Starting phenix.real_space_refine on Fri Jun 13 05:08:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg5_37503/06_2025/8wg5_37503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg5_37503/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wg5_37503/06_2025/8wg5_37503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg5_37503/06_2025/8wg5_37503.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg5_37503/06_2025/8wg5_37503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg5_37503/06_2025/8wg5_37503.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1} 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: 9.18, per 1000 atoms: 0.61 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: 3.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 7.56 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: 8.22 Time building geometry restraints manager: 4.69 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.140 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.700 ------------------------------------------------------------------------------- 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 : 12.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP M 793 HIS 0.006 0.001 HIS M 696 PHE 0.010 0.001 PHE M 359 TYR 0.050 0.002 TYR D 83 ARG 0.007 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.13057 ( 894) hydrogen bonds : angle 5.04900 ( 2271) covalent geometry : bond 0.00342 (15825) covalent geometry : angle 0.59034 (22627) *********************** 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 : 1.919 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: 0.3570 time to fit residues: 199.5256 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 : 1.262 ------------------------------------------------------------------------------- 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 113 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 C 68 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS H 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.089111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.061395 restraints weight = 58895.042| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.72 r_work: 0.3022 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 15825 Z= 0.248 Angle : 0.792 11.548 22627 Z= 0.438 Chirality : 0.043 0.220 2587 Planarity : 0.007 0.090 1848 Dihedral : 29.546 173.754 4452 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 3.68 % Allowed : 17.05 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1101 helix: 0.69 (0.19), residues: 675 sheet: 1.76 (0.61), residues: 67 loop : -0.29 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.006 TRP M 793 HIS 0.009 0.002 HIS H 49 PHE 0.019 0.002 PHE U 45 TYR 0.040 0.003 TYR D 83 ARG 0.015 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05845 ( 894) hydrogen bonds : angle 4.00674 ( 2271) covalent geometry : bond 0.00553 (15825) covalent geometry : angle 0.79206 (22627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 322 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 643 ASN cc_start: 0.7086 (t0) cc_final: 0.6780 (t0) REVERT: M 718 GLU cc_start: 0.7572 (pm20) cc_final: 0.6971 (tm-30) REVERT: M 744 LEU cc_start: 0.6168 (tp) cc_final: 0.5532 (tp) REVERT: M 820 GLU cc_start: 0.7917 (tp30) cc_final: 0.7461 (mm-30) REVERT: A 48 LEU cc_start: 0.8989 (mm) cc_final: 0.8690 (mm) REVERT: B 26 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8373 (tp) REVERT: B 88 TYR cc_start: 0.7278 (m-10) cc_final: 0.7041 (m-10) REVERT: C 61 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8543 (mm-30) REVERT: C 64 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8224 (tt0) REVERT: D 59 MET cc_start: 0.8945 (tpp) cc_final: 0.8727 (tpp) REVERT: D 83 TYR cc_start: 0.8276 (m-10) cc_final: 0.7707 (m-10) REVERT: D 108 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8600 (tmtt) REVERT: D 111 VAL cc_start: 0.8978 (m) cc_final: 0.8773 (t) REVERT: E 120 MET cc_start: 0.9107 (mtp) cc_final: 0.8770 (mtm) REVERT: F 31 LYS cc_start: 0.9238 (tttm) cc_final: 0.8943 (tttp) REVERT: F 53 GLU cc_start: 