Starting phenix.real_space_refine on Thu Aug 6 09:57:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg5_37503/08_2026/8wg5_37503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg5_37503/08_2026/8wg5_37503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wg5_37503/08_2026/8wg5_37503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg5_37503/08_2026/8wg5_37503.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg5_37503/08_2026/8wg5_37503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg5_37503/08_2026/8wg5_37503.cif" } resolution = 3.05 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= 0.000 sd= 0.002 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 294 5.49 5 S 30 5.16 5 C 8509 2.51 5 N 2765 2.21 5 O 3367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 14965 Number of models: 1 Model: "" Number of chains: 12 Chain: "M" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2319 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 281} Chain breaks: 7 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 849 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" 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: "E" 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: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "U" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.95, per 1000 atoms: 0.20 Number of scatterers: 14965 At special positions: 0 Unit cell: (118.14, 113.844, 119.214, 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 30 16.00 P 294 15.00 O 3367 8.00 N 2765 7.00 C 8509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 467.0 milliseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 16 sheets defined 60.6% alpha, 10.7% beta 146 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'M' and resid 204 through 216 removed outlier: 3.623A pdb=" N GLN M 216 " --> pdb=" O GLN M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 229 removed outlier: 3.782A pdb=" N ARG M 221 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU M 222 " --> pdb=" O PRO M 218 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU M 223 " --> pdb=" O VAL M 219 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS M 225 " --> pdb=" O ARG M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 270 removed outlier: 3.632A pdb=" N MET M 261 " --> pdb=" O LEU M 257 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU M 265 " --> pdb=" O MET M 261 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN M 266 " --> pdb=" O SER M 262 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN M 269 " --> pdb=" O LEU M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 278 through 289 removed outlier: 3.627A pdb=" N PHE M 282 " --> pdb=" O PRO M 278 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS M 287 " --> pdb=" O SER M 283 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS M 288 " --> pdb=" O GLN M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 293 Processing helix chain 'M' and resid 299 through 328 removed outlier: 3.717A pdb=" N TYR M 306 " --> pdb=" O GLU M 302 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG M 312 " --> pdb=" O LEU M 308 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU M 315 " --> pdb=" O MET M 311 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER M 320 " --> pdb=" O HIS M 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE M 323 " --> pdb=" O VAL M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 348 removed outlier: 3.535A pdb=" N LYS M 348 " --> pdb=" O ASP M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 358 Processing helix chain 'M' and resid 632 through 641 removed outlier: 3.601A pdb=" N THR M 641 " --> pdb=" O LEU M 637 " (cutoff:3.500A) Processing helix chain 'M' and resid 805 through 811 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.085A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.085A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.155A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.517A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.513A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.711A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.557A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.638A 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 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.944A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.381A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.565A 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 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.656A pdb=" N LYS U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 41 removed outlier: 3.743A pdb=" N GLN U 40 " --> pdb=" O PRO U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'M' and resid 197 through 198 removed outlier: 6.668A pdb=" N GLY M 197 " --> pdb=" O VAL M 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 378 through 382 removed outlier: 6.793A pdb=" N GLU M 362 " --> pdb=" O SER M 687 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 385 through 387 removed outlier: 6.773A pdb=" N TYR M 815 " --> pdb=" O LEU M 697 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL M 748 " --> pdb=" O TYR M 815 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU M 817 " --> pdb=" O GLY M 746 