Starting phenix.real_space_refine on Fri Jul 3 14:56:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg5_37503/07_2026/8wg5_37503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg5_37503/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wg5_37503/07_2026/8wg5_37503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg5_37503/07_2026/8wg5_37503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wg5_37503/07_2026/8wg5_37503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg5_37503/07_2026/8wg5_37503.map" } 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-dev-6108/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: 2.66, per 1000 atoms: 0.18 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: 1.05 Conformation dependent library (CDL) restraints added in 537.8 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: 2.02 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: 3.52 Time building geometry restraints manager: 1.49 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: 21124 1.40 - 2.80: 1368 2.80 - 4.20: 106 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: 1.080 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- 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 : 0.723 7.004 22627 Z= 0.602 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 0.72336 / 0.60 (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 : 0.458 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: 0.5904 (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: 0.6846 (mm) REVERT: C 61 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7649 (mm-30) 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: 0.1616 time to fit residues: 91.4657 Evaluate side-chains 275 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 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 ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS U 25 ASN ** U 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.086122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057441 restraints weight = 57608.687| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.79 r_work: 0.2928 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 15825 Z= 0.362 Angle : 1.043 23.508 22627 Z= 0.564 Chirality : 0.058 0.431 2587 Planarity : 0.009 0.080 1848 Dihedral : 30.394 173.655 4452 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 4.74 % Allowed : 15.79 % 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: -0.43 (0.24), residues: 1101 helix: -0.10 (0.19), residues: 666 sheet: 0.84 (0.63), residues: 67 loop : -0.58 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG A 52 TYR 0.048 0.005 TYR D 83 PHE 0.029 0.004 PHE B 61 TRP 0.022 0.014 TRP M 793 HIS 0.022 0.003 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.36 (15825) covalent geometry : angle 1.04349 / 0.56 (22627) hydrogen bonds : bond 0.08576 / 5.64 ( 894) hydrogen bonds : angle 4.81453 / 3.47 ( 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 357 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 312 time to evaluate : 0.384 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: M 222 GLU cc_start: 0.8253 (mp0) cc_final: 0.8019 (pm20) REVERT: M 281 LEU cc_start: 0.8867 (tt) cc_final: 0.8090 (tt) REVERT: M 306 TYR cc_start: 0.8362 (m-80) cc_final: 0.7779 (m-80) REVERT: M 309 ASP cc_start: 0.8009 (p0) cc_final: 0.7563 (p0) REVERT: M 643 ASN cc_start: 0.7101 (t0) cc_final: 0.6778 (t0) REVERT: M 714 ILE cc_start: 0.5910 (tp) cc_final: 0.5692 (tp) REVERT: M 718 GLU cc_start: 0.7583 (pm20) cc_final: 0.6776 (tm-30) REVERT: M 741 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8098 (mm) REVERT: M 820 GLU cc_start: 0.8255 (tp30) cc_final: 0.7769 (mm-30) REVERT: A 73 GLU cc_start: 0.8101 (tt0) cc_final: 0.7889 (tt0) REVERT: B 26 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8415 (tp) REVERT: B 84 MET cc_start: 0.8692 (tpp) cc_final: 0.8490 (tpt) REVERT: C 56 GLU cc_start: 0.8560 (tt0) cc_final: 0.8327 (tt0) REVERT: C 61 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8734 (mm-30) REVERT: C 64 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: D 59 MET cc_start: 0.9268 (tpp) cc_final: 0.8991 (tpp) REVERT: D 105 GLU cc_start: 0.8488 (pm20) cc_final: 0.8167 (pm20) REVERT: D 108 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8809 (tmtt) REVERT: E 96 CYS cc_start: 0.8977 (m) cc_final: 0.8750 (m) REVERT: E 120 MET cc_start: 0.9169 (mtp) cc_final: 0.8857 (mtm) REVERT: F 25 ASN cc_start: 0.8029 (m110) cc_final: 0.7777 (m110) REVERT: F 31 LYS cc_start: 0.9347 (tttm) cc_final: 0.9029 (tttp) REVERT: G 33 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9301 (mm) REVERT: G 57 TYR cc_start: 0.7952 (t80) cc_final: 0.7527 (t80) REVERT: G 74 LYS cc_start: 0.9003 (ptmt) cc_final: 0.8763 (ptmm) REVERT: G 92 GLU cc_start: 0.8627 (tt0) cc_final: 0.8300 (tt0) REVERT: H 34 LYS cc_start: 0.8710 (mppt) cc_final: 0.8479 (mmmm) REVERT: H 105 GLU cc_start: 0.8932 (tp30) cc_final: 0.8577 (tp30) REVERT: H 108 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.8995 (ptmm) REVERT: U 1 MET cc_start: 0.7192 (ptt) cc_final: 0.6793 (ttt) outliers start: 45 outliers final: 20 residues processed: 338 average time/residue: 0.1521 time to fit residues: 70.0496 Evaluate side-chains 282 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 201 LEU 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 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 64 GLU 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 101 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 108 LYS 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: 0.9980 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 212 GLN M 263 GLN M 635 HIS M 696 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** U 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.086725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.057941 restraints weight = 57575.563| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.69 r_work: 0.2926 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15825 Z= 0.161 Angle : 0.681 11.065 22627 Z= 0.383 Chirality : 0.044 0.323 2587 Planarity : 0.005 0.057 1848 Dihedral : 30.201 176.868 4448 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.26 % Allowed : 21.26 % 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: 0.67 (0.25), residues: 1101 helix: 0.97 (0.20), residues: 674 sheet: 0.49 (0.60), residues: 79 loop : -0.45 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 78 TYR 0.023 0.002 TYR G 57 PHE 0.014 0.001 PHE M 207 TRP 0.004 0.001 TRP M 793 HIS 0.005 0.001 HIS M 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (15825) covalent geometry : angle 0.68052 / 0.38 (22627) hydrogen bonds : bond 0.05079 / 3.43 ( 894) hydrogen bonds : angle 3.87069 / 2.82 ( 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 321 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.463 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: M 309 ASP cc_start: 0.7891 (p0) cc_final: 0.7553 (p0) REVERT: M 635 HIS cc_start: 0.3052 (OUTLIER) cc_final: 0.2031 (t-90) REVERT: M 643 ASN cc_start: 0.7034 (t0) cc_final: 0.6748 (t0) REVERT: M 718 GLU cc_start: 0.7543 (pm20) cc_final: 0.6791 (tm-30) REVERT: M 744 LEU cc_start: 0.6506 (tp) cc_final: 0.6182 (tp) REVERT: M 820 GLU cc_start: 0.8269 (tp30) cc_final: 0.7734 (mm-30) REVERT: B 26 ILE cc_start: 0.8757 (mp) cc_final: 0.8449 (tp) REVERT: B 88 TYR cc_start: 0.7765 (m-10) cc_final: 0.7260 (m-80) REVERT: C 50 TYR cc_start: 0.9064 (t80) cc_final: 0.8839 (t80) REVERT: C 56 GLU cc_start: 0.8588 (tt0) cc_final: 0.8279 (tt0) REVERT: C 61 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8725 (mm-30) REVERT: C 92 GLU cc_start: 0.7408 (tp30) cc_final: 0.6849 (tp30) REVERT: C 104 GLN cc_start: 0.9174 (mp10) cc_final: 0.8275 (mp10) REVERT: D 59 MET cc_start: 0.9266 (tpp) cc_final: 0.9004 (tpp) REVERT: D 71 GLU cc_start: 0.9115 (tp30) cc_final: 0.8869 (tp30) REVERT: D 76 GLU cc_start: 0.8908 (tp30) cc_final: 0.8684 (tp30) REVERT: D 83 TYR cc_start: 0.8487 (m-10) cc_final: 0.7906 (m-80) REVERT: D 105 GLU cc_start: 0.8430 (pm20) cc_final: 0.8131 (pm20) REVERT: D 108 LYS cc_start: 0.9097 (tmtt) cc_final: 0.8783 (tmtt) REVERT: E 55 