Starting phenix.real_space_refine on Sat Aug 23 21:03:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg5_37503/08_2025/8wg5_37503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg5_37503/08_2025/8wg5_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_37503/08_2025/8wg5_37503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg5_37503/08_2025/8wg5_37503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wg5_37503/08_2025/8wg5_37503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg5_37503/08_2025/8wg5_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-2.0-5787/lib/python3.9/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: 3.84, per 1000 atoms: 0.26 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: 1.13 Conformation dependent library (CDL) restraints added in 384.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.68 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: 3.46 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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=" CG1 ILE F 66 " pdb=" CD1 ILE F 66 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.61e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG LEU F 62 " pdb=" CD2 LEU F 62 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CG GLU G 61 " pdb=" CD GLU G 61 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.26e+00 ... (remaining 15820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 21823 1.40 - 2.80: 699 2.80 - 4.20: 77 4.20 - 5.60: 17 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=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.39 117.39 -7.00 1.66e+00 3.63e-01 1.78e+01 angle pdb=" C LEU F 62 " pdb=" N GLU F 63 " pdb=" CA GLU F 63 " ideal model delta sigma weight residual 120.72 114.31 6.41 1.67e+00 3.59e-01 1.47e+01 angle pdb=" N GLN E 125 " pdb=" CA GLN E 125 " pdb=" CB GLN E 125 " ideal model delta sigma weight residual 110.39 116.57 -6.18 1.66e+00 3.63e-01 1.39e+01 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+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: 2149 0.045 - 0.090: 358 0.090 - 0.136: 74 0.136 - 0.181: 5 0.181 - 0.226: 1 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=" 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 chirality pdb=" CA GLN E 125 " pdb=" N GLN E 125 " pdb=" C GLN E 125 " pdb=" CB GLN E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-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: 1.120 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.220 Find NCS groups from input model: 0.120 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.003 0.056 15825 Z= 0.158 Angle : 0.590 7.004 22627 Z= 0.350 Chirality : 0.035 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 aren 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 covalent geometry : bond 0.00342 (15825) covalent geometry : angle 0.59034 (22627) hydrogen bonds : bond 0.13057 ( 894) hydrogen bonds : angle 5.04900 ( 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 : 0.358 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: 0.1431 time to fit residues: 80.9133 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 : 0.429 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 GLN M 635 HIS M 683 GLN M 750 HIS M 758 HIS M 800 HIS C 68 ASN C 84 GLN E 125 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.085733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056791 restraints weight = 57963.082| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.64 r_work: 0.2904 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 15825 Z= 0.347 Angle : 0.878 13.122 22627 Z= 0.488 Chirality : 0.047 0.238 2587 Planarity : 0.008 0.070 1848 Dihedral : 29.765 173.612 4452 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.32 % Allowed : 16.53 % Favored : 79.16 % 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 aren not related in a simple way. whole: 0.04 (0.24), residues: 1101 helix: 0.30 (0.19), residues: 672 sheet: 1.09 (0.54), residues: 85 loop : -0.57 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 134 TYR 0.048 0.003 TYR D 83 PHE 0.018 0.003 PHE A 78 TRP 0.011 0.006 TRP M 793 HIS 0.015 0.002 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00768 (15825) covalent geometry : angle 0.87840 (22627) hydrogen bonds : bond 0.07039 ( 894) hydrogen bonds : angle 4.32064 ( 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 354 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 281 LEU cc_start: 0.8882 (tt) cc_final: 0.8650 (tt) REVERT: M 643 ASN cc_start: 