0.8977 (tp30) cc_final: 0.8665 (tp30) REVERT: G 33 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9220 (mm) REVERT: G 92 GLU cc_start: 0.8622 (tt0) cc_final: 0.8232 (tt0) REVERT: H 34 LYS cc_start: 0.8625 (mppt) cc_final: 0.8151 (mptt) REVERT: H 68 ASP cc_start: 0.8814 (t0) cc_final: 0.8563 (t0) REVERT: H 72 ARG cc_start: 0.9293 (mmm-85) cc_final: 0.9077 (mtt180) outliers start: 35 outliers final: 14 residues processed: 341 average time/residue: 0.3660 time to fit residues: 167.6862 Evaluate side-chains 276 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 286 CYS Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 719 ILE Chi-restraints excluded: chain 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 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 55 GLN F 25 ASN G 24 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.088637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.060588 restraints weight = 57710.814| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.66 r_work: 0.2981 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15825 Z= 0.161 Angle : 0.608 8.555 22627 Z= 0.345 Chirality : 0.037 0.172 2587 Planarity : 0.004 0.047 1848 Dihedral : 29.543 174.446 4448 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.05 % Allowed : 19.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1101 helix: 1.33 (0.20), residues: 677 sheet: 1.45 (0.64), residues: 69 loop : -0.05 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP M 793 HIS 0.006 0.001 HIS H 49 PHE 0.009 0.001 PHE M 716 TYR 0.023 0.002 TYR D 83 ARG 0.008 0.001 ARG M 699 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 894) hydrogen bonds : angle 3.54215 ( 2271) covalent geometry : bond 0.00357 (15825) covalent geometry : angle 0.60817 (22627) *********************** 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 320 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 1.379 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 311 MET cc_start: 0.7287 (mmp) cc_final: 0.7029 (mmm) REVERT: M 325 LYS cc_start: 0.8468 (pptt) cc_final: 0.8259 (pttp) REVERT: M 635 HIS cc_start: 0.3268 (OUTLIER) cc_final: 0.2387 (t-90) REVERT: M 643 ASN cc_start: 0.6969 (t0) cc_final: 0.6688 (t0) REVERT: M 714 ILE cc_start: 0.6270 (tp) cc_final: 0.5863 (tp) REVERT: M 718 GLU cc_start: 0.7403 (pm20) cc_final: 0.6703 (tm-30) REVERT: M 744 LEU cc_start: 0.6392 (tp) cc_final: 0.5680 (tp) REVERT: M 820 GLU cc_start: 0.8117 (tp30) cc_final: 0.7565 (mm-30) REVERT: A 123 ASP cc_start: 0.8959 (m-30) cc_final: 0.8696 (m-30) REVERT: B 26 ILE cc_start: 0.8658 (mp) cc_final: 0.8372 (tp) REVERT: B 31 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8237 (ttpp) REVERT: C 61 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8635 (mm-30) REVERT: C 64 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8405 (tt0) REVERT: C 94 ASN cc_start: 0.8850 (t0) cc_final: 0.8647 (t0) REVERT: C 104 GLN cc_start: 0.9187 (mp10) cc_final: 0.8447 (mp10) REVERT: D 59 MET cc_start: 0.9078 (tpp) cc_final: 0.8749 (tpp) REVERT: D 108 LYS cc_start: 0.8978 (tmtt) cc_final: 0.8708 (tmtt) REVERT: E 73 GLU cc_start: 0.9119 (tt0) cc_final: 0.8760 (tt0) REVERT: E 125 GLN cc_start: 0.9061 (mp10) cc_final: 0.8846 (mp10) REVERT: G 33 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9127 (mm) REVERT: G 104 GLN cc_start: 0.9068 (mp10) cc_final: 0.8855 (mp10) REVERT: H 42 TYR cc_start: 0.8058 (t80) cc_final: 0.7849 (t80) REVERT: H 108 LYS cc_start: 0.9157 (pptt) cc_final: 0.8895 (ptpp) REVERT: H 113 GLU cc_start: 0.9141 (tp30) cc_final: 0.8917 (tp30) REVERT: U 6 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7363 (pptt) outliers start: 29 outliers final: 15 residues processed: 307 average time/residue: 0.4349 time to fit residues: 180.9563 Evaluate side-chains 279 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 719 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain 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 74 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.084221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053936 