Starting phenix.real_space_refine on Thu Aug 6 13:31:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0a_15777/08_2026/8b0a_15777.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0a_15777/08_2026/8b0a_15777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b0a_15777/08_2026/8b0a_15777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0a_15777/08_2026/8b0a_15777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b0a_15777/08_2026/8b0a_15777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0a_15777/08_2026/8b0a_15777.map" } resolution = 3.0 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= 0.022 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: 5 Type Number sf(0) Gaussians P 297 5.49 5 S 27 5.16 5 C 9068 2.51 5 N 2914 2.21 5 O 3537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15843 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3671 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 13, 'TRANS': 445} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3036 Classifications: {'DNA': 149} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3070 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Time building chain proxies: 3.31, per 1000 atoms: 0.21 Number of scatterers: 15843 At special positions: 0 Unit cell: (137.01, 139.595, 107.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 297 15.00 O 3537 8.00 N 2914 7.00 C 9068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 500.5 milliseconds 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 12 sheets defined 66.3% alpha, 5.5% beta 148 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'K' and resid 48 through 63 removed outlier: 4.339A pdb=" N GLU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 91 Processing helix chain 'K' and resid 103 through 105 No H-bonds generated for 'chain 'K' and resid 103 through 105' Processing helix chain 'K' and resid 106 through 118 Processing helix chain 'K' and resid 129 through 140 removed outlier: 3.801A pdb=" N GLN K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 159 Processing helix chain 'K' and resid 159 through 165 removed outlier: 3.763A pdb=" N LEU K 163 " --> pdb=" O ASP K 159 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER K 165 " --> pdb=" O SER K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 181 removed outlier: 3.654A pdb=" N ARG K 178 " --> pdb=" O GLU K 175 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN K 181 " --> pdb=" O ARG K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 193 Processing helix chain 'K' and resid 209 through 219 Processing helix chain 'K' and resid 221 through 230 removed outlier: 6.174A pdb=" N LYS K 227 " --> pdb=" O ASP K 223 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU K 228 " --> pdb=" O LEU K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 237 removed outlier: 3.981A pdb=" N GLN K 235 " --> pdb=" O GLY K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 241 Processing helix chain 'K' and resid 246 through 255 removed outlier: 3.524A pdb=" N LEU K 250 " --> pdb=" O SER K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 267 Processing helix chain 'K' and resid 283 through 294 Processing helix chain 'K' and resid 299 through 304 Processing helix chain 'K' and resid 314 through 324 Processing helix chain 'K' and resid 325 through 328 Processing helix chain 'K' and resid 340 through 345 Processing helix chain 'K' and resid 346 through 362 Processing helix chain 'K' and resid 372 through 387 Processing helix chain 'K' and resid 398 through 410 Processing helix chain 'K' and resid 444 through 453 removed outlier: 3.963A pdb=" N ASP K 448 " --> pdb=" O ASN K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 495 removed outlier: 3.833A pdb=" N ILE K 478 " --> pdb=" O THR K 474 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU K 487 " --> pdb=" O ALA K 483 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N MET K 492 " --> pdb=" O GLN K 488 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE K 493 " --> pdb=" O LEU K 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.589A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.646A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.673A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.766A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.510A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.705A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.617A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.691A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.598A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.758A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.733A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.632A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 119 