cc_final: 0.8965 (ttpp) REVERT: H 79 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8813 (mmtp) REVERT: K 284 ASP cc_start: 0.8611 (t70) cc_final: 0.8278 (t70) REVERT: K 296 MET cc_start: 0.8804 (ppp) cc_final: 0.8315 (ppp) REVERT: K 354 MET cc_start: 0.9034 (pmm) cc_final: 0.8510 (pmm) REVERT: K 452 MET cc_start: 0.8228 (ttp) cc_final: 0.7487 (ttm) REVERT: K 499 HIS cc_start: 0.6241 (p-80) cc_final: 0.5869 (p-80) REVERT: K 622 TRP cc_start: 0.9093 (m100) cc_final: 0.7474 (m100) REVERT: K 626 MET cc_start: 0.9142 (tpp) cc_final: 0.8782 (tpp) REVERT: K 758 MET cc_start: 0.5109 (tpp) cc_final: 0.4467 (tpt) outliers start: 25 outliers final: 16 residues processed: 206 average time/residue: 0.1185 time to fit residues: 36.3465 Evaluate side-chains 194 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL 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 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 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: 0.9980 chunk 86 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 HIS F 68 GLN H 25 ASN ** K 190 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.089082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.057665 restraints weight = 55682.706| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.87 r_work: 0.2843 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17181 Z= 0.204 Angle : 0.604 8.520 24477 Z= 0.338 Chirality : 0.041 0.333 2776 Planarity : 0.004 0.044 2050 Dihedral : 29.714 156.925 4678 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.12 % Allowed : 17.71 % 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: 1.99 (0.24), residues: 1244 helix: 2.51 (0.18), residues: 804 sheet: -1.54 (0.51), residues: 78 loop : -0.82 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.015 0.001 TYR B 48 PHE 0.011 0.001 PHE K 390 TRP 0.015 0.001 TRP K 373 HIS 0.004 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (17181) covalent geometry : angle 0.60440 / 0.34 (24477) hydrogen bonds : bond 0.05385 / 3.80 ( 735) hydrogen bonds : angle 3.65314 / 2.67 ( 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 206 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9129 (mttp) cc_final: 0.8853 (mttp) REVERT: A 47 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8523 (ttp-170) REVERT: A 70 GLU cc_start: 0.8906 (tp30) cc_final: 0.8450 (tp30) REVERT: A 73 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8773 (tm-30) REVERT: A 81 ASP cc_start: 0.9037 (m-30) cc_final: 0.8554 (t0) REVERT: A 83 LYS cc_start: 0.9385 (mptt) cc_final: 0.9152 (mppt) REVERT: A 99 ASP cc_start: 0.8944 (t0) cc_final: 0.8413 (t0) REVERT: A 123 VAL cc_start: 0.9015 (t) cc_final: 0.8814 (m) REVERT: B 73 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8704 (tp30) REVERT: B 99 ASP cc_start: 0.8687 (t0) cc_final: 0.8168 (t0) REVERT: C 88 ASP cc_start: 0.9024 (t0) cc_final: 0.8761 (t0) REVERT: C 91 GLU cc_start: 0.8824 (tt0) cc_final: 0.8552 (tp30) REVERT: C 96 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8324 (mm-30) REVERT: C 113 GLU cc_start: 0.8871 (mp0) cc_final: 0.8070 (mp0) REVERT: D 57 TYR cc_start: 0.9443 (m-80) cc_final: 0.9217 (m-80) REVERT: D 79 MET cc_start: 0.8912 (tpp) cc_final: 0.8586 (tpp) REVERT: D 88 ASP cc_start: 0.9057 (t0) cc_final: 0.8439 (t0) REVERT: D 91 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8579 (tm-30) REVERT: D 113 GLU cc_start: 0.8713 (mp0) cc_final: 0.7921 (mp0) REVERT: E 50 GLU cc_start: 0.8554 (tt0) cc_final: 0.7902 (tt0) REVERT: E 134 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7682 (mmm160) REVERT: F 50 GLU cc_start: 0.9215 (tt0) cc_final: 0.8995 (tt0) REVERT: G 59 LYS cc_start: 0.8931 (tttt) cc_final: 0.8679 (tttm) REVERT: G 100 PHE cc_start: 0.8915 (m-80) cc_final: 0.8643 (m-80) REVERT: H 27 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8717 (mm-40) REVERT: H 59 LYS cc_start: 0.9185 (tttt) cc_final: 0.8955 (ttpp) REVERT: H 79 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8802 (mmtp) REVERT: K 296 MET cc_start: 0.8839 (ppp) cc_final: 0.8261 (ppp) REVERT: K 354 MET cc_start: 0.9017 (pmm) cc_final: 0.8501 (pmm) REVERT: K 373 TRP cc_start: 0.9264 (t60) cc_final: 0.8562 (t60) REVERT: K 452 MET cc_start: 0.8190 (ttp) cc_final: 0.7451 (ttm) REVERT: K 454 ASP cc_start: 0.9480 (p0) cc_final: 0.9087 (t0) REVERT: K 626 MET cc_start: 0.9149 (tpp) cc_final: 0.8782 (tpp) REVERT: K 758 MET cc_start: 0.5029 (tpp) cc_final: 0.4283 (tpt) outliers start: 23 outliers final: 15 residues processed: 200 average time/residue: 0.1206 time to fit residues: 36.3313 Evaluate side-chains 192 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 59 ILE 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 616 ILE Chi-restraints excluded: chain K residue 643 VAL Chi-restraints excluded: chain K residue 671 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 8 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 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: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 3.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 39 HIS F 68 GLN H 25 ASN ** K 190 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.086499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055392 restraints weight = 56307.307| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.87 r_work: 0.2782 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 17181 Z= 0.287 Angle : 0.691 11.872 24477 Z= 0.374 Chirality : 0.044 0.334 2776 Planarity : 0.005 0.048 2050 Dihedral : 29.963 159.519 4678 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.68 % Allowed : 18.27 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1244 helix: 2.43 (0.18), residues: 807 sheet: -1.59 (0.53), residues: 78 loop : -0.78 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 42 TYR 0.019 0.002 TYR B 48 PHE 0.013 0.002 PHE B 34 TRP 0.017 0.002 TRP K 373 HIS 0.006 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.29 (17181) covalent geometry : angle 0.69114 / 0.37 (24477) hydrogen bonds : bond 0.06457 / 4.55 ( 735) hydrogen bonds : angle 3.90491 / 2.85 ( 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 202 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9172 (mttp) cc_final: 0.8842 (mttp) REVERT: A 47 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8505 (ttp-170) REVERT: A 70 GLU cc_start: 0.8947 (tp30) cc_final: 0.8475 (tp30) REVERT: A 73 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8776 (tm-30) REVERT: A 81 ASP cc_start: 0.9033 (m-30) cc_final: 0.8698 (t0) REVERT: A 99 ASP cc_start: 0.8960 (t0) cc_final: 0.8289 (t0) REVERT: B 70 GLU cc_start: 0.9047 (tp30) cc_final: 0.8834 (tp30) REVERT: B 73 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8787 (tp30) REVERT: B 99 ASP cc_start: 0.8747 (t0) cc_final: 0.8302 (t0) REVERT: B 101 GLU cc_start: 0.8124 (pm20) cc_final: 0.7885 (pm20) REVERT: C 88 ASP cc_start: 0.9045 (t0) cc_final: 0.8768 (t0) REVERT: C 91 GLU cc_start: 0.8864 (tt0) cc_final: 0.8587 (tp30) REVERT: C 96 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8343 (mm-30) REVERT: C 113 GLU cc_start: 0.8848 (mp0) cc_final: 0.7975 (mp0) REVERT: C 125 GLU cc_start: 0.8443 (tp30) cc_final: 0.8165 (tp30) REVERT: C 129 HIS cc_start: 0.9234 (OUTLIER) cc_final: 0.8785 (m-70) REVERT: D 88 ASP cc_start: 0.9078 (t0) cc_final: 0.8569 (t0) REVERT: D 91 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8609 (tm-30) REVERT: E 54 TYR cc_start: 0.9014 (m-80) cc_final: 0.8599 (m-80) REVERT: E 115 LYS cc_start: 0.9423 (mttm) cc_final: 0.9169 (mmtt) REVERT: F 50 GLU cc_start: 0.9202 (tt0) cc_final: 0.9001 (tt0) REVERT: G 59 LYS cc_start: 0.8958 (tttt) cc_final: 0.8698 (tttm) REVERT: G 100 PHE cc_start: 0.8971 (m-80) cc_final: 0.8692 (m-80) REVERT: H 27 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8852 (mm-40) REVERT: H 59 LYS cc_start: 0.9199 (tttt) cc_final: 0.8982 (ttpp) REVERT: H 79 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8818 (mmtp) REVERT: H 98 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8461 (m-10) REVERT: K 354 MET cc_start: 0.8997 (pmm) cc_final: 0.8335 (pmm) REVERT: K 452 MET cc_start: 0.8212 (ttp) cc_final: 0.7557 (ttm) REVERT: K 626 MET cc_start: 0.9168 (tpp) cc_final: 0.8824 (tpp) outliers start: 29 outliers final: 23 residues processed: 195 average time/residue: 0.1288 time to fit residues: 37.2560 Evaluate side-chains 194 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 67 GLN 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 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 51 ILE 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 H residue 60 ILE 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 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: 0.7980 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 87 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.087672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.056604 restraints weight = 55516.407| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.84 r_work: 0.2827 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17181 Z= 0.155 Angle : 0.584 9.120 24477 Z= 0.330 Chirality : 0.040 0.335 2776 Planarity : 0.004 0.054 2050 Dihedral : 29.831 160.019 4678 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.75 % Allowed : 19.83 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.24), residues: 1244 helix: 2.62 (0.18), residues: 804 sheet: -1.52 (0.51), residues: 78 loop : -0.63 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 38 TYR 0.014 0.001 TYR B 48 PHE 0.011 0.001 PHE E 67 TRP 0.017 0.001 TRP K 373 HIS 0.017 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (17181) covalent geometry : angle 0.58394 / 0.33 (24477) hydrogen bonds : bond 0.05105 / 3.57 ( 735) hydrogen bonds : angle 3.55172 / 2.58 ( 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 205 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9097 (mttp) cc_final: 0.8608 (mttp) REVERT: A 47 ARG cc_start: 0.8881 (ttp80) cc_final: 0.8522 (ttp-170) REVERT: A 70 GLU cc_start: 0.8881 (tp30) cc_final: 0.8424 (tp30) REVERT: A 73 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 81 ASP cc_start: 0.9039 (m-30) cc_final: 0.8711 (t0) REVERT: A 99 ASP cc_start: 0.9033 (t0) cc_final: 0.8426 (t0) REVERT: B 73 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8641 (tp30) REVERT: B 99 ASP cc_start: 0.8739 (t0) cc_final: 0.8202 (t0) REVERT: C 88 ASP cc_start: 0.9013 (t0) cc_final: 0.8732 (t0) REVERT: C 91 GLU cc_start: 0.8824 (tt0) cc_final: 0.8565 (tp30) REVERT: C 96 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8331 (mm-30) REVERT: C 113 GLU cc_start: 0.8876 (mp0) cc_final: 0.7999 (mp0) REVERT: C 125 GLU cc_start: 0.8363 (tp30) cc_final: 0.8086 (tp30) REVERT: C 129 HIS cc_start: 0.9190 (OUTLIER) cc_final: 0.8740 (m-70) REVERT: D 57 TYR cc_start: 0.9438 (m-80) cc_final: 0.9051 (m-80) REVERT: D 88 ASP cc_start: 0.9061 (t0) cc_final: 0.8443 (t0) REVERT: D 91 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8549 (tm-30) REVERT: D 113 GLU cc_start: 0.8475 (mp0) cc_final: 0.7752 (mp0) REVERT: E 50 GLU cc_start: 0.8612 (tt0) cc_final: 0.7888 (tt0) REVERT: E 54 TYR cc_start: 0.8998 (m-80) cc_final: 0.8609 (m-80) REVERT: E 115 LYS cc_start: 0.9416 (mttm) cc_final: 0.9174 (mmtt) REVERT: E 134 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7722 (mmm160) REVERT: F 50 GLU cc_start: 0.9252 (tt0) cc_final: 0.8985 (tt0) REVERT: G 59 LYS cc_start: 0.8925 (tttt) cc_final: 0.8665 (tttm) REVERT: H 27 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8836 (mm-40) REVERT: H 59 LYS cc_start: 0.9167 (tttt) cc_final: 0.8936 (ttpp) REVERT: H 79 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8902 (mmtm) REVERT: K 296 MET cc_start: 0.8928 (ppp) cc_final: 0.8619 (ppp) REVERT: K 354 MET cc_start: 0.8857 (pmm) cc_final: 0.8278 (pmm) REVERT: K 373 TRP cc_start: 0.9248 (t60) cc_final: 0.8609 (t60) REVERT: K 452 MET cc_start: 0.8171 (ttp) cc_final: 0.7620 (ttm) REVERT: K 626 MET cc_start: 0.9128 (tpp) cc_final: 0.8771 (tpp) REVERT: K 758 MET cc_start: 0.5062 (tpp) cc_final: 0.4475 (mmm) outliers start: 19 outliers final: 15 residues processed: 201 average time/residue: 0.1209 time to fit residues: 36.3086 Evaluate side-chains 194 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 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 516 VAL Chi-restraints excluded: chain K residue 616 ILE Chi-restraints excluded: chain K residue 643 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: 0.9990 chunk 130 optimal weight: 8.9990 chunk 73 optimal weight: 40.0000 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 149 optimal weight: 30.0000 chunk 37 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 HIS F 113 HIS G 93 GLN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 541 HIS K 644 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.088539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.057755 restraints weight = 55363.453| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.86 r_work: 0.2855 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17181 Z= 0.133 Angle : 0.571 11.638 24477 Z= 0.321 Chirality : 0.039 0.340 2776 Planarity : 0.004 0.053 2050 Dihedral : 29.697 160.869 4678 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.85 % Allowed : 20.20 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.24), residues: 1244 helix: 2.68 (0.18), residues: 804 sheet: -1.43 (0.51), residues: 78 loop : -0.51 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 112 TYR 0.012 0.001 TYR C 60 PHE 0.011 0.001 PHE F 67 TRP 0.016 0.001 TRP K 373 HIS 0.004 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (17181) covalent geometry : angle 0.57118 / 0.32 (24477) hydrogen bonds : bond 0.04531 / 3.13 ( 735) hydrogen bonds : angle 3.38601 / 2.45 ( 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 210 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9099 (mttp) cc_final: 0.8518 (mttp) REVERT: A 47 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8508 (ttp-170) REVERT: A 70 GLU cc_start: 0.8875 (tp30) cc_final: 0.8434 (tp30) REVERT: A 73 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8728 (tm-30) REVERT: A 81 ASP cc_start: 0.9039 (m-30) cc_final: 0.8568 (t0) REVERT: A 83 LYS cc_start: 0.9386 (mptt) cc_final: 0.9101 (mppt) REVERT: A 99 ASP cc_start: 0.9021 (t0) cc_final: 0.8324 (t0) REVERT: B 41 ARG cc_start: 0.9534 (ttp-170) cc_final: 0.9175 (ttp80) REVERT: B 73 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8668 (tp30) REVERT: B 99 ASP cc_start: 0.8738 (t0) cc_final: 0.8270 (t0) REVERT: B 101 GLU cc_start: 0.8068 (pm20) cc_final: 0.7697 (pm20) REVERT: C 88 ASP cc_start: 0.9015 (t0) cc_final: 0.8726 (t0) REVERT: C 91 GLU cc_start: 0.8826 (tt0) cc_final: 0.8537 (tp30) REVERT: C 96 