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY M 746 " --> pdb=" O LEU M 817 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TYR M 819 " --> pdb=" O LEU M 744 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU M 744 " --> pdb=" O TYR M 819 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG M 821 " --> pdb=" O TYR M 742 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TYR M 742 " --> pdb=" O ARG M 821 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 385 through 387 removed outlier: 6.773A pdb=" N TYR M 815 " --> pdb=" O LEU M 697 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL M 748 " --> pdb=" O TYR M 815 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU M 817 " --> pdb=" O GLY M 746 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY M 746 " --> pdb=" O LEU M 817 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TYR M 819 " --> pdb=" O LEU M 744 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU M 744 " --> pdb=" O TYR M 819 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG M 821 " --> pdb=" O TYR M 742 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TYR M 742 " --> pdb=" O ARG M 821 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR M 745 " --> pdb=" O LYS M 764 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA M 763 " --> pdb=" O PHE M 794 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 700 through 703 removed outlier: 3.511A pdb=" N GLN M 701 " --> pdb=" O ARG M 708 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.940A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.752A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.512A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.693A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.815A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.536A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.432A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB7, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.967A pdb=" N ARG U 42 " --> pdb=" O VAL U 70 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 1.40 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: 2959 1.33 - 1.45: 4838 1.45 - 1.57: 7393 1.57 - 1.69: 586 1.69 - 1.82: 49 Bond restraints: 15825 Sorted by residual: bond pdb=" C3' DG I -22 " pdb=" C2' DG I -22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA J -22 " pdb=" C2' DA J -22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.54e+00 bond pdb=" C3' DC J 66 " pdb=" C2' DC J 66 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.94e+00 ... (remaining 15820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 21110 1.40 - 2.80: 1379 2.80 - 4.20: 109 4.20 - 5.60: 18 5.60 - 7.00: 11 Bond angle restraints: 22627 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.71 108.01 5.70 9.50e-01 1.11e+00 3.60e+01 angle pdb=" O4' DA I 47 " pdb=" C4' DA I 47 " pdb=" C3' DA I 47 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.28e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT J 71 " pdb=" C4 DT J 71 " pdb=" O4 DT J 71 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 22622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 7382 35.98 - 71.96: 1388 71.96 - 107.94: 12 107.94 - 143.92: 2 143.92 - 179.90: 2 Dihedral angle restraints: 8786 sinusoidal: 5501 harmonic: 3285 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 40.10 179.90 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual -140.00 33.52 -173.52 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual 180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 8783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1904 0.045 - 0.090: 509 0.090 - 0.136: 165 0.136 - 0.181: 7 0.181 - 0.226: 2 Chirality restraints: 2587 Sorted by residual: chirality pdb=" CA GLU G 61 " pdb=" N GLU G 61 " pdb=" C GLU G 61 " pdb=" CB GLU G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' DT I 15 " pdb=" C4' DT I 15 " pdb=" O3' DT I 15 " pdb=" C2' DT I 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 2584 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.021 2.00e-02 2.50e+03 2.11e-02 8.90e+00 pdb=" CG TYR D 83 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 83 " 0.017 2.00e-02 2.50e+03 1.87e-02 7.02e+00 pdb=" CG TYR H 83 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR H 83 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR H 83 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR H 83 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR H 83 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 83 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 83 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE U 36 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO U 37 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO U 37 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO U 37 " 0.035 5.00e-02 4.00e+02 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 363 2.66 - 3.22: 13390 3.22 - 3.78: 28189 3.78 - 4.34: 35412 4.34 - 4.90: 51250 Nonbonded interactions: 128604 Sorted by model distance: nonbonded pdb=" OG SER M 320 " pdb=" OE1 GLU M 346 " model vdw 2.099 3.040 nonbonded pdb=" OE1 GLU M 362 " pdb=" OG SER M 687 " model vdw 2.103 3.040 nonbonded pdb=" N2 DG I -10 " pdb=" O2 DC J 10 " model vdw 2.117 2.496 nonbonded pdb=" O PRO M 690 " pdb=" OH TYR M 742 " model vdw 2.136 