Processing sheet with id=AA1, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.802A pdb=" N PHE K 98 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR K 151 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE K 100 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU K 99 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER K 169 " --> pdb=" O PHE K 197 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU K 199 " --> pdb=" O SER K 169 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU K 171 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU K 201 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL K 173 " --> pdb=" O LEU K 201 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE K 68 " --> pdb=" O LEU K 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 275 through 280 removed outlier: 6.575A pdb=" N VAL K 436 " --> pdb=" O ILE K 467 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU K 469 " --> pdb=" O VAL K 436 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE K 438 " --> pdb=" O LEU K 469 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLY K 471 " --> pdb=" O PHE K 438 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU K 367 " --> pdb=" O ILE K 437 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU K 391 " --> pdb=" O LEU K 418 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER K 420 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL K 393 " --> pdb=" O SER K 420 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.881A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.921A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.817A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.710A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.831A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 560 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 1.55 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: 3054 1.33 - 1.45: 5151 1.45 - 1.57: 7895 1.57 - 1.69: 593 1.69 - 1.81: 46 Bond restraints: 16739 Sorted by residual: bond pdb=" C3' DC I -57 " pdb=" C2' DC I -57 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.72e+01 bond pdb=" C3' DT I -36 " pdb=" C2' DT I -36 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.60e+01 bond pdb=" C3' DT J 5 " pdb=" C2' DT J 5 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.57e+01 bond pdb=" C3' DG J -5 " pdb=" C2' DG J -5 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.08e+01 bond pdb=" C3' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.88e+01 ... (remaining 16734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 22271 2.06 - 4.11: 1441 4.11 - 6.17: 159 6.17 - 8.22: 8 8.22 - 10.28: 2 Bond angle restraints: 23881 Sorted by residual: angle pdb=" O4' DA I 73 " pdb=" C1' DA I 73 " pdb=" N9 DA I 73 " ideal model delta sigma weight residual 108.00 118.28 -10.28 7.00e-01 2.04e+00 2.16e+02 angle pdb=" C4' DA I 73 " pdb=" O4' DA I 73 " pdb=" C1' DA I 73 " ideal model delta sigma weight residual 110.10 101.82 8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" O5' DT I 64 " pdb=" C5' DT I 64 " pdb=" C4' DT I 64 " ideal model delta sigma weight residual 109.40 115.59 -6.19 8.00e-01 1.56e+00 5.99e+01 angle pdb=" O4' DG J 63 " pdb=" C1' DG J 63 " pdb=" N9 DG J 63 " ideal model delta sigma weight residual 108.00 113.13 -5.13 7.00e-01 2.04e+00 5.37e+01 angle pdb=" O5' DA J -41 " pdb=" C5' DA J -41 " pdb=" C4' DA J -41 " ideal model delta sigma weight residual 109.40 115.22 -5.82 8.00e-01 1.56e+00 5.29e+01 ... (remaining 23876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 8144 35.00 - 69.99: 1136 69.99 - 104.99: 32 104.99 - 139.99: 0 139.99 - 174.98: 1 Dihedral angle restraints: 9313 sinusoidal: 5764 harmonic: 3549 Sorted by residual: dihedral pdb=" CA LYS K 307 " pdb=" C LYS K 307 " pdb=" N LYS K 308 " pdb=" CA LYS K 308 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ALA K 306 " pdb=" C ALA K 306 " pdb=" N LYS K 307 " pdb=" CA LYS K 307 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PHE K 409 " pdb=" C PHE K 409 " pdb=" N GLY K 410 " pdb=" CA GLY K 410 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 9310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2349 0.109 - 0.218: 349 0.218 - 0.327: 9 0.327 - 0.436: 1 0.436 - 0.544: 2 Chirality restraints: 2710 Sorted by residual: chirality pdb=" C1' DA I 73 " pdb=" O4' DA I 73 " pdb=" C2' DA I 73 " pdb=" N9 DA I 73 " both_signs ideal model delta sigma weight residual False 2.43 1.89 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" C1' DG I 74 " pdb=" O4' DG I 74 " pdb=" C2' DG I 74 " pdb=" N9 DG I 74 " both_signs ideal model delta sigma weight residual False 2.43 1.92 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" C1' DT I 64 " pdb=" O4' DT I 64 " pdb=" C2' DT I 64 " pdb=" N1 DT I 