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8338 (mm-30) REVERT: C 113 GLU cc_start: 0.8886 (mp0) cc_final: 0.8023 (mp0) REVERT: C 125 GLU cc_start: 0.8302 (tp30) cc_final: 0.8030 (tp30) REVERT: C 129 HIS cc_start: 0.9154 (OUTLIER) cc_final: 0.8721 (m-70) REVERT: D 57 TYR cc_start: 0.9428 (m-80) cc_final: 0.8912 (m-80) REVERT: D 88 ASP cc_start: 0.9048 (t0) cc_final: 0.8541 (t0) REVERT: D 91 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8543 (tm-30) REVERT: D 113 GLU cc_start: 0.8583 (mp0) cc_final: 0.7893 (mp0) REVERT: E 50 GLU cc_start: 0.8570 (tt0) cc_final: 0.7753 (tt0) REVERT: E 54 TYR cc_start: 0.8961 (m-80) cc_final: 0.8555 (m-80) REVERT: E 115 LYS cc_start: 0.9412 (mttm) cc_final: 0.9172 (mmtt) REVERT: E 134 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7726 (mmm160) REVERT: F 50 GLU cc_start: 0.9246 (tt0) cc_final: 0.9008 (tt0) REVERT: F 94 GLU cc_start: 0.9102 (tp30) cc_final: 0.8877 (tt0) REVERT: F 125 GLN cc_start: 0.9569 (mt0) cc_final: 0.9368 (mt0) REVERT: G 59 LYS cc_start: 0.8872 (tttt) cc_final: 0.8625 (tttm) REVERT: G 84 MET cc_start: 0.8838 (tpp) cc_final: 0.8368 (mmm) REVERT: H 27 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8783 (mm-40) REVERT: H 59 LYS cc_start: 0.9076 (tttt) cc_final: 0.8841 (ttpp) REVERT: H 79 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8902 (mmtm) REVERT: H 98 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: K 296 MET cc_start: 0.8943 (ppp) cc_final: 0.8615 (ppp) REVERT: K 354 MET cc_start: 0.8844 (pmm) cc_final: 0.8251 (pmm) REVERT: K 373 TRP cc_start: 0.9241 (t60) cc_final: 0.8639 (t60) REVERT: K 452 MET cc_start: 0.8020 (ttp) cc_final: 0.7409 (ttm) REVERT: K 626 MET cc_start: 0.9109 (tpp) cc_final: 0.8725 (tpp) REVERT: K 758 MET cc_start: 0.4797 (tpp) cc_final: 0.4234 (mmm) outliers start: 20 outliers final: 16 residues processed: 204 average time/residue: 0.1232 time to fit residues: 37.6480 Evaluate side-chains 203 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 60 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 H residue 98 TYR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 555 ILE 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: 1.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 39 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.087913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057137 restraints weight = 55819.678| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.85 r_work: 0.2841 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4301 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= 0.157 Angle : 0.583 12.560 24477 Z= 0.325 Chirality : 0.039 0.339 2776 Planarity : 0.004 0.052 2050 Dihedral : 29.740 162.181 4678 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.94 % Allowed : 20.02 % Favored : 78.04 % 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: 2.33 (0.24), residues: 1244 helix: 2.69 (0.18), residues: 804 sheet: -1.33 (0.52), residues: 78 loop : -0.46 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 38 TYR 0.013 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 TRP 0.015 0.001 TRP K 373 HIS 0.016 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (17181) covalent geometry : angle 0.58273 / 0.33 (24477) hydrogen bonds : bond 0.04682 / 3.23 ( 735) hydrogen bonds : angle 3.42012 / 2.48 ( 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 203 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8533 (ttp-170) REVERT: A 70 GLU cc_start: 0.8881 (tp30) cc_final: 0.8437 (tp30) REVERT: A 73 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8734 (tm-30) REVERT: A 81 ASP cc_start: 0.9032 (m-30) cc_final: 0.8558 (t0) REVERT: A 83 LYS cc_start: 