3.040 nonbonded pdb=" NZ LYS M 288 " pdb=" O TYR M 306 " model vdw 2.141 3.120 ... (remaining 128599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.120 Find NCS groups from input model: 0.130 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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 : 0.005 0.056 15825 Z= 0.457 Angle : 0.728 7.004 22627 Z= 0.606 Chirality : 0.045 0.226 2587 Planarity : 0.004 0.064 1848 Dihedral : 26.060 179.903 6658 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.32 % Allowed : 0.11 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 1.36 (0.26), residues: 1101 helix: 1.48 (0.21), residues: 653 sheet: 1.22 (0.57), residues: 85 loop : -0.12 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.050 0.002 TYR D 83 PHE 0.010 0.001 PHE M 359 TRP 0.004 0.001 TRP M 793 HIS 0.006 0.001 HIS M 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.46 (15825) covalent geometry : angle 0.72845 / 0.61 (22627) hydrogen bonds : bond 0.13057 / 8.22 ( 894) hydrogen bonds : angle 5.04900 / 3.70 ( 2271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 417 time to evaluate : 0.440 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 259 LEU cc_start: 0.9548 (mt) cc_final: 0.9344 (mt) REVERT: A 46 VAL cc_start: 0.6296 (p) cc_final: 0.5907 (p) REVERT: A 48 LEU cc_start: 0.7597 (mm) cc_final: 0.6990 (mm) REVERT: A 122 LYS cc_start: 0.7564 (pttt) cc_final: 0.7053 (ptmm) REVERT: A 123 ASP cc_start: 0.8097 (m-30) cc_final: 0.7489 (m-30) REVERT: B 50 ILE cc_start: 0.7377 (mm) cc_final: 0.6847 (mm) REVERT: B 80 THR cc_start: 0.6953 (m) cc_final: 0.6299 (m) REVERT: C 61 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7649 (mm-30) REVERT: D 33 ARG cc_start: 0.7223 (mmm160) cc_final: 0.6760 (mmm160) REVERT: D 42 TYR cc_start: 0.6833 (t80) cc_final: 0.6574 (t80) REVERT: D 108 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7915 (tmtt) REVERT: E 73 GLU cc_start: 0.7350 (pt0) cc_final: 0.6822 (pt0) REVERT: F 31 LYS cc_start: 0.8516 (tttm) cc_final: 0.8148 (ttpp) REVERT: G 39 TYR cc_start: 0.8577 (m-80) cc_final: 0.7826 (m-80) outliers start: 3 outliers final: 0 residues processed: 419 average time/residue: 0.1623 time to fit residues: 92.2758 Evaluate side-chains 276 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 212 GLN M 635 HIS M 683 GLN ** M 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 800 HIS C 84 GLN D 95 GLN E 125 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS U 25 ASN U 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.086424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.057836 restraints weight = 57610.367| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.69 r_work: 0.2938 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 15825 Z= 0.334 Angle : 1.022 22.530 22627 Z= 0.543 Chirality : 0.057 0.411 2587 Planarity : 0.009 0.091 1848 Dihedral : 30.233 175.012 4452 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 4.42 % Allowed : 16.11 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: -0.21 (0.24), residues: 1101 helix: 0.11 (0.19), residues: 670 sheet: 0.97 (0.62), residues: 67 loop : -0.58 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG G 99 TYR 0.048 0.005 TYR M 762 PHE 0.026 0.004 PHE B 61 TRP 0.025 0.015 TRP M 793 HIS 0.021 0.003 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.33 (15825) covalent geometry : angle 1.02181 / 0.54 (22627) hydrogen bonds : bond 0.08088 / 5.31 ( 894) hydrogen bonds : angle 4.63443 / 3.35 ( 2271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 311 time to evaluate : 0.531 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 222 GLU cc_start: 0.8203 (mp0) cc_final: 0.7949 (pm20) REVERT: M 280 GLU cc_start: 0.9037 (pm20) cc_final: 0.8837 (pm20) REVERT: M 281 LEU cc_start: 0.8872 (tt) cc_final: 0.8101 (tt) REVERT: M 309 ASP cc_start: 0.7975 (p0) cc_final: 0.7620 (p0) REVERT: M 643 ASN cc_start: 0.7091 (t0) cc_final: 0.6770 (t0) REVERT: M 718 GLU cc_start: 0.7590 (pm20) cc_final: 0.6784 (tm-30) REVERT: M 741 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8138 (mm) REVERT: A 48 LEU cc_start: 0.9199 (mm) cc_final: 0.8994 (mm) REVERT: A 73 GLU cc_start: 0.7992 (tt0) cc_final: 0.7787 (tt0) REVERT: B 26 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8305 (tp) REVERT: B 35 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8152 (mtp-110) REVERT: B 87 VAL cc_start: 0.9421 (t) cc_final: 0.9218 (t) REVERT: C 56 GLU cc_start: 0.8508 (tt0) cc_final: 0.8262 (tt0) REVERT: C 61 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8709 (mm-30) REVERT: C 64 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: D 59 MET cc_start: 0.9247 (tpp) cc_final: 0.8925 (tpp) REVERT: D 83 TYR cc_start: 0.8625 (m-10) cc_final: 0.8296 (m-80) REVERT: D 105 GLU cc_start: 0.8475 (pm20) cc_final: 0.8151 (pm20) REVERT: D 108 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8744 (tmtt) REVERT: E 96 CYS cc_start: 0.8966 (m) cc_final: 0.8736 (m) REVERT: E 120 MET cc_start: 0.9151 (mtp) cc_final: 0.8843 (mtm) REVERT: F 25 ASN cc_start: 0.8000 (m110) cc_final: 0.7709 (m110) REVERT: F 31 LYS cc_start: 0.9321 (tttm) cc_final: 0.9002 (tttp) REVERT: F 53 GLU cc_start: 0.9134 (tp30) cc_final: 0.8817 (tp30) REVERT: G 33 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9247 (mm) REVERT: G 57 TYR cc_start: 