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.9144 (tt0) REVERT: F 88 TYR cc_start: 0.8451 (m-10) cc_final: 0.8230 (m-10) REVERT: G 33 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9146 (mm) REVERT: G 68 ASN cc_start: 0.8508 (m-40) cc_final: 0.8251 (m-40) REVERT: G 104 GLN cc_start: 0.9137 (mp10) cc_final: 0.8849 (mp10) REVERT: H 33 ARG cc_start: 0.6962 (mmm160) cc_final: 0.6710 (mtt-85) REVERT: H 34 LYS cc_start: 0.8550 (mppt) cc_final: 0.8339 (mptt) REVERT: H 51 ASP cc_start: 0.8612 (t0) cc_final: 0.8358 (p0) REVERT: H 68 ASP cc_start: 0.9060 (t0) cc_final: 0.8634 (t0) REVERT: H 105 GLU cc_start: 0.8794 (tp30) cc_final: 0.8574 (tp30) REVERT: H 108 LYS cc_start: 0.9263 (pptt) cc_final: 0.8990 (ptpp) REVERT: U 25 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8695 (p0) REVERT: U 48 LYS cc_start: 0.4433 (OUTLIER) cc_final: 0.4214 (mmtt) outliers start: 31 outliers final: 15 residues processed: 304 average time/residue: 0.1479 time to fit residues: 61.6171 Evaluate side-chains 278 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 258 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 286 CYS 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 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 55 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 61 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR 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: 0.9980 chunk 132 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 55 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.085935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056654 restraints weight = 57647.627| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.68 r_work: 0.2886 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15825 Z= 0.155 Angle : 0.642 10.001 22627 Z= 0.364 Chirality : 0.043 0.334 2587 Planarity : 0.004 0.055 1848 Dihedral : 30.107 176.882 4448 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.89 % Allowed : 20.42 % Favored : 75.68 % 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: 1.12 (0.25), residues: 1101 helix: 1.29 (0.20), residues: 671 sheet: 0.83 (0.67), residues: 69 loop : -0.18 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 35 TYR 0.018 0.002 TYR H 83 PHE 0.013 0.001 PHE M 716 TRP 0.009 0.002 TRP M 793 HIS 0.005 0.001 HIS M 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (15825) covalent geometry : angle 0.64228 / 0.36 (22627) hydrogen bonds : bond 0.04825 / 3.24 ( 894) hydrogen bonds : angle 3.70375 / 2.70 ( 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 305 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.427 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 309 ASP cc_start: 0.7812 (p0) cc_final: 0.7582 (p0) REVERT: M 643 ASN cc_start: 0.6956 (t0) cc_final: 0.6671 (t0) REVERT: M 718 GLU cc_start: 0.7467 (pm20) cc_final: 0.6514 (tm-30) REVERT: M 719 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8088 (mt) REVERT: M 744 LEU cc_start: 0.6621 (tp) cc_final: 0.6414 (tp) REVERT: A 123 ASP cc_start: 0.9116 (m-30) cc_final: 0.8915 (m-30) REVERT: B 26 ILE cc_start: 0.8877 (mp) cc_final: 0.8667 (tp) REVERT: B 88 TYR cc_start: 0.8104 (m-10) cc_final: 0.7744 (m-10) REVERT: C 92 GLU cc_start: 0.7444 (tp30) cc_final: 0.7128 (tp30) REVERT: C 112 GLN cc_start: 0.9068 (mm110) cc_final: 0.8848 (mm-40) REVERT: D 59 MET cc_start: 0.9315 (tpp) cc_final: 0.9081 (tpp) REVERT: D 108 LYS cc_start: 0.9175 (tmtt) cc_final: 0.8902 (tmtt) REVERT: E 79 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8294 (ttmm) REVERT: G 33 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9175 (mm) REVERT: G 92 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: H 79 ARG cc_start: 0.8951 (ttp-110) cc_final: 0.8647 (mtm-85) REVERT: H 105 GLU cc_start: 0.8797 (tp30) cc_final: 0.8521 (tp30) REVERT: H 108 LYS cc_start: 0.9221 (pptt) cc_final: 0.8950 (ptpp) outliers start: 37 outliers final: 20 residues processed: 285 average time/residue: 0.1562 time to fit residues: 60.9332 Evaluate side-chains 278 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 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 