0.9385 (mptt) cc_final: 0.9150 (mppt) REVERT: A 99 ASP cc_start: 0.9025 (t0) cc_final: 0.8318 (t0) REVERT: B 41 ARG cc_start: 0.9571 (ttp-170) cc_final: 0.9268 (ttp80) REVERT: B 73 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8694 (tp30) REVERT: B 99 ASP cc_start: 0.8732 (t0) cc_final: 0.8179 (t0) REVERT: C 88 ASP cc_start: 0.9003 (t0) cc_final: 0.8722 (t0) REVERT: C 91 GLU cc_start: 0.8823 (tt0) cc_final: 0.8537 (tp30) REVERT: C 96 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8325 (mm-30) REVERT: C 113 GLU cc_start: 0.8845 (mp0) cc_final: 0.8006 (mp0) REVERT: C 125 GLU cc_start: 0.8331 (tp30) cc_final: 0.8090 (tp30) REVERT: C 129 HIS cc_start: 0.9157 (OUTLIER) cc_final: 0.8750 (m-70) REVERT: D 57 TYR cc_start: 0.9435 (m-80) cc_final: 0.9058 (m-80) REVERT: D 88 ASP cc_start: 0.9055 (t0) cc_final: 0.8432 (t0) REVERT: D 91 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8553 (tm-30) REVERT: D 113 GLU cc_start: 0.8452 (mp0) cc_final: 0.7992 (mp0) REVERT: E 50 GLU cc_start: 0.8582 (tt0) cc_final: 0.7852 (tt0) REVERT: E 54 TYR cc_start: 0.8975 (m-80) cc_final: 0.8570 (m-80) REVERT: E 115 LYS cc_start: 0.9408 (mttm) cc_final: 0.9160 (mptt) REVERT: F 50 GLU cc_start: 0.9261 (tt0) cc_final: 0.9022 (tt0) REVERT: G 59 LYS cc_start: 0.8909 (tttt) cc_final: 0.8677 (tttm) REVERT: H 27 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8811 (mm-40) REVERT: H 79 LYS cc_start: 0.9185 (mmtt) cc_final: 0.8933 (mmtm) REVERT: K 296 MET cc_start: 0.8939 (ppp) cc_final: 0.8600 (ppp) REVERT: K 354 MET cc_start: 0.8849 (pmm) cc_final: 0.8184 (pmm) REVERT: K 373 TRP cc_start: 0.9248 (t60) cc_final: 0.8658 (t60) REVERT: K 452 MET cc_start: 0.8049 (ttp) cc_final: 0.7451 (ttm) REVERT: K 626 MET cc_start: 0.9149 (tpp) cc_final: 0.8750 (tpp) REVERT: K 758 MET cc_start: 0.4818 (tpp) cc_final: 0.4283 (mmm) outliers start: 21 outliers final: 19 residues processed: 196 average time/residue: 0.1330 time to fit residues: 38.6473 Evaluate side-chains 197 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL 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 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 185 THR Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 555 ILE 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: 0.0000 chunk 12 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** 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 = 0.088216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.057481 restraints weight = 55221.439| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.83 r_work: 0.2852 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17181 Z= 0.142 Angle : 0.567 11.483 24477 Z= 0.320 Chirality : 0.039 0.339 2776 Planarity : 0.004 0.049 2050 Dihedral : 29.681 164.007 4678 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.75 % Allowed : 20.39 % Favored : 77.86 % 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: 2.35 (0.24), residues: 1244 helix: 2.69 (0.18), residues: 804 sheet: -1.30 (0.51), residues: 78 loop : -0.42 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.012 0.001 TYR C 57 PHE 0.010 0.001 PHE F 67 TRP 0.015 0.001 TRP K 373 HIS 0.004 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (17181) covalent geometry : angle 0.56694 / 0.32 (24477) hydrogen bonds : bond 0.04469 / 3.06 ( 735) hydrogen bonds : angle 3.35719 / 2.43 ( 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 205 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8525 (ttp-170) REVERT: A 70 GLU cc_start: 0.8858 (tp30) cc_final: 0.8412 (tp30) REVERT: A 73 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 81 ASP cc_start: 0.9027 (m-30) cc_final: 0.8558 (t0) REVERT: A 83 LYS