0.7919 (t80) cc_final: 0.7596 (t80) REVERT: G 92 GLU cc_start: 0.8608 (tt0) cc_final: 0.8260 (tt0) REVERT: H 34 LYS cc_start: 0.8732 (mppt) cc_final: 0.8226 (mptt) REVERT: H 105 GLU cc_start: 0.8880 (tp30) cc_final: 0.8651 (tp30) REVERT: H 108 LYS cc_start: 0.9332 (pptt) cc_final: 0.8997 (ptpp) REVERT: U 1 MET cc_start: 0.6925 (ptt) cc_final: 0.6546 (ttt) REVERT: U 27 LYS cc_start: 0.8453 (ptpp) cc_final: 0.8078 (ptpp) outliers start: 42 outliers final: 22 residues processed: 336 average time/residue: 0.1565 time to fit residues: 71.7211 Evaluate side-chains 295 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 264 PHE Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 719 ILE Chi-restraints excluded: chain M residue 741 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain U residue 25 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 75 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 212 GLN M 635 HIS ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 55 GLN F 25 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.087050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058642 restraints weight = 58833.131| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.74 r_work: 0.2937 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15825 Z= 0.156 Angle : 0.665 9.935 22627 Z= 0.376 Chirality : 0.043 0.338 2587 Planarity : 0.005 0.054 1848 Dihedral : 30.081 176.418 4448 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.16 % Allowed : 20.95 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.80 (0.25), residues: 1101 helix: 1.07 (0.20), residues: 674 sheet: 0.62 (0.61), residues: 79 loop : -0.40 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 35 TYR 0.028 0.002 TYR G 57 PHE 0.017 0.001 PHE M 716 TRP 0.006 0.003 TRP M 793 HIS 0.006 0.001 HIS M 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (15825) covalent geometry : angle 0.66546 / 0.38 (22627) hydrogen bonds : bond 0.05018 / 3.38 ( 894) hydrogen bonds : angle 3.81853 / 2.77 ( 2271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 0.418 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: symmetry clash revert: symmetry clash REVERT: M 309 ASP cc_start: 0.7906 (p0) cc_final: 0.7586 (p0) REVERT: M 643 ASN cc_start: 0.6949 (t0) cc_final: 0.6648 (t0) REVERT: M 684 MET cc_start: 0.7937 (mmm) cc_final: 0.7655 (mmp) REVERT: M 718 GLU cc_start: 0.7468 (pm20) cc_final: 0.6716 (tm-30) REVERT: M 744 LEU cc_start: 0.6539 (tp) cc_final: 0.6275 (tp) REVERT: A 59 GLU cc_start: 0.7364 (pm20) cc_final: 0.7092 (pm20) REVERT: A 85 GLN cc_start: 0.7685 (mm110) cc_final: 0.6910 (mt0) REVERT: B 26 ILE cc_start: 0.8731 (mp) cc_final: 0.8389 (tp) REVERT: B 31 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8299 (ttpp) REVERT: C 50 TYR cc_start: 0.8983 (t80) cc_final: 0.8726 (t80) REVERT: C 61 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8722 (mm-30) REVERT: C 92 GLU cc_start: 0.7472 (tp30) cc_final: 0.7102 (tp30) REVERT: C 94 ASN cc_start: 0.8928 (t0) cc_final: 0.8705 (t0) REVERT: C 104 GLN cc_start: 0.9192 (mp10) cc_final: 0.8396 (mp10) REVERT: D 59 MET cc_start: 0.9230 (tpp) cc_final: 0.8953 (tpp) REVERT: D 71 GLU cc_start: 0.9074 (tp30) cc_final: 0.8809 (tp30) REVERT: D 76 GLU cc_start: 0.8938 (tp30) cc_final: 0.8710 (tp30) REVERT: D 79 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8310 (mtm-85) REVERT: D 105 GLU cc_start: 0.8427 (pm20) cc_final: 0.8088 (pm20) REVERT: D 108 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8849 (tmtt) REVERT: G 33 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9150 (mm) REVERT: H 34 LYS cc_start: 0.8533 (mppt) cc_final: 0.8312 (mptt) REVERT: H 105 GLU cc_start: 0.8778 (tp30) cc_final: 0.8470 (tp30) REVERT: H 108 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8910 (ptpp) REVERT: U 25 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8806 (p0) REVERT: U 27 LYS cc_start: 0.8396 (ptpp) cc_final: 0.7926 (ptpp) REVERT: U 48 LYS cc_start: 0.4514 (OUTLIER) cc_final: 0.4287 (mmtt) outliers start: 30 outliers final: 16 residues processed: 308 average time/residue: 0.1487 time to fit residues: 63.5648 Evaluate side-chains 285 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 286 CYS Chi-restraints excluded: chain M residue 311 MET Chi-restraints excluded: chain M residue 358 ILE Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 719 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain U residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 18 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 101 optimal weight: 30.0000 chunk 127 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 696 HIS B 27 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** H 49 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 = 0.3861 r_free = 0.3861 target = 0.086187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057291 restraints weight = 57529.727| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.65 r_work: 0.2897 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15825 Z= 0.155 Angle : 0.635 10.328 22627 Z= 0.362 Chirality : 0.043 0.351 2587 Planarity : 0.004 0.054 1848 Dihedral : 29.985 176.249 4448 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.53 % Allowed : 20.00 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 1.22 (0.25), residues: 1101 helix: 