64 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 2707 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 74 " -0.085 2.00e-02 2.50e+03 3.58e-02 3.84e+01 pdb=" N9 DG I 74 " 0.082 2.00e-02 2.50e+03 pdb=" C8 DG I 74 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DG I 74 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 74 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 74 " -0.012 2.00e-02 2.50e+03 pdb=" O6 DG I 74 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG I 74 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 74 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 74 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DG I 74 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG I 74 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 73 " 0.059 2.00e-02 2.50e+03 2.91e-02 2.32e+01 pdb=" N9 DA I 73 " -0.073 2.00e-02 2.50e+03 pdb=" C8 DA I 73 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I 73 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 73 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 73 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 73 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 73 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA I 73 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 73 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 73 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -57 " 0.058 2.00e-02 2.50e+03 3.20e-02 2.31e+01 pdb=" N1 DC I -57 " -0.073 2.00e-02 2.50e+03 pdb=" C2 DC I -57 " 0.009 2.00e-02 2.50e+03 pdb=" O2 DC I -57 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I -57 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I -57 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC I -57 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DC I -57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC I -57 " -0.007 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4145 2.84 - 3.36: 14086 3.36 - 3.87: 28705 3.87 - 4.39: 34388 4.39 - 4.90: 49476 Nonbonded interactions: 130800 Sorted by model distance: nonbonded pdb=" OH TYR K 289 " pdb=" OE1 GLU K 304 " model vdw 2.331 3.040 nonbonded pdb=" OD1 ASP K 353 " pdb=" OH TYR K 382 " model vdw 2.375 3.040 nonbonded pdb=" OG SER K 226 " pdb=" OE2 GLU K 229 " model vdw 2.404 3.040 nonbonded pdb=" O5' DA I -72 " pdb=" O4 DT J 72 " model vdw 2.447 3.040 nonbonded pdb=" OD1 ASP K 394 " pdb=" N GLY K 395 " model vdw 2.460 3.120 ... (remaining 130795 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 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 20 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = chain 'H' } 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: 1.210 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.200 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 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 : 0.008 0.057 16739 Z= 0.722 Angle : 1.040 10.280 23881 Z= 0.827 Chirality : 0.071 0.544 2710 Planarity : 0.011 0.113 1998 Dihedral : 23.863 174.983 7023 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.66 % Favored : 96.93 % Rotamer: Outliers : 0.58 % Allowed : 1.93 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1204 helix: 0.24 (0.17), residues: 767 sheet: 1.14 (0.65), residues: 75 loop : -0.58 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG A 83 TYR 0.036 0.004 TYR K 214 PHE 0.016 0.002 PHE K 162 TRP 0.020 0.004 TRP K 110 HIS 0.006 0.002 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00829 / 0.72 (16739) covalent geometry : angle 1.03980 / 0.83 (23881) hydrogen bonds : bond 0.17617 / 11.53 ( 939) hydrogen bonds : angle 5.33553 / 3.84 ( 2393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: K 72 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: K 73 MET cc_start: 0.7434 (mtp) cc_final: 0.6812 (mmm) REVERT: K 113 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8522 (mp0) REVERT: K 329 ASP cc_start: 0.8945 (m-30) cc_final: 0.8654 (p0) REVERT: K 428 MET cc_start: 0.8954 (mtm) cc_final: 0.8688 (mtm) REVERT: A 59 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 24 ASP cc_start: 0.8910 (t0) cc_final: 0.8665 (t0) REVERT: C 64 GLU cc_start: 0.9086 (tt0) cc_final: 0.8410 (tp30) REVERT: C 72 ASP cc_start: 0.9035 (m-30) cc_final: 0.8835 (m-30) REVERT: C 92 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8528 (mt-10) REVERT: D 49 THR cc_start: 0.9360 (m) cc_final: 0.9005 (p) REVERT: D 65 ASP cc_start: 0.9550 (t0) cc_final: 0.9220 (t0) REVERT: F 85 ASP cc_start: 0.9237 (m-30) cc_final: 0.8983 (m-30) REVERT: G 64 GLU cc_start: 0.8980 (tt0) cc_final: 0.8347 (tm-30) REVERT: G 90 ASP cc_start: 0.8418 (t70) cc_final: 0.8115 (t0) outliers start: 6 outliers final: 5 residues processed: 221 average time/residue: 0.8370 time to fit residues: 198.0264 Evaluate