268 MET 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 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 101 THR Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 55 GLN 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 79 ILE 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: 40.0000 chunk 97 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 266 ASN M 284 GLN M 297 GLN E 93 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.082359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051403 restraints weight = 57312.398| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.56 r_work: 0.2739 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 15825 Z= 0.242 Angle : 0.715 12.864 22627 Z= 0.397 Chirality : 0.045 0.360 2587 Planarity : 0.006 0.063 1848 Dihedral : 30.238 176.357 4448 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.42 % Allowed : 22.42 % 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: 1.05 (0.25), residues: 1101 helix: 1.29 (0.20), residues: 676 sheet: 0.79 (0.67), residues: 69 loop : -0.35 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 305 TYR 0.041 0.002 TYR D 83 PHE 0.024 0.002 PHE U 45 TRP 0.002 0.001 TRP M 793 HIS 0.006 0.001 HIS M 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (15825) covalent geometry : angle 0.71514 / 0.40 (22627) hydrogen bonds : bond 0.06107 / 4.05 ( 894) hydrogen bonds : angle 3.70327 / 2.70 ( 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 302 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 0.423 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: 0.9108 (mm-40) cc_final: 0.8712 (mm110) REVERT: M 643 ASN cc_start: 0.6905 (t0) cc_final: 0.6620 (t0) REVERT: M 684 MET cc_start: 0.7955 (mmp) cc_final: 0.7495 (mmp) REVERT: M 718 GLU cc_start: 0.7630 (pm20) cc_final: 0.7344 (pm20) REVERT: M 821 ARG cc_start: 0.7153 (tpt90) cc_final: 0.6155 (mmm160) REVERT: B 77 LYS cc_start: 0.9460 (mttt) cc_final: 0.9231 (mttm) REVERT: B 88 TYR cc_start: 0.8888 (m-10) cc_final: 0.8220 (m-10) REVERT: C 73 ASN cc_start: 0.9207 (t0) cc_final: 0.8933 (t0) REVERT: C 94 ASN cc_start: 0.9338 (t0) cc_final: 0.9127 (t0) REVERT: D 51 ASP cc_start: 0.8947 (m-30) cc_final: 0.8496 (p0) REVERT: D 83 TYR cc_start: 0.8593 (m-10) cc_final: 0.8383 (m-80) REVERT: E 79 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8605 (ttmm) REVERT: G 33 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9238 (mm) REVERT: G 41 GLU cc_start: 0.8785 (pm20) cc_final: 0.8472 (mp0) REVERT: G 68 ASN cc_start: 0.8866 (m-40) cc_final: 0.8143 (m-40) REVERT: G 72 ASP cc_start: 0.8617 (m-30) cc_final: 0.8402 (m-30) REVERT: G 90 ASP cc_start: 0.9203 (t0) cc_final: 0.8914 (t0) REVERT: H 68 ASP cc_start: 0.9232 (t0) cc_final: 0.8969 (t0) REVERT: H 71 GLU cc_start: 0.9176 (tp30) cc_final: 0.8635 (mp0) REVERT: H 105 GLU cc_start: 0.8847 (tp30) cc_final: 0.8478 (tp30) REVERT: H 108 LYS cc_start: 0.9291 (pptt) cc_final: 0.8968 (ptpp) outliers start: 42 outliers final: 24 residues processed: 281 average time/residue: 0.1495 time to fit residues: 57.2292 Evaluate side-chains 269 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 307 LEU Chi-restraints excluded: chain M residue 385 LEU Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 61 LEU 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 33 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 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 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 212 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 = 0.3786 r_free = 0.3786 target = 0.082723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.052850 restraints weight = 56170.202| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.60 r_work: 0.2760 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15825 Z= 0.152 Angle : 0.646 14.027 22627 Z= 0.363 Chirality : 0.043 0.329 2587 Planarity : 0.004 0.055 1848 Dihedral : 30.192 177.371 4448 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.26 % Allowed : 22.21 % Favored : 74.53 % 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: 1.23 (0.26), residues: 1101 helix: 1.46 (0.20), residues: 675 sheet: 0.82 (0.66), residues: 69 loop : -0.33 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG M 305 TYR 0.036 0.002 TYR D 83 PHE 0.012 0.001 PHE M 207 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 0.00295 / 0.15 (15825) covalent geometry : angle 0.64604 / 0.36 (22627) hydrogen bonds : bond 0.04607 / 3.10 ( 894) hydrogen bonds : angle 3.53505 / 2.58 ( 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 293 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.278 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 643 ASN cc_start: 0.6921 (t0) cc_final: 0.6692 (t0) REVERT: M 684 MET cc_start: 0.7923 (mmp) cc_final: 0.7452 (mmp) REVERT: M 766 ARG cc_start: 0.5867 (ptp90) cc_final: 0.5606 (ptp90) REVERT: M 821 ARG cc_start: 0.7263 (tpt90) cc_final: 0.5944 (mmp-170) REVERT: A 59 GLU cc_start: 0.8245 (pm20) cc_final: 0.8020 (pm20) REVERT: B 77 LYS cc_start: 0.9489 (mttt) cc_final: 0.9235 (mttm) REVERT: B 88 TYR cc_start: 0.8959 (m-10) cc_final: 0.8183 (m-10) REVERT: B 97 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9077 (pt) REVERT: C 73 ASN cc_start: 0.9232 (t0) cc_final: 0.8945 (t0) REVERT: C 92 GLU cc_start: 0.8003 (tp30) cc_final: 0.7635 (tp30) REVERT: C 99 ARG cc_start: 0.8932 (mmt180) cc_final: 0.8662 (mmm-85) REVERT: D 47 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8925 (mt0) REVERT: D 51 ASP cc_start: 0.8979 (m-30) cc_final: 0.8631 (p0) REVERT: D 83 TYR cc_start: 0.8645 (m-10) cc_final: 0.8387 (m-80) REVERT: D 105 GLU cc_start: 0.8578 (pm20) cc_final: 0.8349 (pm20) REVERT: D 108 LYS cc_start: 0.9358 (tmtt) cc_final: 0.8928 (tmtt) REVERT: E 79 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8615 (ttmm) REVERT: G 68 ASN cc_start: 0.8880 (m-40) cc_final: 0.8062 (m-40) REVERT: G 72 ASP cc_start: 0.8667 (m-30) cc_final: 0.8415 (m-30) REVERT: H 68 ASP cc_start: 0.9268 (t0) cc_final: 0.9003 (t0) REVERT: H 71 GLU cc_start: 0.9188 (tp30) cc_final: 0.8627 (mp0) REVERT: H 105 GLU cc_start: 0.8723 (tp30) cc_final: 0.8252 (tp30) REVERT: H 108 LYS cc_start: 0.9254 (pptt) cc_final: 0.8926 (ptpp) REVERT: U 67 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8632 (pp) REVERT: U 76 CYS cc_start: 0.8552 (t) cc_final: 0.8279 (t) outliers start: 31 outliers final: 21 residues processed: 276 average time/residue: 0.1406 time to fit residues: 52.7750 Evaluate side-chains 272 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain M residue 389 VAL Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 97 LEU 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 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 G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.082996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053079 restraints weight = 57067.646| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.61 r_work: 0.2771 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.7334 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= 0.138 Angle : 0.656 15.867 22627 Z= 0.362 Chirality : 0.042 0.324 2587 Planarity : 0.004 0.054 1848 Dihedral : 30.092 177.480 4448 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.74 % Allowed : 23.58 % Favored : 73.68 % 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: 1.32 (0.26), residues: 1101 helix: 1.54 (0.20), residues: 675 sheet: 0.83 (0.65), residues: 69 loop : -0.32 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG M 305 TYR 0.034 0.001 TYR D 83 PHE 0.009 0.001 PHE M 716 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 0.00262 / 0.14 (15825) covalent geometry : angle 0.65551 / 0.36 (22627) hydrogen bonds : bond 0.04406 / 2.97 ( 894) hydrogen bonds : angle 3.43775 / 2.51 ( 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 285 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.355 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: M 261 MET cc_start: 0.9129 (tpt) cc_final: 0.8766 (mtt) REVERT: M 284 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8645 (mm110) REVERT: M 684 MET cc_start: 0.7917 (mmp) cc_final: 0.7483 (mmp) REVERT: M 718 GLU cc_start: 