0.7175 (t0) cc_final: 0.6874 (t0) REVERT: M 718 GLU cc_start: 0.7629 (pm20) cc_final: 0.6763 (tm-30) REVERT: M 741 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8020 (mm) REVERT: M 744 LEU cc_start: 0.6526 (tp) cc_final: 0.6195 (tp) REVERT: M 820 GLU cc_start: 0.8112 (tp30) cc_final: 0.7617 (mm-30) REVERT: A 78 PHE cc_start: 0.8833 (m-80) cc_final: 0.8544 (m-80) REVERT: B 26 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8656 (tp) REVERT: B 78 ARG cc_start: 0.7636 (ptt90) cc_final: 0.7342 (ptt90) REVERT: B 88 TYR cc_start: 0.8187 (m-10) cc_final: 0.7552 (m-10) REVERT: C 56 GLU cc_start: 0.8617 (tt0) cc_final: 0.8312 (tt0) REVERT: C 61 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8702 (mm-30) REVERT: C 99 ARG cc_start: 0.8872 (mmt180) cc_final: 0.8647 (mmm-85) REVERT: D 59 MET cc_start: 0.9277 (tpp) cc_final: 0.9051 (tpp) REVERT: D 68 ASP cc_start: 0.9167 (t70) cc_final: 0.8935 (t0) REVERT: D 83 TYR cc_start: 0.8515 (m-10) cc_final: 0.8103 (m-80) REVERT: D 108 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8767 (tmtt) REVERT: E 96 CYS cc_start: 0.8913 (m) cc_final: 0.8699 (m) REVERT: E 120 MET cc_start: 0.9250 (mtp) cc_final: 0.8920 (mtm) REVERT: F 25 ASN cc_start: 0.8203 (m110) cc_final: 0.7921 (m110) REVERT: F 53 GLU cc_start: 0.9071 (tp30) cc_final: 0.8753 (tp30) REVERT: F 88 TYR cc_start: 0.8345 (m-10) cc_final: 0.8085 (m-10) REVERT: G 33 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9270 (mm) REVERT: G 57 TYR cc_start: 0.7906 (t80) cc_final: 0.7603 (t80) REVERT: G 92 GLU cc_start: 0.8873 (tt0) cc_final: 0.8552 (tt0) REVERT: H 34 LYS cc_start: 0.8776 (mppt) cc_final: 0.8566 (mmmm) REVERT: H 51 ASP cc_start: 0.8577 (t0) cc_final: 0.8331 (p0) REVERT: H 105 GLU cc_start: 0.8864 (tp30) cc_final: 0.8659 (tp30) REVERT: H 108 LYS cc_start: 0.9426 (pptt) cc_final: 0.9124 (ptpp) REVERT: U 27 LYS cc_start: 0.8360 (ptpp) cc_final: 0.7915 (ptpp) outliers start: 41 outliers final: 16 residues processed: 337 average time/residue: 0.1329 time to fit residues: 60.5957 Evaluate side-chains 287 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 268 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 741 LEU Chi-restraints excluded: chain M residue 758 HIS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 43 VAL 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 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 75 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 635 HIS M 696 HIS M 800 HIS A 85 GLN A 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 55 GLN F 25 ASN U 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.086191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.056944 restraints weight = 57312.138| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.73 r_work: 0.2895 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15825 Z= 0.160 Angle : 0.616 8.523 22627 Z= 0.350 Chirality : 0.036 0.161 2587 Planarity : 0.004 0.050 1848 Dihedral : 29.732 174.825 4448 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.16 % Allowed : 18.95 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1101 helix: 1.25 (0.20), residues: 679 sheet: 1.33 (0.60), residues: 78 loop : -0.28 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 699 TYR 0.025 0.002 TYR D 83 PHE 0.012 0.001 PHE B 100 TRP 0.005 0.002 TRP M 793 HIS 0.021 0.002 HIS M 758 Details of bonding type rmsd covalent geometry : bond 0.00354 (15825) covalent geometry : angle 0.61640 (22627) hydrogen bonds : bond 0.04329 ( 894) hydrogen bonds : angle 3.59976 ( 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 312 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.383 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 635 HIS cc_start: 0.3496 (OUTLIER) cc_final: 0.2669 (t-90) REVERT: M 643 ASN cc_start: 0.7100 (t0) cc_final: 0.6809 (t0) REVERT: M 714 ILE cc_start: 0.6310 (tp) cc_final: 0.6107 (tp) REVERT: M 718 GLU cc_start: 0.7294 (pm20) cc_final: 0.6514 (tm-30) REVERT: M 719 ILE cc_start: 0.8135 (mt) cc_final: 0.7801 (mp) REVERT: M 744 LEU cc_start: 0.6609 (tp) cc_final: 0.5896 (tp) REVERT: M 793 TRP cc_start: 0.7705 (m100) cc_final: 0.7499 (m100) REVERT: M 820 GLU cc_start: 0.8179 (tp30) cc_final: 0.7886 (mm-30) REVERT: B 88 TYR cc_start: 0.8171 (m-10) cc_final: 0.7863 (m-10) REVERT: B 97 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8986 (pt) REVERT: C 57 TYR cc_start: 0.9051 (t80) cc_final: 0.8794 (t80) REVERT: C 61 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8741 (mm-30) REVERT: C 94 ASN cc_start: 