1.37 (0.20), residues: 677 sheet: 1.03 (0.68), residues: 69 loop : -0.22 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 699 TYR 0.020 0.002 TYR G 57 PHE 0.012 0.001 PHE B 100 TRP 0.008 0.002 TRP M 793 HIS 0.014 0.001 HIS M 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (15825) covalent geometry : angle 0.63512 / 0.36 (22627) hydrogen bonds : bond 0.04784 / 3.21 ( 894) hydrogen bonds : angle 3.64965 / 2.66 ( 2271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 0.422 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 284 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8011 (mt0) REVERT: M 309 ASP cc_start: 0.7813 (p0) cc_final: 0.7576 (p0) REVERT: M 643 ASN cc_start: 0.6972 (t0) cc_final: 0.6682 (t0) REVERT: M 718 GLU cc_start: 0.7452 (pm20) cc_final: 0.6668 (tm-30) REVERT: M 744 LEU cc_start: 0.6566 (tp) cc_final: 0.6358 (tp) REVERT: M 766 ARG cc_start: 0.5840 (ptp90) cc_final: 0.5593 (ptp90) REVERT: A 85 GLN cc_start: 0.7628 (mm110) cc_final: 0.7333 (mt0) REVERT: A 123 ASP cc_start: 0.9098 (m-30) cc_final: 0.8891 (m-30) REVERT: B 26 ILE cc_start: 0.8863 (mp) cc_final: 0.8620 (tp) REVERT: B 31 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8472 (ttpp) REVERT: B 88 TYR cc_start: 0.8083 (m-10) cc_final: 0.7615 (m-10) REVERT: C 61 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8786 (mm-30) REVERT: C 92 GLU cc_start: 0.7552 (tp30) cc_final: 0.7024 (tp30) REVERT: C 104 GLN cc_start: 0.9207 (mp10) cc_final: 0.8988 (mm-40) REVERT: C 112 GLN cc_start: 0.9124 (mm110) cc_final: 0.8892 (mm-40) REVERT: D 59 MET cc_start: 0.9236 (tpp) cc_final: 0.9006 (tpp) REVERT: D 68 ASP cc_start: 0.9185 (t70) cc_final: 0.8953 (t0) REVERT: D 79 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8306 (mtm-85) REVERT: D 105 GLU cc_start: 0.8444 (pm20) cc_final: 0.8115 (pm20) REVERT: D 108 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8925 (tmtt) REVERT: E 79 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8336 (ttmm) REVERT: E 125 GLN cc_start: 0.9045 (mp10) cc_final: 0.8844 (mp10) REVERT: G 33 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9178 (mm) REVERT: G 92 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8411 (mt-10) REVERT: H 34 LYS cc_start: 0.8603 (mppt) cc_final: 0.8308 (mptt) REVERT: H 71 GLU cc_start: 0.9110 (tp30) cc_final: 0.8496 (mp0) REVERT: H 105 GLU cc_start: 0.8758 (tp30) cc_final: 0.8418 (tp30) REVERT: H 108 LYS cc_start: 0.9338 (pptt) cc_final: 0.8982 (ptpp) REVERT: U 27 LYS cc_start: 0.8390 (ptpp) cc_final: 0.7851 (ptpp) REVERT: U 76 CYS cc_start: 0.8615 (t) cc_final: 0.8317 (t) outliers start: 43 outliers final: 23 residues processed: 293 average time/residue: 0.1487 time to fit residues: 60.4653 Evaluate side-chains 283 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 719 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 48 LYS Chi-restraints excluded: chain U residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 30.0000 chunk 97 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 29 optimal weight: 0.0670 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.084676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055134 restraints weight = 57168.668| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.61 r_work: 0.2836 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15825 Z= 0.169 Angle : 0.649 10.913 22627 Z= 0.365 Chirality : 0.043 0.352 2587 Planarity : 0.005 0.056 1848 Dihedral : 29.998 175.979 4448 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.32 % Allowed : 21.47 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 1.34 (0.25), residues: 1101 helix: 1.55 (0.20), residues: 675 sheet: 0.81 (0.67), residues: 69 loop : -0.28 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 35 TYR 0.039 0.002 TYR D 83 PHE 0.014 0.001 PHE U 45 TRP 0.002 0.001 TRP M 793 HIS 0.005 0.001 HIS M 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (15825) covalent geometry : angle 0.64865 / 0.36 (22627) hydrogen bonds : bond 0.04821 / 3.25 ( 894) hydrogen bonds : angle 3.54380 / 2.59 ( 2271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.424 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: symmetry clash revert: symmetry clash REVERT: M 643 ASN cc_start: 0.6920 (t0) cc_final: 0.6695 (t0) REVERT: M 684 MET cc_start: 0.7957 (mmm) cc_final: 0.7528 (mmm) REVERT: M 695 LEU cc_start: 0.7828 (mm) cc_final: 0.7540 (mt) REVERT: M 718 GLU cc_start: 0.7509 (pm20) cc_final: 0.6588 (tm-30) REVERT: M 719 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7914 (mp) REVERT: M 766 ARG cc_start: 0.5738 (ptp90) cc_final: 0.5432 (ptp90) REVERT: M 821 ARG cc_start: 0.7143 (tpt90) cc_final: 0.5828 (mmp-170) REVERT: A 73 GLU cc_start: 0.8562 (tt0) cc_final: 0.8106 (tt0) REVERT: B 31 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8537 (ttpp) REVERT: B 88 TYR cc_start: 0.8548 (m-10) cc_final: 0.8075 (m-10) REVERT: C 92 GLU cc_start: 0.7542 (tp30) cc_final: 0.7342 (tp30) REVERT: C 94 ASN cc_start: 0.9098 (t0) cc_final: 0.8848 (t0) REVERT: C 112 GLN cc_start: 0.9103 (mm110) cc_final: 0.8902 (mm-40) REVERT: D 68 ASP cc_start: 0.9253 (t70) cc_final: 0.9021 (t0) REVERT: D 105 GLU cc_start: 0.8463 (pm20) cc_final: 0.8082 (pm20) REVERT: D 108 LYS cc_start: 0.9299 (tmtt) cc_final: 0.9042 (tmtt) REVERT: E 79 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8387 (ttmm) REVERT: E 125 GLN cc_start: 0.9104 (mp10) cc_final: 0.8853 (mp10) REVERT: G 33 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9191 (mm) REVERT: G 64 GLU cc_start: 0.8911 (tp30) cc_final: 0.8616 (tp30) REVERT: G 92 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8596 (mt-10) REVERT: H 34 LYS cc_start: 0.8734 (mppt) cc_final: 0.8416 (mptt) REVERT: H 68 ASP cc_start: 0.9167 (t0) cc_final: 0.8845 (t0) REVERT: H 79 ARG cc_start: 0.8974 (ttp-110) cc_final: 0.8676 (mtm-85) REVERT: H 105 GLU cc_start: 0.8816 (tp30) cc_final: 0.8381 (tp30) REVERT: H 108 LYS cc_start: 0.9322 (pptt) cc_final: 0.8987 (ptpp) REVERT: U 27 LYS cc_start: 0.8477 (ptpp) cc_final: 0.8060 (ptpp) REVERT: U 76 CYS cc_start: 0.8536 (t) cc_final: 0.8253 (t) outliers start: 41 outliers final: 23 residues processed: 290 average time/residue: 0.1594 time to fit residues: 63.7836 Evaluate side-chains 286 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 279 LYS Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 311 MET Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 719 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 76 optimal weight: 0.1980 chunk 115 optimal weight: 30.0000 chunk 18 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 25 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.085238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056137 restraints weight = 56759.179| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.63 r_work: 0.2862 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15825 Z= 0.132 Angle : 0.634 12.448 22627 Z= 0.355 Chirality : 0.043 0.412 2587 Planarity : 0.004 0.052 1848 Dihedral : 29.931 176.358 4448 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.74 % Allowed : 24.11 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 1.42 (0.26), residues: 1101 helix: 1.65 (0.20), residues: 676 sheet: 0.84 (0.63), residues: 78 loop : -0.37 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.016 0.001 TYR C 50 PHE 0.011 0.001 PHE A 67 TRP 0.002 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (15825) covalent geometry : angle 0.63435 / 0.35 (22627) hydrogen bonds : bond 0.04330 / 2.94 ( 894) hydrogen bonds : angle 3.43690 / 2.51 ( 2271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.424 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 284 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8557 (mm110) REVERT: M 643 ASN cc_start: 0.7012 (t0) cc_final: 0.6800 (t0) REVERT: M 718 GLU cc_start: 0.7494 (pm20) cc_final: 0.6567 (tm-30) REVERT: M 719 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7991 (mp) REVERT: M 766 ARG cc_start: 0.5784 (ptp90) cc_final: 0.5493 (ptp90) REVERT: M 821 ARG cc_start: 0.7384 (tpt90) cc_final: 0.6047 (mmp-170) REVERT: C 61 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8935 (mm-30) REVERT: C 73 ASN cc_start: 0.9133 (t0) cc_final: 0.8899 (t0) REVERT: C 78 ILE cc_start: 0.8713 (pt) cc_final: 0.8436 (mt) REVERT: C 92 GLU cc_start: 0.7662 (tp30) cc_final: 0.7434 (tp30) REVERT: C 94 ASN cc_start: 0.9142 (t0) cc_final: 0.8886 (t0) REVERT: D 51 ASP cc_start: 0.8848 (m-30) cc_final: 0.8381 (p0) REVERT: D 59 MET cc_start: 0.9302 (tpp) cc_final: 0.8966 (tpp) REVERT: D 68 ASP cc_start: 0.9265 (t70) cc_final: 0.9026 (t0) REVERT: D 105 GLU cc_start: 0.8497 (pm20) cc_final: 0.8138 (pm20) REVERT: E 79 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8529 (ttmm) REVERT: E 125 GLN cc_start: 0.9003 (mp10) cc_final: 0.8658 (mm-40) REVERT: G 33 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9178 (mm) REVERT: H 34 LYS cc_start: 0.8730 (mppt) cc_final: 0.8443 (mptt) REVERT: H 68 ASP cc_start: 0.9202 (t0) cc_final: 0.8881 (t0) REVERT: H 79 ARG cc_start: 0.8992 (ttp-110) cc_final: 0.8707 (mtm-85) REVERT: H 105 GLU cc_start: 0.8653 (tp30) cc_final: 0.8193 (tp30) REVERT: H 108 LYS cc_start: 0.9304 (pptt) cc_final: 0.8941 (ptpp) REVERT: U 76 CYS cc_start: 0.8544 (t) cc_final: 0.8261 (t) outliers start: 26 outliers final: 16 residues processed: 284 average time/residue: 0.1533 time to fit residues: 60.0980 Evaluate side-chains 282 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 719 ILE Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.0770 chunk 22 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 212 GLN M 266 ASN G 110 ASN ** H 49 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 = 0.3834 r_free = 0.3834 target = 0.084963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055688 restraints weight = 56447.504| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.61 r_work: 0.2846 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15825 Z= 0.136 Angle : 0.631 11.071 22627 Z= 0.354 Chirality : 0.042 0.341 2587 Planarity : 0.004 0.051 1848 Dihedral : 29.869 176.012 4448 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.53 % Allowed : 24.95 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 1.46 (0.26), residues: 1101 helix: 1.67 (0.20), residues: 676 sheet: 0.79 (0.58), residues: 87 loop : -0.35 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.020 0.002 TYR D 83 PHE 0.012 0.001 PHE U 45 TRP 0.003 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (15825) covalent geometry : angle 0.63150 / 0.35 (22627) hydrogen bonds : bond 0.04387 / 2.96 ( 894) hydrogen bonds : angle 3.37776 / 2.46 