cc_start: 0.9391 (mptt) cc_final: 0.9152 (mppt) REVERT: A 99 ASP cc_start: 0.9014 (t0) cc_final: 0.8307 (t0) REVERT: B 41 ARG cc_start: 0.9558 (ttp-170) cc_final: 0.9238 (ttp80) REVERT: B 73 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8688 (tp30) REVERT: B 99 ASP cc_start: 0.8724 (t0) cc_final: 0.8288 (t0) REVERT: B 101 GLU cc_start: 0.8116 (pm20) cc_final: 0.7758 (pm20) REVERT: C 88 ASP cc_start: 0.9005 (t0) cc_final: 0.8719 (t0) REVERT: C 91 GLU cc_start: 0.8824 (tt0) cc_final: 0.8547 (tp30) REVERT: C 96 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8323 (mm-30) REVERT: C 113 GLU cc_start: 0.8855 (mp0) cc_final: 0.8007 (mp0) REVERT: C 125 GLU cc_start: 0.8317 (tp30) cc_final: 0.8080 (tp30) REVERT: C 129 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8740 (m-70) REVERT: D 57 TYR cc_start: 0.9421 (m-80) cc_final: 0.8886 (m-80) REVERT: D 88 ASP cc_start: 0.9050 (t0) cc_final: 0.8419 (t0) REVERT: D 91 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8531 (tm-30) REVERT: D 113 GLU cc_start: 0.8540 (mp0) cc_final: 0.8077 (mp0) REVERT: E 50 GLU cc_start: 0.8574 (tt0) cc_final: 0.7762 (tt0) REVERT: E 54 TYR cc_start: 0.8963 (m-80) cc_final: 0.8559 (m-80) REVERT: E 115 LYS cc_start: 0.9440 (mttm) cc_final: 0.9170 (mptt) REVERT: F 50 GLU cc_start: 0.9265 (tt0) cc_final: 0.9025 (tt0) REVERT: G 59 LYS cc_start: 0.8894 (tttt) cc_final: 0.8662 (tttm) REVERT: G 84 MET cc_start: 0.8830 (tpp) cc_final: 0.8365 (mmm) REVERT: H 27 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8797 (mm-40) REVERT: H 79 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8924 (mmtm) REVERT: K 296 MET cc_start: 0.8936 (ppp) cc_final: 0.8612 (ppp) REVERT: K 354 MET cc_start: 0.8785 (pmm) cc_final: 0.8080 (pmm) REVERT: K 373 TRP cc_start: 0.9242 (t60) cc_final: 0.8680 (t60) REVERT: K 452 MET cc_start: 0.8018 (ttp) cc_final: 0.7391 (ttm) REVERT: K 454 ASP cc_start: 0.9535 (p0) cc_final: 0.9177 (t0) REVERT: K 626 MET cc_start: 0.9049 (tpp) cc_final: 0.8632 (tpp) REVERT: K 758 MET cc_start: 0.4818 (tpp) cc_final: 0.4308 (mmm) outliers start: 19 outliers final: 17 residues processed: 198 average time/residue: 0.1281 time to fit residues: 38.0234 Evaluate side-chains 200 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain C residue 54 VAL 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 E residue 60 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 502 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: 0.8980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** 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 = 0.087472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056712 restraints weight = 54825.949| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.80 r_work: 0.2836 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17181 Z= 0.179 Angle : 0.591 11.047 24477 Z= 0.329 Chirality : 0.039 0.340 2776 Planarity : 0.004 0.049 2050 Dihedral : 29.767 165.741 4678 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.94 % Allowed : 20.48 % Favored : 77.58 % 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: 2.43 (0.24), residues: 1244 helix: 2.76 (0.18), residues: 797 sheet: -1.33 (0.52), residues: 78 loop : -0.32 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 38 TYR 0.015 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 TRP 0.015 0.001 TRP K 373 HIS 0.005 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (17181) covalent geometry : angle 0.59140 / 0.33 (24477) hydrogen bonds : bond 0.04792 / 3.30 ( 735) hydrogen bonds : angle 3.44673 / 2.50 ( 2045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4348.58 seconds wall clock time: 75 minutes 1.19 seconds (4501.19 seconds total)