restraints weight = 57733.449| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.58 r_work: 0.2804 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 15825 Z= 0.222 Angle : 0.646 9.135 22627 Z= 0.368 Chirality : 0.039 0.193 2587 Planarity : 0.005 0.054 1848 Dihedral : 29.602 173.972 4448 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.32 % Allowed : 19.16 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1101 helix: 1.35 (0.20), residues: 676 sheet: 1.01 (0.59), residues: 78 loop : -0.16 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 793 HIS 0.027 0.002 HIS M 635 PHE 0.010 0.001 PHE M 282 TYR 0.050 0.002 TYR H 83 ARG 0.007 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 894) hydrogen bonds : angle 3.55073 ( 2271) covalent geometry : bond 0.00510 (15825) covalent geometry : angle 0.64625 (22627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 2.095 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 261 MET cc_start: 0.9029 (tpt) cc_final: 0.8569 (mtt) REVERT: M 284 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8027 (mt0) REVERT: M 303 LEU cc_start: 0.8985 (tp) cc_final: 0.8720 (tt) REVERT: M 325 LYS cc_start: 0.8418 (pptt) cc_final: 0.8217 (pttp) REVERT: M 684 MET cc_start: 0.8333 (mmm) cc_final: 0.7543 (tpp) REVERT: M 718 GLU cc_start: 0.7640 (pm20) cc_final: 0.7371 (pm20) REVERT: M 820 GLU cc_start: 0.8261 (tp30) cc_final: 0.7688 (mm-30) REVERT: B 44 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9217 (mmmt) REVERT: B 77 LYS cc_start: 0.9433 (mttt) cc_final: 0.9214 (mttm) REVERT: B 88 TYR cc_start: 0.8804 (m-10) cc_final: 0.7845 (m-10) REVERT: C 57 TYR cc_start: 0.9147 (t80) cc_final: 0.8938 (t80) REVERT: C 78 ILE cc_start: 0.8834 (pt) cc_final: 0.8606 (mt) REVERT: C 94 ASN cc_start: 0.9195 (t0) cc_final: 0.8983 (t0) REVERT: C 99 ARG cc_start: 0.8891 (mmt180) cc_final: 0.8681 (mmm-85) REVERT: D 68 ASP cc_start: 0.9326 (t70) cc_final: 0.9077 (t0) REVERT: D 83 TYR cc_start: 0.8638 (m-10) cc_final: 0.8359 (m-80) REVERT: E 79 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8500 (ttmm) REVERT: E 125 GLN cc_start: 0.9094 (mp10) cc_final: 0.8260 (mp10) REVERT: G 33 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9210 (mm) REVERT: G 72 ASP cc_start: 0.8485 (m-30) cc_final: 0.8279 (m-30) REVERT: G 92 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8638 (mt-10) REVERT: G 104 GLN cc_start: 0.9196 (mp10) cc_final: 0.8775 (mp10) REVERT: H 34 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8678 (mptt) REVERT: H 42 TYR cc_start: 0.8577 (t80) cc_final: 0.8367 (t80) REVERT: H 51 ASP cc_start: 0.8816 (t0) cc_final: 0.8576 (p0) REVERT: H 68 ASP cc_start: 0.9219 (t0) cc_final: 0.8876 (t0) REVERT: H 108 LYS cc_start: 0.9239 (pptt) cc_final: 0.8981 (ptpp) REVERT: U 76 CYS cc_start: 0.8452 (t) cc_final: 0.8159 (t) outliers start: 41 outliers final: 20 residues processed: 296 average time/residue: 0.4227 time to fit residues: 169.9577 Evaluate side-chains 275 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 279 LYS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 101 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 56 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN E 55 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.082411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.052474 restraints weight = 56683.895| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.50 r_work: 0.2770 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.7659 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= 0.191 Angle : 0.623 9.388 22627 Z= 0.352 Chirality : 0.038 0.180 2587 Planarity : 0.004 0.050 1848 Dihedral : 29.677 175.691 4448 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.42 % Allowed : 20.84 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1101 helix: 1.52 (0.20), residues: 676 sheet: 0.85 (0.60), residues: 71 loop : -0.20 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 793 HIS 0.017 0.001 HIS M 635 PHE 0.013 0.001 PHE M 207 TYR 0.026 0.002 TYR H 83 ARG 0.009 0.001 ARG M 312 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 