0.9117 (t0) cc_final: 0.8904 (t0) REVERT: C 99 ARG cc_start: 0.8891 (mmt180) cc_final: 0.8635 (mmm-85) REVERT: C 104 GLN cc_start: 0.9184 (mp10) cc_final: 0.8963 (mm-40) REVERT: D 59 MET cc_start: 0.9254 (tpp) cc_final: 0.9036 (tpp) REVERT: D 108 LYS cc_start: 0.9116 (tmtt) cc_final: 0.8875 (tmtt) REVERT: E 96 CYS cc_start: 0.9028 (m) cc_final: 0.8699 (m) REVERT: E 125 GLN cc_start: 0.9135 (mp10) cc_final: 0.8236 (mp10) REVERT: G 33 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9157 (mm) REVERT: G 92 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: H 34 LYS cc_start: 0.8718 (mppt) cc_final: 0.8486 (mptt) REVERT: H 108 LYS cc_start: 0.9349 (pptt) cc_final: 0.9038 (ptpp) outliers start: 30 outliers final: 20 residues processed: 297 average time/residue: 0.1660 time to fit residues: 67.0859 Evaluate side-chains 283 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 259 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 279 LYS Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 758 HIS Chi-restraints excluded: chain M residue 800 HIS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain 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 101 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 18 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 635 HIS M 758 HIS M 800 HIS F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.084400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054997 restraints weight = 58483.074| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.72 r_work: 0.2824 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15825 Z= 0.187 Angle : 0.621 9.681 22627 Z= 0.353 Chirality : 0.037 0.181 2587 Planarity : 0.004 0.050 1848 Dihedral : 29.597 174.645 4448 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.58 % Allowed : 19.47 % Favored : 76.95 % 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 aren not related in a simple way. whole: 1.32 (0.25), residues: 1101 helix: 1.49 (0.20), residues: 677 sheet: 1.12 (0.61), residues: 78 loop : -0.33 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.034 0.002 TYR D 83 PHE 0.011 0.001 PHE M 716 TRP 0.003 0.001 TRP M 793 HIS 0.029 0.002 HIS M 800 Details of bonding type rmsd covalent geometry : bond 0.00423 (15825) covalent geometry : angle 0.62088 (22627) hydrogen bonds : bond 0.04585 ( 894) hydrogen bonds : angle 3.48270 ( 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: 34 poor density : 271 time to evaluate : 0.475 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 284 GLN cc_start: 0.8890 (mm-40) cc_final: 0.7891 (mt0) REVERT: M 643 ASN cc_start: 0.7004 (t0) cc_final: 0.6753 (t0) REVERT: M 718 GLU cc_start: 0.7328 (pm20) cc_final: 0.6485 (tm-30) REVERT: M 719 ILE cc_start: 0.8166 (mt) cc_final: 0.7831 (mp) REVERT: B 77 LYS cc_start: 0.9402 (mttt) cc_final: 0.9190 (mttm) REVERT: B 97 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8945 (pt) REVERT: C 78 ILE cc_start: 0.8768 (pt) cc_final: 0.8510 (mt) REVERT: C 94 ASN cc_start: 0.9255 (t0) cc_final: 0.9037 (t0) REVERT: C 99 ARG cc_start: 0.8954 (mmt180) cc_final: 0.8678 (mmm-85) REVERT: D 33 ARG cc_start: 0.8276 (mmm160) cc_final: 0.8062 (mmm160) REVERT: D 71 GLU cc_start: 0.9171 (tp30) cc_final: 0.8823 (tp30) REVERT: D 90 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8444 (p) REVERT: E 96 CYS cc_start: 0.9024 (m) cc_final: 0.8733 (m) REVERT: E 125 GLN cc_start: 0.9094 (mp10) cc_final: 0.8246 (mp10) REVERT: G 33 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9199 (mm) REVERT: G 72 ASP cc_start: 0.8467 (m-30) cc_final: 0.8257 (m-30) REVERT: G 92 GLU cc_start: 0.8996 (tt0) cc_final: 0.8698 (mt-10) REVERT: H 33 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7953 (mtm180) REVERT: H 34 LYS cc_start: 0.8824 (mppt) cc_final: 0.8579 (mptt) REVERT: H 68 ASP cc_start: 0.9232 (t0) cc_final: 0.8909 (t0) REVERT: H 79 ARG cc_start: 0.9043 (ttp-110) cc_final: 0.8748 (mtm-85) REVERT: H 105 GLU cc_start: 0.8727 (tp30) cc_final: 0.8273 (tp30) REVERT: H 108 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8952 (ptpp) REVERT: U 76 CYS cc_start: 0.8860 (t) cc_final: 0.8638 (t) outliers start: 34 outliers final: 19 residues processed: 288 average time/residue: 0.1556 time to fit residues: 60.9453 Evaluate side-chains 286 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 263 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 279 LYS Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 758 HIS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 