0.7225 (pm20) cc_final: 0.6976 (mt-10) REVERT: M 766 ARG cc_start: 0.5863 (ptp90) cc_final: 0.5586 (ptp90) REVERT: M 821 ARG cc_start: 0.7319 (tpt90) cc_final: 0.6101 (mmp-170) REVERT: B 77 LYS cc_start: 0.9486 (mttt) cc_final: 0.9251 (mttm) REVERT: B 97 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9036 (pt) REVERT: C 73 ASN cc_start: 0.9223 (t0) cc_final: 0.8936 (t0) REVERT: C 92 GLU cc_start: 0.7983 (tp30) cc_final: 0.7526 (tp30) REVERT: C 99 ARG cc_start: 0.8950 (mmt180) cc_final: 0.8654 (mmm-85) REVERT: D 47 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9019 (mt0) REVERT: D 51 ASP cc_start: 0.8989 (m-30) cc_final: 0.8704 (p0) REVERT: D 83 TYR cc_start: 0.8590 (m-10) cc_final: 0.8223 (m-80) REVERT: D 105 GLU cc_start: 0.8578 (pm20) cc_final: 0.8328 (pm20) REVERT: D 108 LYS cc_start: 0.9387 (tmtt) cc_final: 0.8971 (tmtt) REVERT: G 41 GLU cc_start: 0.8741 (pm20) cc_final: 0.8450 (mp0) REVERT: G 68 ASN cc_start: 0.8870 (m-40) cc_final: 0.8029 (m-40) REVERT: G 72 ASP cc_start: 0.8682 (m-30) cc_final: 0.8429 (m-30) REVERT: H 34 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8668 (mmtm) REVERT: H 68 ASP cc_start: 0.9277 (t0) cc_final: 0.9025 (t0) REVERT: H 105 GLU cc_start: 0.8598 (tp30) cc_final: 0.8105 (tp30) REVERT: H 108 LYS cc_start: 0.9235 (pptt) cc_final: 0.8914 (ptpp) REVERT: U 76 CYS cc_start: 0.8549 (t) cc_final: 0.8289 (t) outliers start: 26 outliers final: 18 residues processed: 270 average time/residue: 0.1438 time to fit residues: 53.0762 Evaluate side-chains 270 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 A residue 48 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 97 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 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR 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: 2.9990 chunk 110 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 131 optimal weight: 0.2980 chunk 104 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 100 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 212 GLN ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 758 HIS D 84 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** 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 = 0.3699 r_free = 0.3699 target = 0.077611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047495 restraints weight = 55843.042| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.45 r_work: 0.2605 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.8729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 15825 Z= 0.349 Angle : 0.842 12.658 22627 Z= 0.455 Chirality : 0.052 0.403 2587 Planarity : 0.007 0.071 1848 Dihedral : 30.634 176.329 4448 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.37 % Allowed : 22.53 % Favored : 74.11 % 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: 0.68 (0.25), residues: 1101 helix: 1.04 (0.20), residues: 676 sheet: 0.81 (0.65), residues: 67 loop : -0.65 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 33 TYR 0.047 0.003 TYR M 306 PHE 0.019 0.002 PHE C 25 TRP 0.003 0.001 TRP M 793 HIS 0.007 0.002 HIS U 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.35 (15825) covalent geometry : angle 0.84250 / 0.45 (22627) hydrogen bonds : bond 0.08891 / 5.83 ( 894) hydrogen bonds : angle 3.88146 / 2.81 ( 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 268 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.433 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: M 684 MET cc_start: 0.7921 (mmp) cc_final: 0.7357 (mmm) REVERT: B 77 LYS cc_start: 0.9558 (mttt) cc_final: 0.9317 (mttm) REVERT: B 88 TYR cc_start: 0.9478 (m-10) cc_final: 0.8255 (m-80) REVERT: C 73 ASN cc_start: 0.9349 (t0) cc_final: 0.8954 (t0) REVERT: C 92 GLU cc_start: 0.8315 (tp30) cc_final: 0.8069 (tp30) REVERT: D 83 TYR cc_start: 0.8651 (m-10) cc_final: 0.7983 (m-80) REVERT: D 108 LYS cc_start: 0.9404 (tmtt) cc_final: 0.9157 (ttpp) REVERT: E 79 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8824 (ttmm) REVERT: F 88 TYR cc_start: 0.9482 (m-10) cc_final: 0.9000 (m-10) REVERT: G 41 GLU cc_start: 0.8881 (pm20) cc_final: 