side-chains 150 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 187 HIS Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain K residue 394 ASP Chi-restraints excluded: chain E residue 122 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 303 ASN B 75 HIS B 93 GLN E 76 GLN E 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.054025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.034253 restraints weight = 72709.771| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 2.94 r_work: 0.2400 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16739 Z= 0.198 Angle : 0.813 14.520 23881 Z= 0.460 Chirality : 0.053 0.419 2710 Planarity : 0.005 0.050 1998 Dihedral : 28.491 176.033 4620 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.74 % Favored : 98.09 % Rotamer: Outliers : 3.18 % Allowed : 10.31 % Favored : 86.51 % 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: 1.31 (0.24), residues: 1204 helix: 1.53 (0.19), residues: 778 sheet: 1.66 (0.65), residues: 73 loop : -0.77 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 236 TYR 0.027 0.002 TYR K 214 PHE 0.017 0.002 PHE K 233 TRP 0.006 0.001 TRP K 56 HIS 0.020 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.20 (16739) covalent geometry : angle 0.81326 / 0.46 (23881) hydrogen bonds : bond 0.07281 / 4.87 ( 939) hydrogen bonds : angle 3.69864 / 2.66 ( 2393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7708 (mmm) REVERT: K 329 ASP cc_start: 0.8962 (m-30) cc_final: 0.8528 (p0) REVERT: K 428 MET cc_start: 0.8802 (mtm) cc_final: 0.8473 (mtm) REVERT: K 489 LEU cc_start: 0.9280 (pp) cc_final: 0.8938 (pt) REVERT: A 59 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8506 (mt-10) REVERT: B 20 LYS cc_start: 0.8707 (tppp) cc_final: 0.8248 (tptp) REVERT: B 24 ASP cc_start: 0.8839 (t0) cc_final: 0.8586 (t0) REVERT: C 64 GLU cc_start: 0.9182 (tt0) cc_final: 0.8538 (tp30) REVERT: C 90 ASP cc_start: 0.8749 (t0) cc_final: 0.8379 (t0) REVERT: D 65 ASP cc_start: 0.9501 (t0) cc_final: 0.9245 (t0) REVERT: F 77 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9304 (mttp) REVERT: G 64 GLU cc_start: 0.9193 (tt0) cc_final: 0.8650 (tm-30) REVERT: G 90 ASP cc_start: 0.8548 (t70) cc_final: 0.8226 (t70) REVERT: G 101 THR cc_start: 0.9151 (t) cc_final: 0.8930 (p) REVERT: H 73 GLU cc_start: 0.9505 (tp30) cc_final: 0.9283 (mm-30) outliers start: 33 outliers final: 7 residues processed: 180 average time/residue: 0.7876 time to fit residues: 152.7746 Evaluate side-chains 150 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 187 HIS Chi-restraints excluded: chain K residue 214 TYR Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 77 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 139 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.053840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033928 restraints weight = 73052.129| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 2.95 r_work: 0.2400 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16739 Z= 0.172 Angle : 0.719 10.438 23881 Z= 0.406 Chirality : 0.049 0.384 2710 Planarity : 0.005 0.067 1998 Dihedral : 28.739 176.207 4608 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.91 % Favored : 97.92 % Rotamer: Outliers : 3.18 % Allowed : 13.10 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.25), residues: 1204 helix: 1.90 (0.19), residues: 786 sheet: 1.39 (0.61), residues: 77 loop : -0.89 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 116 TYR 0.020 0.002 TYR K 214 PHE 0.013 0.001 PHE K 225 TRP 0.006 0.001 TRP K 110 HIS 0.009 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (16739) covalent geometry : angle 0.71864 / 0.41 (23881) hydrogen bonds : bond 0.06336 / 4.25 ( 939) hydrogen bonds : angle 3.38580 / 2.42 ( 2393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: K 112 GLU cc_start: 0.9494 (tp30) cc_final: 0.9265 (tp30) REVERT: K 113 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8776 (pm20) REVERT: K 329 ASP cc_start: 0.8945 (m-30) cc_final: 0.8426 (p0) REVERT: K 428 MET cc_start: 0.8862 (mtm) cc_final: 0.8570 (ptp) REVERT: K 450 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8957 (mm-40) REVERT: B 20 LYS cc_start: 0.8822 (tppp) cc_final: 0.8402 (tptp) REVERT: B 24 ASP cc_start: 0.8805 (t0) cc_final: 0.8557 (t0) REVERT: C 64 GLU cc_start: 0.9195 (tt0) cc_final: 0.8670 (tp30) REVERT: C 72 ASP cc_start: 0.8817 (m-30) cc_final: 0.8583 (m-30) REVERT: C 90 ASP cc_start: 0.8746 (t0) cc_final: 0.8256 (t0) REVERT: D 65 ASP cc_start: 0.9511 (t0) cc_final: 0.9242 (t0) REVERT: D 102 GLU cc_start: 0.8530 (pm20) cc_final: 0.8306 (pm20) REVERT: E 59 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: E 73 GLU cc_start: 0.9298 (tm-30) cc_final: 0.9030 (tt0) REVERT: F 59 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8822 (ttmt) REVERT: G 64 GLU cc_start: 0.9255 (tt0) cc_final: 0.8751 (tm-30) REVERT: G 90 ASP cc_start: 0.8601 (t70) cc_final: 0.8284 (t70) REVERT: G 101 THR cc_start: 0.9154 (t) cc_final: 0.8941 (p) REVERT: H 73 GLU cc_start: 0.9566 (tp30) cc_final: 0.9345 (mm-30) outliers start: 33 outliers final: 12 residues processed: 173 average time/residue: 0.8615 time to fit residues: 160.1236 Evaluate side-chains 153 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain H residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 127 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS B 93 GLN D 44 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.032446 restraints weight = 73519.729| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 2.95 r_work: 0.2341 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 16739 Z= 0.278 Angle : 0.772 11.047 23881 Z= 0.420 Chirality : 0.050 0.310 2710 Planarity : 0.005 0.050 1998 Dihedral : 29.009 176.717 4606 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.16 % Favored : 97.67 % Rotamer: Outliers : 2.89 % Allowed : 13.39 % Favored : 83.72 % 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: 1.49 (0.25), residues: 1204 helix: 1.87 (0.19), residues: 785 sheet: 1.04 (0.60), residues: 77 loop : -1.14 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.043 0.002 TYR K 214 PHE 0.013 0.002 PHE K 225 TRP 0.005 0.001 TRP K 168 HIS 0.015 0.001 HIS K 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.28 (16739) covalent geometry : angle 0.77182 / 0.42 (23881) hydrogen bonds : bond 0.07074 / 4.73 ( 939) hydrogen bonds : angle 3.62042 / 2.58 ( 2393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: K 73 MET cc_start: 0.8092 (mmm) cc_final: 0.7444 (mpt) REVERT: K 112 GLU cc_start: 0.9476 (tp30) cc_final: 0.9275 (tp30) REVERT: K 113 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8834 (pm20) REVERT: K 227 LYS cc_start: 0.9362 (mppt) cc_final: 0.9152 (tmtt) REVERT: K 428 MET cc_start: 0.8870 (mtm) cc_final: 0.8510 (mtm) REVERT: A 59 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8790 (pm20) REVERT: B 20 LYS cc_start: 0.8823 (tppp) cc_final: 0.8451 (tptp) REVERT: B 24 ASP cc_start: 0.8856 (t0) cc_final: 0.8601 (t0) REVERT: B 40 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.7794 (ttp-170) REVERT: C 64 GLU cc_start: 0.9212 (tt0) cc_final: 0.8615 (tp30) REVERT: C 72 ASP cc_start: 0.8841 (m-30) cc_final: 0.8539 (m-30) REVERT: C 90 ASP cc_start: 0.8964 (t0) cc_final: 0.8224 (t0) REVERT: D 65 ASP cc_start: 0.9521 (t0) cc_final: 0.9258 (t0) REVERT: E 59 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8744 (pm20) REVERT: G 64 GLU cc_start: 0.9250 (tt0) cc_final: 0.8792 (tm-30) outliers start: 30 outliers final: 11 residues processed: 161 average time/residue: 0.8950 time to fit residues: 154.7489 Evaluate side-chains 145 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS D 44 GLN G 73 ASN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.053157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.033106 restraints weight = 73122.416| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 2.93 r_work: 0.2377 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16739 Z= 0.183 Angle : 0.694 12.269 23881 Z= 0.385 Chirality : 0.046 0.264 2710 Planarity : 0.004 0.046 1998 Dihedral : 28.891 176.446 4606 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 3.37 % Allowed : 14.93 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.25), residues: 1204 helix: 2.03 (0.19), residues: 785 sheet: 0.95 (0.60), residues: 77 loop : -1.03 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.036 0.001 TYR K 214 PHE 0.010 0.001 PHE K 415 TRP 0.003 0.000 TRP K 168 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (16739) covalent geometry : angle 0.69405 / 0.38 (23881) hydrogen bonds : bond 0.06038 / 4.04 ( 939) hydrogen bonds : angle 3.35522 / 2.39 ( 2393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 112 GLU cc_start: 0.9474 (tp30) cc_final: 0.9229 (tp30) REVERT: K 187 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8369 (t-170) REVERT: K 214 TYR cc_start: 0.8398 (p90) cc_final: 0.8174 (p90) REVERT: K 428 MET cc_start: 0.8917 (mtm) cc_final: 0.8580 (mtm) REVERT: B 20 LYS cc_start: 0.8855 (tppp) cc_final: 0.8533 (tptp) REVERT: B 24 ASP cc_start: 0.8815 (t0) cc_final: 0.8563 (t0) REVERT: B 40 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.7596 (ttp-170) REVERT: C 64 GLU cc_start: 0.9207 (tt0) cc_final: 0.8644 (tp30) REVERT: C 72 ASP cc_start: 0.8796 (m-30) cc_final: 0.8488 (m-30) REVERT: C 90 ASP cc_start: 0.8859 (t0) cc_final: 0.8368 (t0) REVERT: D 65 ASP cc_start: 0.9515 (t0) cc_final: 0.9280 (t0) REVERT: D 102 GLU cc_start: 0.8506 (pm20) cc_final: 0.8034 (pm20) REVERT: E 59 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8679 (pm20) REVERT: E 73 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9044 (tt0) REVERT: E 120 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8916 (mtp) REVERT: G 64 GLU cc_start: 0.9247 (tt0) cc_final: 0.8798 (tm-30) outliers start: 35 outliers final: 11 residues processed: 167 average time/residue: 0.8593 time to fit residues: 154.4436 Evaluate side-chains 147 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 187 HIS Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 111 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 chunk 123 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.033222 restraints weight = 73267.958| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 2.96 r_work: 0.2393 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16739 Z= 0.183 Angle : 0.688 12.215 23881 Z= 0.379 Chirality : 0.045 0.338 2710 Planarity : 0.004 0.059 1998 Dihedral : 28.856 176.507 4606 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 2.99 % Allowed : 15.70 % Favored : 81.31 % 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: 1.72 (0.25), residues: 1204 helix: 2.07 (0.19), residues: 786 sheet: 0.84 (0.61), residues: 77 loop : -1.04 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.034 0.001 TYR K 214 PHE 0.009 0.001 PHE B 61 TRP 0.004 0.001 TRP K 168 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (16739) covalent geometry : angle 0.68793 / 0.38 (23881) hydrogen bonds : bond 0.05791 / 3.89 ( 939) hydrogen bonds : angle 3.29052 / 2.35 ( 2393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8905 (pm20) REVERT: K 428 MET cc_start: 0.8938 (mtm) cc_final: 0.8576 (mtm) REVERT: A 59 GLU cc_start: 0.8984 (pt0) cc_final: 0.8678 (pm20) REVERT: B 20 LYS cc_start: 0.8882 (tppp) cc_final: 0.8473 (tptp) REVERT: B 24 ASP cc_start: 0.8812 (t0) cc_final: 0.8578 (t0) REVERT: C 64 GLU cc_start: 0.9208 (tt0) cc_final: 0.8671 (tp30) REVERT: C 72 ASP cc_start: 0.8782 (m-30) cc_final: 0.8474 (m-30) REVERT: C 90 ASP cc_start: 0.8990 (t0) cc_final: 0.8308 (t0) REVERT: C 92 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8376 (mt-10) REVERT: D 65 ASP cc_start: 0.9522 (t0) cc_final: 0.9300 (t0) REVERT: E 59 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8722 (pm20) REVERT: E 73 GLU cc_start: 0.9436 (tm-30) cc_final: 0.9001 (tt0) REVERT: F 22 LEU cc_start: 0.8477 (mt) cc_final: 0.8151 (mp) REVERT: F 85 ASP cc_start: 0.9419 (m-30) cc_final: 0.9138 (m-30) REVERT: G 64 GLU cc_start: 0.9262 (tt0) cc_final: 0.8844 (tm-30) REVERT: H 102 GLU cc_start: 0.8633 (tp30) cc_final: 0.8160 (tm-30) outliers start: 31 outliers final: 14 residues processed: 164 average time/residue: 0.8447 time to fit residues: 149.0836 Evaluate side-chains 148 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 91 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 26 optimal weight: 30.0000 chunk 54 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.053228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033437 restraints weight = 72566.998| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 2.94 r_work: 0.2403 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16739 Z= 0.171 Angle : 0.673 11.670 23881 Z= 0.372 Chirality : 0.044 0.289 2710 Planarity : 0.004 0.055 1998 Dihedral : 28.840 176.498 4606 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 2.31 % Allowed : 17.05 % Favored : 80.64 % 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: 1.82 (0.25), residues: 1204 helix: 2.15 (0.19), residues: 785 sheet: 0.82 (0.61), residues: 77 loop : -1.00 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 23 TYR 0.026 0.001 TYR K 214 PHE 0.009 0.001 PHE B 61 TRP 0.003 0.001 TRP K 168 HIS 0.017 0.001 HIS K 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (16739) covalent geometry : angle 0.67341 / 0.37 (23881) hydrogen bonds : bond 0.05568 / 3.74 ( 939) hydrogen bonds : angle 3.23880 / 2.29 ( 2393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8911 (pm20) REVERT: K 310 LYS cc_start: 0.9101 (mptt) cc_final: 0.8725 (mmmt) REVERT: K 372 MET cc_start: 0.8093 (mtm) cc_final: 0.7683 (mpt) REVERT: K 428 MET cc_start: 0.8976 (mtm) cc_final: 0.8638 (mtm) REVERT: A 59 GLU cc_start: 0.8994 (pt0) cc_final: 0.8682 (pm20) REVERT: B 20 LYS cc_start: 0.8887 (tppp) cc_final: 0.8461 (tmtt) REVERT: B 24 ASP cc_start: 0.8798 (t0) cc_final: 0.8573 (t0) REVERT: C 64 GLU cc_start: 0.9193 (tt0) cc_final: 0.8677 (tp30) REVERT: C 72 ASP cc_start: 0.8787 (m-30) cc_final: 0.8490 (m-30) REVERT: C 90 ASP cc_start: 0.8905 (t0) cc_final: 0.8226 (t0) REVERT: D 65 ASP cc_start: 0.9524 (t0) cc_final: 0.9308 (t0) REVERT: E 59 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8776 (pm20) REVERT: E 105 GLU cc_start: 0.9266 (tt0) cc_final: 0.8946 (tp30) REVERT: F 85 ASP cc_start: 0.9418 (m-30) cc_final: 0.9112 (m-30) REVERT: G 64 GLU cc_start: 0.9252 (tt0) cc_final: 0.8839 (tm-30) outliers start: 24 outliers final: 14 residues processed: 155 average time/residue: 0.8796 time to fit residues: 146.5616 Evaluate side-chains 149 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 141 optimal weight: 30.0000 chunk 115 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 HIS A 68 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.053494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033504 restraints weight = 73996.055| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 3.00 r_work: 0.2409 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16739 Z= 0.161 Angle : 0.661 11.894 23881 Z= 0.366 Chirality : 0.043 0.281 2710 Planarity : 0.004 0.055 1998 Dihedral : 28.794 176.093 4606 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.99 % Favored : 97.84 % Rotamer: Outliers : 2.22 % Allowed : 17.82 % Favored : 79.96 % 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: 1.90 (0.25), residues: 1204 helix: 2.23 (0.19), residues: 783 sheet: 0.87 (0.62), residues: 77 loop : -0.98 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 23 TYR 0.026 0.001 TYR K 214 PHE 0.009 0.001 PHE B 61 TRP 0.004 0.001 TRP K 168 HIS 0.015 0.001 HIS K 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (16739) covalent geometry : angle 0.66129 / 0.37 (23881) hydrogen bonds : bond 0.05228 / 3.52 ( 939) hydrogen bonds : angle 3.14248 / 2.23 ( 2393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8879 (pm20) REVERT: K 310 LYS cc_start: 0.9121 (mptt) cc_final: 0.8715 (mmmt) REVERT: K 372 MET cc_start: 0.8157 (mtm) cc_final: 0.7633 (mpt) REVERT: K 383 MET cc_start: 0.8833 (tpp) cc_final: 0.8630 (tpt) REVERT: K 428 MET cc_start: 0.8982 (mtm) cc_final: 0.8588 (mtm) REVERT: A 59 GLU cc_start: 0.9061 (pt0) cc_final: 0.8771 (pm20) REVERT: B 20 LYS cc_start: 0.8928 (tppp) cc_final: 0.8559 (tptp) REVERT: B 24 ASP cc_start: 0.8765 (t0) cc_final: 0.8554 (t0) REVERT: C 64 GLU cc_start: 0.9202 (tt0) cc_final: 0.8733 (tp30) REVERT: C 79 ILE cc_start: 0.9192 (pt) cc_final: 0.8983 (pp) REVERT: C 90 ASP cc_start: 0.8961 (t0) cc_final: 0.8348 (t0) REVERT: D 65 ASP cc_start: 0.9517 (t0) cc_final: 0.9315 (t0) REVERT: D 102 GLU cc_start: 0.8449 (pm20) cc_final: 0.8184 (pm20) REVERT: E 59 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8769 (pm20) REVERT: E 73 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9099 (tt0) REVERT: E 105 GLU cc_start: 0.9259 (tt0) cc_final: 0.8960 (tp30) REVERT: F 22 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8172 (mp) REVERT: F 85 ASP cc_start: 0.9398 (m-30) cc_final: 0.9096 (m-30) REVERT: G 64 GLU cc_start: 0.9248 (tt0) cc_final: 0.8852 (tm-30) REVERT: H 102 GLU cc_start: 0.8562 (tp30) cc_final: 0.8035 (tm-30) outliers start: 23 outliers final: 13 residues processed: 158 average time/residue: 0.8859 time to fit residues: 150.4486 Evaluate side-chains 149 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 70 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 0.0570 chunk 131 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 139 optimal weight: 30.0000 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 144 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033377 restraints weight = 73192.480| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 2.97 r_work: 0.2407 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16739 Z= 0.171 Angle : 0.668 11.504 23881 Z= 0.369 Chirality : 0.043 0.262 2710 Planarity : 0.004 0.065 1998 Dihedral : 28.805 175.772 4606 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 2.70 % Allowed : 18.11 % Favored : 79.19 % 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 (0.25), residues: 1204 helix: 2.29 (0.19), residues: 781 sheet: 0.69 (0.62), residues: 79 loop : -0.97 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.016 0.001 TYR F 88 PHE 0.009 0.001 PHE B 61 TRP 0.004 0.001 TRP K 168 HIS 0.006 0.001 HIS K 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (16739) covalent geometry : angle 0.66824 / 0.37 (23881) hydrogen bonds : bond 0.05278 / 3.55 ( 939) hydrogen bonds : angle 3.14545 / 2.22 ( 2393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8828 (pm20) REVERT: K 310 LYS cc_start: 0.9084 (mptt) cc_final: 0.8733 (mmpt) REVERT: K 372 MET cc_start: 0.8160 (mtm) cc_final: 0.7661 (mpt) REVERT: K 428 MET cc_start: 0.8973 (mtm) cc_final: 0.8568 (mtm) REVERT: A 59 GLU cc_start: 0.9043 (pt0) cc_final: 0.8762 (pm20) REVERT: B 20 LYS cc_start: 0.8939 (tppp) cc_final: 0.8575 (tptp) REVERT: B 24 ASP cc_start: 0.8768 (t0) cc_final: 0.8538 (t0) REVERT: C 64 GLU cc_start: 0.9199 (tt0) cc_final: 0.8716 (tp30) REVERT: C 79 ILE cc_start: 0.9184 (pt) cc_final: 0.8968 (pp) REVERT: C 90 ASP cc_start: 0.9002 (t0) cc_final: 0.8442 (t0) REVERT: C 92 