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 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 50 GLU 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 108 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain U residue 6 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: 50.0000 chunk 97 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 635 HIS M 758 HIS ** M 800 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 = 0.3809 r_free = 0.3809 target = 0.083060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053060 restraints weight = 57217.480| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.47 r_work: 0.2793 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15825 Z= 0.189 Angle : 0.615 10.644 22627 Z= 0.348 Chirality : 0.037 0.213 2587 Planarity : 0.004 0.048 1848 Dihedral : 29.624 174.913 4448 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.89 % Allowed : 20.21 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.25), residues: 1101 helix: 1.58 (0.20), residues: 676 sheet: 1.41 (0.61), residues: 76 loop : -0.34 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 305 TYR 0.021 0.002 TYR D 83 PHE 0.010 0.001 PHE B 100 TRP 0.001 0.000 TRP M 793 HIS 0.030 0.002 HIS M 758 Details of bonding type rmsd covalent geometry : bond 0.00425 (15825) covalent geometry : angle 0.61500 (22627) hydrogen bonds : bond 0.04378 ( 894) hydrogen bonds : angle 3.42639 ( 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 304 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 309 ASP cc_start: 0.8086 (p0) cc_final: 0.7586 (p0) REVERT: M 635 HIS cc_start: 0.3232 (OUTLIER) cc_final: 0.2342 (t-90) REVERT: M 718 GLU cc_start: 0.7230 (pm20) cc_final: 0.6414 (tm-30) REVERT: B 77 LYS cc_start: 0.9471 (mttt) cc_final: 0.9238 (mttm) REVERT: B 88 TYR cc_start: 0.8795 (m-10) cc_final: 0.8556 (m-80) REVERT: B 97 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8937 (pt) REVERT: C 73 ASN cc_start: 0.9229 (t0) cc_final: 0.8971 (t0) REVERT: C 99 ARG cc_start: 0.8983 (mmt180) cc_final: 0.8685 (mmm-85) REVERT: D 51 ASP cc_start: 0.8910 (m-30) cc_final: 0.8539 (p0) REVERT: D 71 GLU cc_start: 0.9122 (tp30) cc_final: 0.8844 (tp30) REVERT: D 108 LYS cc_start: 0.9336 (tmtt) cc_final: 0.8865 (tmtt) REVERT: E 96 CYS cc_start: 0.8988 (m) cc_final: 0.8721 (m) REVERT: E 125 GLN cc_start: 0.9098 (mp10) cc_final: 0.8119 (mp10) REVERT: G 72 ASP cc_start: 0.8627 (m-30) cc_final: 0.8401 (m-30) REVERT: G 92 GLU cc_start: 0.9002 (tt0) cc_final: 0.8714 (mt-10) REVERT: H 34 LYS cc_start: 0.8930 (mppt) cc_final: 0.8703 (mptt) REVERT: H 68 ASP cc_start: 0.9221 (t0) cc_final: 0.8926 (t0) REVERT: H 79 ARG cc_start: 0.9097 (ttp-110) cc_final: 0.8881 (mtm-85) REVERT: H 105 GLU cc_start: 0.8667 (tp30) cc_final: 0.8353 (tp30) REVERT: H 108 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9104 (ptpp) outliers start: 37 outliers final: 22 residues processed: 284 average time/residue: 0.1403 time to fit residues: 53.8938 Evaluate side-chains 273 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 279 LYS Chi-restraints excluded: chain M residue 291 ARG Chi-restraints excluded: chain M residue 635 HIS 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 A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR 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 87 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 112 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: 0.9980 chunk 96 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 635 HIS M 758 HIS ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.082705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.052829 restraints weight = 56400.230| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.47 r_work: 0.2787 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15825 Z= 0.164 Angle : 0.618 12.585 22627 Z= 0.343 Chirality : 0.036 0.189 2587 Planarity : 0.004 0.048 1848 Dihedral : 29.577 175.385 4448 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.47 % Allowed : 20.74 % Favored : 75.79 % 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 aren not related in a simple way. whole: 1.54 (0.25), residues: 1101 helix: 1.67 (0.20), residues: 674 sheet: 1.52 (0.61), residues: 75 loop : -0.30 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 305 TYR 0.033 0.002 TYR G 57 PHE 0.018 0.001 PHE U 45 TRP 0.002 0.001 TRP M 793 HIS 0.013 0.001 HIS M 758 Details of bonding type rmsd covalent geometry : bond 0.00369 (15825) covalent geometry : angle 0.61823 (22627) hydrogen