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.420 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: symmetry clash REVERT: M 261 MET cc_start: 0.9090 (tpt) cc_final: 0.8823 (mtt) REVERT: M 351 MET cc_start: 0.5702 (tmm) cc_final: 0.5238 (tmm) REVERT: M 718 GLU cc_start: 0.7596 (pm20) cc_final: 0.6602 (tm-30) REVERT: M 719 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8049 (mp) REVERT: M 766 ARG cc_start: 0.5861 (ptp90) cc_final: 0.5589 (ptp90) REVERT: M 821 ARG cc_start: 0.7358 (tpt90) cc_final: 0.6150 (mmp-170) REVERT: A 50 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8326 (pt0) REVERT: C 73 ASN cc_start: 0.9152 (t0) cc_final: 0.8905 (t0) REVERT: C 78 ILE cc_start: 0.8770 (pt) cc_final: 0.8519 (mt) REVERT: C 92 GLU cc_start: 0.7793 (tp30) cc_final: 0.7477 (tp30) REVERT: C 94 ASN cc_start: 0.9169 (t0) cc_final: 0.8936 (t0) REVERT: D 51 ASP cc_start: 0.8904 (m-30) cc_final: 0.8455 (p0) REVERT: D 59 MET cc_start: 0.9334 (tpp) cc_final: 0.9010 (tpp) REVERT: D 68 ASP cc_start: 0.9290 (t70) cc_final: 0.9034 (t0) REVERT: D 105 GLU cc_start: 0.8502 (pm20) cc_final: 0.8160 (pm20) REVERT: D 108 LYS cc_start: 0.9317 (tmtt) cc_final: 0.8846 (tmtt) REVERT: E 79 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8496 (ttmm) REVERT: G 33 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9183 (mm) REVERT: H 34 LYS cc_start: 0.8785 (mppt) cc_final: 0.8566 (mmtm) REVERT: H 68 ASP cc_start: 0.9238 (t0) cc_final: 0.8926 (t0) REVERT: H 79 ARG cc_start: 0.8981 (ttp-110) cc_final: 0.8730 (mtm-85) REVERT: H 105 GLU cc_start: 0.8615 (tp30) cc_final: 0.8077 (tp30) REVERT: H 108 LYS cc_start: 0.9304 (pptt) cc_final: 0.8974 (ptpp) REVERT: U 76 CYS cc_start: 0.8579 (t) cc_final: 0.8317 (t) outliers start: 24 outliers final: 17 residues processed: 284 average time/residue: 0.1505 time to fit residues: 58.8571 Evaluate side-chains 272 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 719 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 758 HIS C 112 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.079000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048202 restraints weight = 55489.806| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.43 r_work: 0.2645 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.176 15825 Z= 0.337 Angle : 0.858 15.109 22627 Z= 0.466 Chirality : 0.056 1.012 2587 Planarity : 0.007 0.073 1848 Dihedral : 30.405 174.808 4448 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.16 % Allowed : 24.32 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.77 (0.25), residues: 1101 helix: 1.13 (0.20), residues: 677 sheet: 0.66 (0.57), residues: 85 loop : -0.68 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 42 TYR 0.028 0.003 TYR D 83 PHE 0.020 0.002 PHE U 45 TRP 0.013 0.003 TRP M 793 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.34 (15825) covalent geometry : angle 0.85755 / 0.47 (22627) hydrogen bonds : bond 0.08746 / 5.75 ( 894) hydrogen bonds : angle 3.94783 / 2.85 ( 2271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.414 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: M 284 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8643 (mm-40) REVERT: M 718 GLU cc_start: 0.7665 (pm20) cc_final: 0.7378 (pm20) REVERT: M 766 ARG cc_start: 0.6016 (ptp90) cc_final: 0.5724 (ptp90) REVERT: M 821 ARG cc_start: 0.7428 (tpt90) cc_final: 0.6312 (mmm160) REVERT: A 81 ASP cc_start: 0.8908 (p0) cc_final: 0.8658 (p0) REVERT: C 73 ASN cc_start: 0.9313 (t0) cc_final: 0.8949 (t0) REVERT: C 92 GLU cc_start: 0.8363 (tp30) cc_final: 0.8061 (tp30) REVERT: D 33 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8526 (mmm-85) REVERT: D 108 LYS cc_start: 0.9387 (tmtt) cc_final: 0.9003 (tmtt) REVERT: E 79 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8623 (ttmm) REVERT: E 120 MET cc_start: 0.9242 (mtp) cc_final: 0.9026 (mtt) REVERT: G 41 GLU cc_start: 0.8811 (pm20) cc_final: 0.8550 (mp0) REVERT: H 68 ASP cc_start: 0.9220 (t0) cc_final: 0.8946 (t0) outliers start: 30 outliers final: 23 residues processed: 256 average time/residue: 0.1603 time to fit residues: 55.9170 Evaluate side-chains 238 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 385 LEU Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 758 HIS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 0.1980 chunk 132 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 129 optimal weight: 0.0050 chunk 114 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 48 optimal weight: 0.0170 chunk 15 optimal weight: 5.9990 overall best weight: 1.