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8649 (mp0) REVERT: D 65 ASP cc_start: 0.9517 (t0) cc_final: 0.9306 (t0) REVERT: E 59 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: E 73 GLU cc_start: 0.9484 (tm-30) cc_final: 0.9116 (tt0) REVERT: E 105 GLU cc_start: 0.9242 (tt0) cc_final: 0.8943 (tp30) REVERT: F 22 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8305 (mp) REVERT: F 85 ASP cc_start: 0.9416 (m-30) cc_final: 0.9115 (m-30) REVERT: G 64 GLU cc_start: 0.9240 (tt0) cc_final: 0.8827 (tm-30) outliers start: 28 outliers final: 15 residues processed: 155 average time/residue: 0.8542 time to fit residues: 142.7132 Evaluate side-chains 155 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 143 optimal weight: 30.0000 chunk 100 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 21 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 126 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN E 68 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.032854 restraints weight = 73032.955| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 2.95 r_work: 0.2379 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16739 Z= 0.217 Angle : 0.705 11.821 23881 Z= 0.383 Chirality : 0.045 0.365 2710 Planarity : 0.004 0.063 1998 Dihedral : 28.875 175.359 4606 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.49 % Favored : 97.34 % Rotamer: Outliers : 1.83 % Allowed : 18.88 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.25), residues: 1204 helix: 2.20 (0.19), residues: 778 sheet: 0.55 (0.62), residues: 79 loop : -1.02 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.017 0.001 TYR F 88 PHE 0.010 0.001 PHE B 61 TRP 0.004 0.001 TRP K 168 HIS 0.008 0.001 HIS K 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (16739) covalent geometry : angle 0.70535 / 0.38 (23881) hydrogen bonds : bond 0.05819 / 3.90 ( 939) hydrogen bonds : angle 3.30364 / 2.33 ( 2393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8867 (pm20) REVERT: K 310 LYS cc_start: 0.9099 (mptt) cc_final: 0.8731 (mmpt) REVERT: K 372 MET cc_start: 0.8230 (mtm) cc_final: 0.7629 (mpt) REVERT: K 428 MET cc_start: 0.8995 (mtm) cc_final: 0.8626 (mtm) REVERT: K 489 LEU cc_start: 0.9495 (tm) cc_final: 0.9282 (pp) REVERT: A 59 GLU cc_start: 0.9071 (pt0) cc_final: 0.8787 (pm20) REVERT: B 20 LYS cc_start: 0.8971 (tppp) cc_final: 0.8572 (tmtt) REVERT: B 24 ASP cc_start: 0.8820 (t0) cc_final: 0.8591 (t0) REVERT: C 41 GLU cc_start: 0.9196 (tt0) cc_final: 0.8951 (tm-30) REVERT: C 64 GLU cc_start: 0.9198 (tt0) cc_final: 0.8715 (tp30) REVERT: C 90 ASP cc_start: 0.9081 (t0) cc_final: 0.8675 (t0) REVERT: D 65 ASP cc_start: 0.9535 (t0) cc_final: 0.9325 (t0) REVERT: E 59 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8906 (pm20) REVERT: E 105 GLU cc_start: 0.9256 (tt0) cc_final: 0.8938 (tp30) REVERT: F 85 ASP cc_start: 0.9400 (m-30) cc_final: 0.9110 (m-30) REVERT: G 64 GLU cc_start: 0.9245 (tt0) cc_final: 0.8844 (tm-30) REVERT: H 102 GLU cc_start: 0.8608 (tp30) cc_final: 0.8166 (tm-30) outliers start: 19 outliers final: 14 residues processed: 150 average time/residue: 0.8909 time to fit residues: 143.8500 Evaluate side-chains 147 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 135 CYS Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 239 ASP Chi-restraints excluded: chain K residue 293 ILE Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 113 optimal weight: 4.9990 chunk 139 optimal weight: 30.0000 chunk 138 optimal weight: 30.0000 chunk 64 optimal weight: 0.0050 chunk 119 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 overall best weight: 6.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.052480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.032358 restraints weight = 72669.628| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 2.94 r_work: 0.2359 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16739 Z= 0.250 Angle : 0.736 10.820 23881 Z= 0.397 Chirality : 0.046 0.322 2710 Planarity : 0.004 0.064 1998 Dihedral : 28.938 174.794 4606 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.66 % Favored : 97.18 % Rotamer: Outliers : 1.73 % Allowed : 19.46 % Favored : 78.81 % 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: 1.72 (0.25), residues: 1204 helix: 2.11 (0.19), residues: 781 sheet: 0.47 (0.61), residues: 79 loop : -1.02 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.018 0.001 TYR F 88 PHE 0.011 0.001 PHE B 61 TRP 0.005 0.001 TRP K 168 HIS 0.008 0.001 HIS K 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (16739) covalent geometry : angle 0.73636 / 0.40 (23881) hydrogen bonds : bond 0.06112 / 4.10 ( 939) hydrogen bonds : angle 3.41080 / 2.41 ( 2393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5365.26 seconds wall clock time: 92 minutes 5.66 seconds (5525.66 seconds total)