894) hydrogen bonds : angle 3.44947 ( 2271) covalent geometry : bond 0.00437 (15825) covalent geometry : angle 0.62298 (22627) *********************** 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 305 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 1.160 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 684 MET cc_start: 0.8350 (mmm) cc_final: 0.7705 (tpp) REVERT: B 88 TYR cc_start: 0.9308 (m-10) cc_final: 0.8262 (m-10) REVERT: C 73 ASN cc_start: 0.9304 (t0) cc_final: 0.9016 (t0) REVERT: C 99 ARG cc_start: 0.8910 (mmt180) cc_final: 0.8703 (mmm-85) REVERT: D 51 ASP cc_start: 0.8940 (m-30) cc_final: 0.8714 (p0) REVERT: D 59 MET cc_start: 0.9474 (tpp) cc_final: 0.9213 (tpp) REVERT: D 68 ASP cc_start: 0.9345 (t70) cc_final: 0.9105 (t0) REVERT: D 83 TYR cc_start: 0.8544 (m-10) cc_final: 0.8193 (m-10) REVERT: D 108 LYS cc_start: 0.9375 (tmtt) cc_final: 0.8962 (tmtt) REVERT: E 125 GLN cc_start: 0.9131 (mp10) cc_final: 0.8099 (mp10) REVERT: G 41 GLU cc_start: 0.8758 (pm20) cc_final: 0.8556 (mp0) REVERT: G 72 ASP cc_start: 0.8718 (m-30) cc_final: 0.8449 (m-30) REVERT: H 68 ASP cc_start: 0.9222 (t0) cc_final: 0.8940 (t0) REVERT: H 105 GLU cc_start: 0.8711 (tp30) cc_final: 0.8261 (tp30) REVERT: H 108 LYS cc_start: 0.9240 (pptt) cc_final: 0.9035 (ptpp) REVERT: U 6 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7314 (pptt) REVERT: U 76 CYS cc_start: 0.8514 (t) cc_final: 0.8244 (t) outliers start: 42 outliers final: 20 residues processed: 291 average time/residue: 0.3449 time to fit residues: 136.0676 Evaluate side-chains 266 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 263 GLN 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 A residue 118 THR 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 C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 0.0040 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.082318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.052354 restraints weight = 56481.103| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.46 r_work: 0.2772 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.7863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15825 Z= 0.159 Angle : 0.609 10.470 22627 Z= 0.341 Chirality : 0.036 0.177 2587 Planarity : 0.004 0.050 1848 Dihedral : 29.571 175.683 4448 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.42 % Allowed : 23.16 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1101 helix: 1.70 (0.20), residues: 674 sheet: 0.84 (0.62), residues: 71 loop : -0.12 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 PHE 0.011 0.001 PHE M 716 TYR 0.026 0.001 TYR H 83 ARG 0.009 0.001 ARG M 305 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 894) hydrogen bonds : angle 3.31503 ( 2271) covalent geometry : bond 0.00357 (15825) covalent geometry : angle 0.60866 (22627) *********************** 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 281 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 1.210 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 198 LEU cc_start: 0.8172 (tp) cc_final: 0.7864 (tp) REVERT: M 284 GLN cc_start: 0.9205 (mm110) cc_final: 0.8819 (mm110) REVERT: M 684 MET cc_start: 0.8303 (mmm) cc_final: 0.7634 (tpp) REVERT: M 718 GLU cc_start: 0.7221 (pm20) cc_final: 0.6671 (tp30) REVERT: C 73 ASN cc_start: 0.9307 (t0) cc_final: 0.8979 (t0) REVERT: C 99 ARG cc_start: 0.8910 (mmt180) cc_final: 0.8676 (mmm-85) REVERT: D 33 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7850 (mmm160) REVERT: D 59 MET cc_start: 0.9420 (tpp) cc_final: 0.9126 (tpp) REVERT: D 68 ASP cc_start: 0.9398 (t70) cc_final: 0.9153 (t0) REVERT: D 83 TYR cc_start: 0.8580 (m-10) cc_final: 0.8181 (m-10) REVERT: E 79 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8711 (ttmm) REVERT: E 125 GLN cc_start: 0.8981 (mp10) cc_final: 0.8667 (mm-40) REVERT: F 53 GLU cc_start: 0.8802 (tp30) cc_final: 0.8528 (tt0) REVERT: H 34 LYS cc_start: 0.9073 (mmmm) cc_final: 0.8779 (mptt) REVERT: H 68 ASP cc_start: 0.9261 (t0) cc_final: 0.8986 (t0) REVERT: H 105 GLU cc_start: 0.8668 (tp30) cc_final: 0.8158 (tp30) outliers start: 