bonds : bond 0.04101 ( 894) hydrogen bonds : angle 3.32047 ( 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 291 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.432 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 635 HIS cc_start: 0.3556 (OUTLIER) cc_final: 0.2649 (t-90) REVERT: M 718 GLU cc_start: 0.7245 (pm20) cc_final: 0.6451 (tm-30) REVERT: B 97 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8917 (pt) REVERT: C 73 ASN cc_start: 0.9189 (t0) cc_final: 0.8902 (t0) REVERT: C 99 ARG cc_start: 0.8934 (mmt180) cc_final: 0.8656 (mmm-85) REVERT: D 33 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8201 (mmm160) REVERT: D 51 ASP cc_start: 0.8950 (m-30) cc_final: 0.8701 (p0) REVERT: D 108 LYS cc_start: 0.9352 (tmtt) cc_final: 0.8915 (tmtt) REVERT: E 96 CYS cc_start: 0.8970 (m) cc_final: 0.8714 (m) REVERT: E 125 GLN cc_start: 0.9034 (mp10) cc_final: 0.8827 (mm-40) REVERT: G 41 GLU cc_start: 0.8719 (pm20) cc_final: 0.8464 (mp0) REVERT: G 72 ASP cc_start: 0.8695 (m-30) cc_final: 0.8456 (m-30) REVERT: G 92 GLU cc_start: 0.8981 (tt0) cc_final: 0.8704 (mt-10) REVERT: H 34 LYS cc_start: 0.8949 (mppt) cc_final: 0.8746 (mptt) REVERT: H 68 ASP cc_start: 0.9242 (t0) cc_final: 0.8953 (t0) REVERT: H 105 GLU cc_start: 0.8587 (tp30) cc_final: 0.8231 (tp30) REVERT: U 6 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7355 (pptt) outliers start: 33 outliers final: 16 residues processed: 275 average time/residue: 0.1684 time to fit residues: 62.6009 Evaluate side-chains 271 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 635 HIS 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 A residue 60 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 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 D residue 84 ASN Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 117 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 635 HIS M 758 HIS ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.083032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053111 restraints weight = 55829.399| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.48 r_work: 0.2795 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.7690 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= 0.150 Angle : 0.614 12.985 22627 Z= 0.339 Chirality : 0.036 0.204 2587 Planarity : 0.004 0.046 1848 Dihedral : 29.511 175.581 4448 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.05 % Allowed : 20.95 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.26), residues: 1101 helix: 1.69 (0.20), residues: 676 sheet: 1.48 (0.61), residues: 77 loop : -0.24 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 305 TYR 0.018 0.001 TYR D 83 PHE 0.014 0.001 PHE U 45 TRP 0.002 0.001 TRP M 793 HIS 0.006 0.001 HIS M 758 Details of bonding type rmsd covalent geometry : bond 0.00335 (15825) covalent geometry : angle 0.61422 (22627) hydrogen bonds : bond 0.03928 ( 894) hydrogen bonds : angle 3.28156 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 0.429 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 718 GLU cc_start: 0.7276 (pm20) cc_final: 0.6456 (tm-30) REVERT: B 97 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8864 (pt) REVERT: C 73 ASN cc_start: 0.9184 (t0) cc_final: 0.8850 (t0) REVERT: C 99 ARG cc_start: 0.8961 (mmt180) cc_final: 0.8673 (mmm-85) REVERT: D 51 ASP cc_start: 0.8963 (m-30) cc_final: 0.8725 (p0) REVERT: D 59 MET cc_start: 0.9365 (tpp) cc_final: 0.8996 (tpp) REVERT: D 108 LYS cc_start: 0.9350 (tmtt) cc_final: 0.8912 (tmtt) REVERT: E 96 CYS cc_start: 0.8985 (m) cc_final: 0.8736 (m) REVERT: G 41 GLU cc_start: 0.8745 (pm20) cc_final: 0.8501 (mp0) REVERT: G 72 ASP cc_start: 0.8777 (m-30) cc_final: 0.8515 (m-30) REVERT: G 92 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: H 34 LYS cc_start: 0.8956 (mppt) cc_final: 0.8739 (mptt) REVERT: H 68 ASP cc_start: 0.9255 (t0) cc_final: 0.8974 (t0) REVERT: U 6 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6945 (pttp) outliers start: 29 outliers final: 20 residues processed: 279 average time/residue: 0.1613 time to fit residues: 61.1591 Evaluate side-chains 271 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 385 LEU Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR 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 B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 635 HIS ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.077891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.046925 restraints weight = 54925.084| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.46 