0.8672 (mp0) REVERT: G 72 ASP cc_start: 0.8932 (m-30) cc_final: 0.8729 (m-30) REVERT: H 68 ASP cc_start: 0.9271 (t0) cc_final: 0.8858 (t0) REVERT: H 80 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9476 (mp) REVERT: H 83 TYR cc_start: 0.8816 (m-10) cc_final: 0.8583 (m-10) REVERT: U 6 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7152 (pptt) REVERT: U 27 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8465 (ptpp) outliers start: 32 outliers final: 21 residues processed: 254 average time/residue: 0.1584 time to fit residues: 54.8187 Evaluate side-chains 241 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 A residue 48 LEU 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 87 ILE Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 50 ILE 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 80 LEU 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: 2.9990 chunk 132 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 32 optimal weight: 0.0970 chunk 129 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 212 GLN 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 = 0.3710 r_free = 0.3710 target = 0.078480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047830 restraints weight = 55555.915| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.44 r_work: 0.2628 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.8944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15825 Z= 0.236 Angle : 0.736 12.847 22627 Z= 0.400 Chirality : 0.046 0.373 2587 Planarity : 0.005 0.051 1848 Dihedral : 30.604 178.649 4448 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.74 % Allowed : 23.05 % 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: 0.96 (0.25), residues: 1101 helix: 1.30 (0.20), residues: 674 sheet: 0.58 (0.64), residues: 69 loop : -0.53 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.038 0.002 TYR D 83 PHE 0.015 0.002 PHE B 100 TRP 0.009 0.002 TRP M 793 HIS 0.043 0.002 HIS M 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (15825) covalent geometry : angle 0.73633 / 0.40 (22627) hydrogen bonds : bond 0.05600 / 3.70 ( 894) hydrogen bonds : angle 3.63934 / 2.63 ( 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 262 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.446 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: M 261 MET cc_start: 0.9088 (tpt) cc_final: 0.8793 (mmm) REVERT: M 284 GLN cc_start: 0.9296 (mm-40) cc_final: 0.8436 (mm110) REVERT: M 684 MET cc_start: 0.8050 (mmp) cc_final: 0.7378 (mmt) REVERT: M 766 ARG cc_start: 0.6088 (ptp90) cc_final: 0.5887 (ptp90) REVERT: M 821 ARG cc_start: 0.7185 (tpt90) cc_final: 0.6433 (mmp-170) REVERT: A 125 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8919 (mp10) REVERT: B 77 LYS cc_start: 0.9547 (mttt) cc_final: 0.9337 (mttm) REVERT: B 88 TYR cc_start: 0.9478 (m-10) cc_final: 0.8313 (m-80) REVERT: C 59 THR cc_start: 0.9779 (m) cc_final: 0.9578 (m) REVERT: C 73 ASN cc_start: 0.9309 (t0) cc_final: 0.8872 (t0) REVERT: D 33 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8216 (mmt90) REVERT: D 83 TYR cc_start: 0.8679 (m-10) cc_final: 0.8042 (m-80) REVERT: D 108 LYS cc_start: 0.9393 (tmtt) cc_final: 0.9169 (ttpp) REVERT: E 79 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8920 (ttmm) REVERT: G 112 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8843 (mm110) REVERT: H 68 ASP cc_start: 0.9299 (t0) cc_final: 0.9076 (t0) REVERT: H 83 TYR cc_start: 0.8782 (m-10) cc_final: 0.8443 (m-10) outliers start: 26 outliers final: 18 residues processed: 252 average time/residue: 0.1571 time to fit residues: 53.4105 Evaluate side-chains 248 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 385 LEU Chi-restraints excluded: chain M residue 389 VAL Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE 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 C residue 108 LEU Chi-restraints excluded: chain G residue 43 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 85 LYS 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: 3.