23 outliers final: 15 residues processed: 273 average time/residue: 0.3587 time to fit residues: 132.2576 Evaluate side-chains 262 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 279 LYS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 266 ASN ** M 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 297 GLN M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 84 ASN E 55 GLN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.082281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.052462 restraints weight = 56466.046| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.49 r_work: 0.2777 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.8131 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= 0.154 Angle : 0.610 10.545 22627 Z= 0.341 Chirality : 0.036 0.188 2587 Planarity : 0.004 0.047 1848 Dihedral : 29.482 175.713 4448 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.58 % Allowed : 22.11 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1101 helix: 1.70 (0.20), residues: 674 sheet: 0.89 (0.64), residues: 71 loop : -0.04 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 793 HIS 0.003 0.001 HIS U 68 PHE 0.017 0.001 PHE U 45 TYR 0.025 0.001 TYR H 83 ARG 0.005 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 894) hydrogen bonds : angle 3.30818 ( 2271) covalent geometry : bond 0.00341 (15825) covalent geometry : angle 0.60998 (22627) *********************** 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 290 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 1.314 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 198 LEU cc_start: 0.8016 (tp) cc_final: 0.7711 (tp) REVERT: M 684 MET cc_start: 0.8375 (mmm) cc_final: 0.7739 (tpp) REVERT: A 60 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8116 (mp) REVERT: A 129 ARG cc_start: 0.9042 (mmm160) cc_final: 0.8834 (mmm160) REVERT: C 73 ASN cc_start: 0.9310 (t0) cc_final: 0.8909 (t0) REVERT: C 99 ARG cc_start: 0.8910 (mmt180) cc_final: 0.8682 (mmm-85) REVERT: D 59 MET cc_start: 0.9416 (tpp) cc_final: 0.9128 (tpp) REVERT: D 68 ASP cc_start: 0.9404 (t70) cc_final: 0.9148 (t0) REVERT: D 71 GLU cc_start: 0.9147 (tp30) cc_final: 0.8883 (tp30) REVERT: E 125 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8753 (mm-40) REVERT: G 72 ASP cc_start: 0.8603 (m-30) cc_final: 0.8328 (m-30) REVERT: H 34 LYS cc_start: 0.9095 (mmmm) cc_final: 0.8870 (mptt) REVERT: H 68 ASP cc_start: 0.9254 (t0) cc_final: 0.9031 (t0) REVERT: U 6 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7287 (pptt) outliers start: 34 outliers final: 19 residues processed: 274 average time/residue: 0.3768 time to fit residues: 138.3580 Evaluate side-chains 267 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 686 ILE Chi-restraints excluded: chain M residue 747 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 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 263 GLN M 284 GLN M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 49 HIS D 84 ASN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.081958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051933 restraints weight = 56157.485| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.45 r_work: 0.2767 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.8281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15825 Z= 0.162 Angle : 0.619 11.517 22627 Z= 0.344 Chirality : 0.036 0.192 2587 Planarity : 0.004 0.047 1848 Dihedral : 29.467 175.773 4448 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.37 % Allowed : 23.05 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1101 helix: 1.66 (0.20), residues: 677 sheet: 0.87 (0.65), residues: 71 loop : -0.03 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 PHE 0.011 0.001 PHE M 716 TYR 0.042 0.002 TYR B 88 ARG 0.005 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 894) hydrogen bonds : angle 3.31948 ( 2271) covalent geometry : bond 0.00366 (15825) covalent geometry : angle 0.61860 (22627) *********************** 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 275 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.300 