r_work: 0.2613 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.9085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15825 Z= 0.324 Angle : 0.731 11.425 22627 Z= 0.407 Chirality : 0.044 0.296 2587 Planarity : 0.006 0.059 1848 Dihedral : 30.036 174.580 4448 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.79 % Allowed : 21.58 % Favored : 74.63 % 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 aren not related in a simple way. whole: 1.08 (0.25), residues: 1101 helix: 1.31 (0.20), residues: 676 sheet: 0.91 (0.57), residues: 78 loop : -0.39 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 305 TYR 0.045 0.003 TYR D 83 PHE 0.023 0.002 PHE U 45 TRP 0.006 0.002 TRP M 793 HIS 0.007 0.002 HIS M 635 Details of bonding type rmsd covalent geometry : bond 0.00743 (15825) covalent geometry : angle 0.73079 (22627) hydrogen bonds : bond 0.07672 ( 894) hydrogen bonds : angle 3.72256 ( 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 274 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 212 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7568 (mt0) REVERT: C 72 ASP cc_start: 0.8935 (m-30) cc_final: 0.8724 (m-30) REVERT: C 73 ASN cc_start: 0.9332 (t0) cc_final: 0.8909 (t0) REVERT: C 99 ARG cc_start: 0.9033 (mmt180) cc_final: 0.8757 (mmm-85) REVERT: D 33 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.8375 (mmt90) REVERT: D 59 MET cc_start: 0.9529 (tpp) cc_final: 0.9201 (tpp) REVERT: D 101 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9450 (mm) REVERT: D 108 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9091 (ttpp) REVERT: E 79 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8865 (ttmm) REVERT: F 91 LYS cc_start: 0.9609 (OUTLIER) cc_final: 0.9373 (tttm) REVERT: G 92 GLU cc_start: 0.8977 (tt0) cc_final: 0.8732 (mt-10) REVERT: H 34 LYS cc_start: 0.9176 (mppt) cc_final: 0.8940 (mmtm) REVERT: H 68 ASP cc_start: 0.9245 (t0) cc_final: 0.8960 (t0) REVERT: U 6 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6782 (pttp) outliers start: 36 outliers final: 22 residues processed: 255 average time/residue: 0.1685 time to fit residues: 57.8632 Evaluate side-chains 252 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 291 ARG Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 758 HIS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR 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 B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 91 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 266 ASN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS E 93 GLN ** U 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.077998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047744 restraints weight = 55444.570| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.43 r_work: 0.2621 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.9454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15825 Z= 0.264 Angle : 0.691 12.591 22627 Z= 0.385 Chirality : 0.040 0.231 2587 Planarity : 0.005 0.073 1848 Dihedral : 29.989 177.208 4448 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.53 % Allowed : 24.00 % 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 aren not related in a simple way. whole: 1.12 (0.26), residues: 1101 helix: 1.36 (0.20), residues: 675 sheet: 0.75 (0.59), residues: 80 loop : -0.37 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 305 TYR 0.027 0.002 TYR D 83 PHE 0.013 0.001 PHE U 45 TRP 0.002 0.001 TRP M 793 HIS 0.008 0.001 HIS M 635 Details of bonding type rmsd covalent geometry : bond 0.00605 (15825) covalent geometry : angle 0.69106 (22627) hydrogen bonds : bond 0.04718 ( 894) hydrogen bonds : angle 3.50847 ( 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 272 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.459 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 212 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7589 (mt0) REVERT: M 261 MET cc_start: 0.9186 (tpt) cc_final: 0.8909 (mmm) REVERT: M 718 GLU cc_start: 0.7420 (pm20) cc_final: 0.6084 (tm-30) REVERT: M 719 ILE cc_start: 0.8574 (mt) cc_final: 0.8113 (mm) REVERT: M 743 SER cc_start: 0.8867 (p) cc_final: 0.8531 (p) REVERT: C 73 ASN cc_start: 0.9302 (t0) cc_final: 0.8895 (t0) REVERT: C 104 GLN cc_start: 0.9284 (mm-40) cc_final: 0.9037 (mm110) REVERT: D 33 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8395 (mmt90) REVERT: D 59 MET cc_start: 0.9513 (tpp) cc_final: 0.9207 (tpp) REVERT: D 108 LYS cc_start: 0.9341 (tmtt) cc_final: 0.9072 (ttpp) REVERT: G 92 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8764 (mt-10) REVERT: H 59 MET cc_start: 0.9503 (tpp) cc_final: 0.9297 (mmm) REVERT: H 68 ASP cc_start: 0.9254 (t0) cc_final: 0.9017 (t0) REVERT: U 6 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6718 (pttp) outliers start: 24 outliers final: 17 residues processed: 260 average time/residue: 0.1705 time to fit residues: 59.9504 Evaluate side-chains 257 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 305 ARG 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 A residue 60 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 18 SER 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 92 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 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN D 84 ASN G 104 GLN U 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.079520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.049442 restraints weight = 55012.654| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.40 r_work: 0.2682 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.9550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15825 Z= 0.159 Angle : 0.676 12.654 22627 Z= 0.369 Chirality : 0.037 0.221 2587 Planarity : 0.004 0.057 1848 Dihedral : 29.711 177.225 4448 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.42 % Allowed : 24.53 % Favored : 73.05 % 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 aren not related in a simple way. whole: 1.24 (0.26), residues: 1101 helix: 1.43 (0.20), residues: 675 sheet: 0.94 (0.58), residues: 79 loop : -0.30 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 305 TYR 0.021 0.002 TYR B 88 PHE 0.010 0.001 PHE M 716 TRP 0.001 0.000 TRP M 793 HIS 0.003 0.001 HIS M 316 Details of bonding type rmsd covalent geometry : bond 0.00357 (15825) covalent geometry : angle 0.67556 (22627) hydrogen bonds : bond 0.04034 ( 894) hydrogen bonds : angle 3.39321 ( 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 280 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 0.295 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 212 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7683 (mt0) REVERT: M 261 MET cc_start: 0.9193 (tpt) cc_final: 0.8961 (mmm) REVERT: M 351 MET cc_start: 0.6389 (tmm) cc_final: 0.6160 (tmm) REVERT: C 73 ASN cc_start: 0.9265 (t0) cc_final: 0.8837 (t0) REVERT: C 104 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8927 (mm110) REVERT: D 33 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8565 (mmt90) REVERT: D 59 MET cc_start: 0.9461 (tpp) cc_final: 0.9190 (tpp) REVERT: D 108 LYS cc_start: 0.9347 (tmtt) cc_final: 0.9049 (ttpp) REVERT: U 6 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.6793 (pttp) REVERT: U 27 LYS cc_start: 0.8752 (ptpp) cc_final: 0.8526 (ptpp) outliers start: 23 outliers final: 16 residues processed: 266 average time/residue: 0.1433 time to fit residues: 51.9762 Evaluate side-chains 264 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 305 ARG 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 A residue 60 LEU 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 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 85 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 31 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 2 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN D 84 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.079235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.049205 restraints weight = 55090.170| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.42 r_work: 0.2677 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.9549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15825 Z= 0.186 Angle : 0.851 59.188 22627 Z= 0.489 Chirality : 0.038 0.388 2587 Planarity : 0.004 0.057 1848 Dihedral : 29.708 177.214 4448 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.00 % Allowed : 24.63 % Favored : 73.37 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: 1.22 (0.26), residues: 1101 helix: 1.40 (0.20), residues: 675 sheet: 0.95 (0.58), residues: 79 loop : -0.30 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 305 TYR 0.018 0.002 TYR D 83 PHE 0.010 0.001 PHE M 716 TRP 0.002 0.001 TRP M 793 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (15825) covalent geometry : angle 0.85141 (22627) hydrogen bonds : bond 0.04061 ( 894) hydrogen bonds : angle 3.39395 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4420.97 seconds wall clock time: 76 minutes 5.10 seconds (4565.10 seconds total)