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 758 HIS D 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.079302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048808 restraints weight = 55134.786| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.43 r_work: 0.2666 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.9070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15825 Z= 0.160 Angle : 0.701 12.994 22627 Z= 0.384 Chirality : 0.044 0.384 2587 Planarity : 0.004 0.051 1848 Dihedral : 30.333 179.474 4448 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.32 % Allowed : 24.21 % Favored : 73.47 % 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: 1.16 (0.25), residues: 1101 helix: 1.45 (0.20), residues: 670 sheet: 0.57 (0.62), residues: 69 loop : -0.39 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.035 0.002 TYR D 83 PHE 0.020 0.001 PHE U 45 TRP 0.008 0.002 TRP M 793 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (15825) covalent geometry : angle 0.70061 / 0.38 (22627) hydrogen bonds : bond 0.04610 / 3.08 ( 894) hydrogen bonds : angle 3.46619 / 2.52 ( 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 268 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 261 MET cc_start: 0.9156 (tpt) cc_final: 0.8748 (mmm) REVERT: M 684 MET cc_start: 0.8137 (mmp) cc_final: 0.7852 (mmp) REVERT: M 821 ARG cc_start: 0.7453 (tpt90) cc_final: 0.5898 (mmp-170) REVERT: B 77 LYS cc_start: 0.9537 (mttt) cc_final: 0.9337 (mttm) REVERT: B 88 TYR cc_start: 0.9497 (m-10) cc_final: 0.8342 (m-80) REVERT: B 97 LEU cc_start: 0.9257 (pt) cc_final: 0.9057 (pt) REVERT: C 59 THR cc_start: 0.9780 (m) cc_final: 0.9554 (m) REVERT: C 72 ASP cc_start: 0.8908 (m-30) cc_final: 0.8668 (m-30) REVERT: C 73 ASN cc_start: 0.9308 (t0) cc_final: 0.8859 (t0) REVERT: C 92 GLU cc_start: 0.8384 (tp30) cc_final: 0.8065 (tp30) REVERT: C 104 GLN cc_start: 0.9370 (mm-40) cc_final: 0.9088 (mm110) REVERT: D 33 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8215 (mmt90) REVERT: D 83 TYR cc_start: 0.8454 (m-10) cc_final: 0.8114 (m-80) REVERT: D 108 LYS cc_start: 0.9363 (tmtt) cc_final: 0.9158 (ttpp) REVERT: H 68 ASP cc_start: 0.9278 (t0) cc_final: 0.9077 (t0) outliers start: 22 outliers final: 17 residues processed: 259 average time/residue: 0.1681 time to fit residues: 59.0515 Evaluate side-chains 252 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 235 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 304 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 48 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE 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 C residue 108 LEU Chi-restraints excluded: chain G residue 43 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 79 optimal weight: 0.0060 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 102 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 0.7836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 284 GLN M 758 HIS 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 = 0.3736 r_free = 0.3736 target = 0.079694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.048667 restraints weight = 55690.879| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.46 r_work: 0.2672 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.9129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15825 Z= 0.148 Angle : 0.707 13.099 22627 Z= 0.389 Chirality : 0.043 0.338 2587 Planarity : 0.004 0.052 1848 Dihedral : 30.267 179.087 4448 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.21 % Allowed : 25.05 % Favored : 72.74 % 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: 1.51 (0.20), residues: 672 sheet: 0.90 (0.59), residues: 78 loop : -0.52 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 766 TYR 0.032 0.002 TYR D 83 PHE 0.010 0.001 PHE B 100 TRP 0.007 0.002 TRP M 793 HIS 0.015 0.001 HIS M 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (15825) covalent geometry : angle 0.70661 / 0.39 (22627) hydrogen bonds : bond 0.04466 / 3.00 ( 894) hydrogen bonds : angle 3.43239 / 2.49 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4282.69 seconds wall clock time: 73 minutes 50.26 seconds (4430.26 seconds total)