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 198 LEU cc_start: 0.8048 (tp) cc_final: 0.7734 (tp) REVERT: M 684 MET cc_start: 0.8400 (mmm) cc_final: 0.7759 (tpp) REVERT: M 718 GLU cc_start: 0.7081 (pm20) cc_final: 0.6569 (tp30) REVERT: M 821 ARG cc_start: 0.7302 (tpt90) cc_final: 0.6032 (mmp-170) REVERT: A 129 ARG cc_start: 0.9052 (mmm160) cc_final: 0.8844 (mmm160) REVERT: B 88 TYR cc_start: 0.9112 (m-10) cc_final: 0.8879 (m-10) REVERT: B 97 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9050 (pt) REVERT: C 73 ASN cc_start: 0.9319 (t0) cc_final: 0.8904 (t0) REVERT: C 99 ARG cc_start: 0.8915 (mmt180) cc_final: 0.8692 (mmm-85) REVERT: D 59 MET cc_start: 0.9429 (tpp) cc_final: 0.9137 (tpp) REVERT: D 68 ASP cc_start: 0.9411 (t70) cc_final: 0.9154 (t0) REVERT: D 71 GLU cc_start: 0.9151 (tp30) cc_final: 0.8935 (tp30) REVERT: E 113 HIS cc_start: 0.9278 (OUTLIER) cc_final: 0.8842 (t-90) REVERT: E 125 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8747 (mm-40) REVERT: H 34 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8875 (mptt) REVERT: H 68 ASP cc_start: 0.9263 (t0) cc_final: 0.9025 (t0) REVERT: U 6 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7384 (pptt) REVERT: U 70 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7417 (m) outliers start: 32 outliers final: 18 residues processed: 263 average time/residue: 0.3583 time to fit residues: 127.2488 Evaluate side-chains 259 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 279 LYS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 85 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 263 GLN M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 84 ASN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.081681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.051595 restraints weight = 56118.467| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.45 r_work: 0.2753 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.8448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15825 Z= 0.171 Angle : 0.630 12.927 22627 Z= 0.348 Chirality : 0.037 0.267 2587 Planarity : 0.004 0.045 1848 Dihedral : 29.470 175.831 4448 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.37 % Allowed : 23.37 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1101 helix: 1.68 (0.20), residues: 677 sheet: 1.09 (0.65), residues: 69 loop : -0.07 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 PHE 0.012 0.001 PHE M 716 TYR 0.031 0.002 TYR H 83 ARG 0.011 0.001 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 894) hydrogen bonds : angle 3.34491 ( 2271) covalent geometry : bond 0.00388 (15825) covalent geometry : angle 0.62964 (22627) *********************** 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 274 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 198 LEU cc_start: 0.8213 (tp) cc_final: 0.7876 (tp) REVERT: M 280 GLU cc_start: 0.8370 (pm20) cc_final: 0.8156 (pm20) REVERT: M 684 MET cc_start: 0.8383 (mmm) cc_final: 0.7758 (tpp) REVERT: M 821 ARG cc_start: 0.7367 (tpt90) cc_final: 0.6192 (mmp-170) REVERT: A 60 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8374 (mt) REVERT: A 97 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8456 (mt-10) REVERT: B 88 TYR cc_start: 0.9236 (m-10) cc_final: 0.8994 (m-80) REVERT: C 73 ASN cc_start: 0.9321 (t0) cc_final: 0.8888 (t0) REVERT: C 99 ARG cc_start: 0.8933 (mmt180) cc_final: 0.8702 (mmm-85) REVERT: D 59 MET cc_start: 0.9444 (tpp) cc_final: 0.9155 (tpp) REVERT: D 68 ASP cc_start: 0.9415 (t70) cc_final: 0.9162 (t0) REVERT: D 86 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8628 (tpp80) REVERT: E 79 LYS cc_start: 0.8983 (ttmm) cc_final: 0.8768 (ttmm) REVERT: E 113 HIS cc_start: 0.9286 (OUTLIER) cc_final: 0.8907 (t-90) REVERT: H 34 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8868 (mptt) REVERT: H 68 ASP cc_start: 0.9273 (t0) cc_final: 0.9033 (t0) REVERT: U 6 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6918 (pttp) outliers start: 32 outliers final: 20 residues processed: 260 average time/residue: 0.4029 time to fit residues: 