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.080858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.050158 restraints weight = 55204.334| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.45 r_work: 0.2696 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.8419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15825 Z= 0.160 Angle : 0.697 12.166 22627 Z= 0.384 Chirality : 0.044 0.360 2587 Planarity : 0.005 0.055 1848 Dihedral : 30.288 177.713 4448 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.21 % Allowed : 24.95 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 1.09 (0.25), residues: 1101 helix: 1.46 (0.20), residues: 675 sheet: 0.46 (0.56), residues: 87 loop : -0.62 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG M 305 TYR 0.021 0.002 TYR M 306 PHE 0.013 0.001 PHE U 45 TRP 0.001 0.000 TRP M 793 HIS 0.029 0.001 HIS M 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (15825) covalent geometry : angle 0.69709 / 0.38 (22627) hydrogen bonds : bond 0.04791 / 3.21 ( 894) hydrogen bonds : angle 3.53962 / 2.57 ( 2271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 198 LEU cc_start: 0.8144 (tp) cc_final: 0.7908 (tp) REVERT: M 263 GLN cc_start: 0.9624 (OUTLIER) cc_final: 0.9388 (mm-40) REVERT: M 684 MET cc_start: 0.8389 (mmm) cc_final: 0.7600 (tpp) REVERT: M 693 LEU cc_start: 0.7476 (tp) cc_final: 0.6803 (tp) REVERT: M 766 ARG cc_start: 0.5913 (ptp90) cc_final: 0.5653 (ptp90) REVERT: M 821 ARG cc_start: 0.7455 (tpt90) cc_final: 0.6238 (mmp-170) REVERT: A 125 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8925 (mp10) REVERT: C 73 ASN cc_start: 0.9293 (t0) cc_final: 0.8886 (t0) REVERT: C 92 GLU cc_start: 0.8101 (tp30) cc_final: 0.7795 (tp30) REVERT: D 33 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.8257 (mmt90) REVERT: D 59 MET cc_start: 0.9469 (tpp) cc_final: 0.9170 (tpp) REVERT: D 108 LYS cc_start: 0.9376 (tmtt) cc_final: 0.9123 (ttpp) REVERT: E 79 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8697 (ttmm) REVERT: E 120 MET cc_start: 0.9179 (mtp) cc_final: 0.8960 (mtt) REVERT: G 41 GLU cc_start: 0.8810 (pm20) cc_final: 0.8585 (mp0) REVERT: H 68 ASP cc_start: 0.9273 (t0) cc_final: 0.9029 (t0) REVERT: U 27 LYS cc_start: 0.9249 (pptt) cc_final: 0.8810 (ptpp) outliers start: 21 outliers final: 15 residues processed: 260 average time/residue: 0.1618 time to fit residues: 57.0978 Evaluate side-chains 254 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 385 LEU Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 297 GLN ** M 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 758 HIS D 84 ASN G 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.079646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048943 restraints weight = 55207.843| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.42 r_work: 0.2665 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.8657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15825 Z= 0.219 Angle : 0.743 12.414 22627 Z= 0.403 Chirality : 0.045 0.391 2587 Planarity : 0.005 0.051 1848 Dihedral : 30.252 177.420 4448 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.21 % Allowed : 25.79 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 1.01 (0.25), residues: 1101 helix: 1.37 (0.20), residues: 676 sheet: 0.63 (0.60), residues: 78 loop : -0.63 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 305 TYR 0.055 0.002 TYR D 83 PHE 0.016 0.002 PHE U 45 TRP 0.006 0.002 TRP M 793 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (15825) covalent geometry : angle 0.74293 / 0.40 (22627) hydrogen bonds : bond 0.05696 / 3.76 ( 894) hydrogen bonds : angle 3.60876 / 2.63 ( 2271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 198 LEU cc_start: 0.8101 (tp) cc_final: 0.7892 (tp) REVERT: M 684 MET cc_start: 0.8333 (mmm) cc_final: 0.7548 (tpp) REVERT: M 766 ARG cc_start: 0.5964 (ptp90) cc_final: 0.5688 (ptp90) REVERT: M 821 ARG cc_start: 0.7437 (tpt90) cc_final: 0.6234 (mmp-170) REVERT: A 125 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8924 (mp10) REVERT: C 73 ASN cc_start: 0.9300 (t0) cc_final: 0.8877 (t0) REVERT: C 114 VAL cc_start: 0.9618 (OUTLIER) cc_final: 0.9392 (p) REVERT: D 33 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8421 (mmt90) REVERT: D 59 MET cc_start: 0.9474 (tpp) cc_final: 0.9117 (tpp) REVERT: D 108 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9126 (ttpp) REVERT: E 79 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8700 (ttmm) REVERT: E 120 MET cc_start: 0.9154 (mtp) cc_final: 0.8945 (mtt) REVERT: H 68 ASP cc_start: 0.9286 (t0) cc_final: 0.9036 (t0) outliers start: 21 outliers final: 13 residues processed: 246 average time/residue: 0.1536 time to fit residues: 51.1514 Evaluate side-chains 243 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 385 LEU Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 758 HIS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 84 ASN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.080430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.049816 restraints weight = 54795.661| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.45 r_work: 0.2688 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.8701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15825 Z= 0.154 Angle : 0.711 12.271 22627 Z= 0.389 Chirality : 0.044 0.361 2587 Planarity : 0.004 0.050 1848 Dihedral : 30.198 178.014 4448 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.89 % Allowed : 26.21 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 1.09 (0.25), residues: 1101 helix: 1.42 (0.20), residues: 676 sheet: 0.61 (0.61), residues: 78 loop : -0.57 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 33 TYR 0.050 0.002 TYR D 83 PHE 0.011 0.001 PHE A 67 TRP 0.002 0.001 TRP M 793 HIS 0.013 0.001 HIS M 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (15825) covalent geometry : angle 0.71145 / 0.39 (22627) hydrogen bonds : bond 0.04615 / 3.08 ( 894) hydrogen bonds : angle 3.53272 / 2.57 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4275.02 seconds wall clock time: 73 minutes 41.78 seconds (4421.78 seconds total)