142.9908 Evaluate side-chains 260 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 279 LYS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 747 VAL 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 73 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 124 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 0.0020 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 104 GLN D 84 ASN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.081662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.051780 restraints weight = 56185.201| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.45 r_work: 0.2759 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.8461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 15825 Z= 0.208 Angle : 0.824 59.193 22627 Z= 0.475 Chirality : 0.038 0.355 2587 Planarity : 0.004 0.068 1848 Dihedral : 29.475 175.846 4448 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.84 % Allowed : 23.89 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1101 helix: 1.69 (0.20), residues: 677 sheet: 1.09 (0.65), residues: 69 loop : -0.07 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 PHE 0.012 0.001 PHE M 716 TYR 0.036 0.002 TYR H 83 ARG 0.019 0.001 ARG U 74 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 894) hydrogen bonds : angle 3.37005 ( 2271) covalent geometry : bond 0.00454 (15825) covalent geometry : angle 0.82421 (22627) ********************** 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 264 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.341 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 198 LEU cc_start: 0.8187 (tp) cc_final: 0.7860 (tp) REVERT: M 684 MET cc_start: 0.8341 (mmm) cc_final: 0.7712 (tpp) REVERT: M 821 ARG cc_start: 0.7362 (tpt90) cc_final: 0.6134 (mmp-170) REVERT: A 97 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8453 (mt-10) REVERT: B 88 TYR cc_start: 0.9229 (m-10) cc_final: 0.8989 (m-80) REVERT: C 73 ASN cc_start: 0.9313 (t0) cc_final: 0.8886 (t0) REVERT: C 99 ARG cc_start: 0.8909 (mmt180) cc_final: 0.8691 (mmm-85) REVERT: D 59 MET cc_start: 0.9431 (tpp) cc_final: 0.9139 (tpp) REVERT: D 68 ASP cc_start: 0.9420 (t70) cc_final: 0.9167 (t0) REVERT: D 86 ARG cc_start: 0.8931 (tpp80) cc_final: 0.8620 (tpp80) REVERT: E 79 LYS cc_start: 0.8983 (ttmm) cc_final: 0.8730 (ttmm) REVERT: E 113 HIS cc_start: 0.9284 (OUTLIER) cc_final: 0.8908 (t-90) REVERT: H 34 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8832 (mmtm) REVERT: H 68 ASP cc_start: 0.9266 (t0) cc_final: 0.9024 (t0) REVERT: U 6 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.6834 (pttp) outliers start: 27 outliers final: 21 residues processed: 252 average time/residue: 0.3429 time to fit residues: 117.3275 Evaluate side-chains 259 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 279 LYS Chi-restraints excluded: chain M residue 311 MET Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN G 38 ASN G 112 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.081498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051608 restraints weight = 56921.290| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.47 r_work: 0.2752 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.8469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.444 15825 Z= 0.386 Angle : 1.043 59.189 22627 Z= 0.670 Chirality : 0.049 1.171 2587 Planarity : 0.006 0.169 1848 Dihedral : 29.472 175.842 4448 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.63 % Allowed : 24.63 % Favored : 72.74 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1101 helix: 1.69 (0.20), residues: 677 sheet: 1.08 (0.65), residues: 69 loop : -0.08 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 PHE 0.012 0.001 PHE M 716 TYR 0.031 0.002 TYR H 83 ARG 0.044 0.001 ARG U 74 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 894) hydrogen bonds : angle 3.38384 ( 2271) covalent geometry : bond 0.00758 (15825) covalent geometry : angle 1.04300 (22627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9710.19 seconds wall clock time: 168 minutes 29.99 seconds (10109.99 seconds total)