Starting phenix.real_space_refine on Mon Aug 5 23:22:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/08_2024/8wg5_37503.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/08_2024/8wg5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/08_2024/8wg5_37503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/08_2024/8wg5_37503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/08_2024/8wg5_37503.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/08_2024/8wg5_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 Residue "M GLU 302": "OE1" <-> "OE2" Residue "M PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "U PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.39, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 7.67 Conformation dependent library (CDL) restraints added in 1.5 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: 7.38 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: 7.27 Time building geometry restraints manager: 8.22 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: 98.73 - 105.76: 1600 105.76 - 112.80: 8713 112.80 - 119.83: 5361 119.83 - 126.87: 6127 126.87 - 133.90: 826 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 49.860 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15825 Z= 0.197 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 417 time to evaluate : 1.209 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: 0.3515 time to fit residues: 196.6264 Evaluate side-chains 275 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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: 3.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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= 0.336 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 *********************** 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 fitting. rotamer outliers: 35 poor density : 322 time to evaluate : 1.252 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: 0.7003 (t0) cc_final: 0.6776 (t0) REVERT: M 718 GLU cc_start: 0.7240 (pm20) cc_final: 0.6808 (tm-30) REVERT: M 744 LEU cc_start: 0.5408 (tp) cc_final: 0.4908 (tp) REVERT: M 820 GLU cc_start: 0.7521 (tp30) cc_final: 0.7125 (mm-30) REVERT: A 48 LEU cc_start: 0.8773 (mm) cc_final: 0.8490 (mm) REVERT: A 73 GLU cc_start: 0.7296 (tt0) cc_final: 0.7032 (tt0) REVERT: B 26 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8228 (tp) REVERT: B 45 ARG cc_start: 0.8527 (ttt-90) cc_final: 0.8303 (ttt-90) REVERT: B 88 TYR cc_start: 0.6719 (m-10) cc_final: 0.6419 (m-10) REVERT: C 56 GLU cc_start: 0.8101 (tt0) cc_final: 0.7774 (tt0) REVERT: C 61 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8314 (mm-30) REVERT: C 64 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7707 (tt0) REVERT: D 59 MET cc_start: 0.8820 (tpp) cc_final: 0.8529 (tpp) REVERT: D 83 TYR cc_start: 0.8198 (m-10) cc_final: 0.7551 (m-10) REVERT: D 108 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8371 (tmtt) REVERT: E 120 MET cc_start: 0.8680 (mtp) cc_final: 0.8201 (mtm) REVERT: F 31 LYS cc_start: 0.8980 (tttm) cc_final: 0.8644 (tttp) REVERT: F 53 GLU cc_start: 0.8927 (tp30) cc_final: 0.8594 (tp30) REVERT: G 33 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9044 (mm) REVERT: G 74 LYS cc_start: 0.8641 (ptmt) cc_final: 0.8418 (ptmm) REVERT: G 92 GLU cc_start: 0.8363 (tt0) cc_final: 0.7911 (tt0) REVERT: H 34 LYS cc_start: 0.8500 (mppt) cc_final: 0.8009 (mptt) REVERT: H 68 ASP cc_start: 0.8727 (t0) cc_final: 0.8378 (t0) REVERT: H 72 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8748 (mtt180) outliers start: 35 outliers final: 14 residues processed: 341 average time/residue: 0.3136 time to fit residues: 143.7786 Evaluate side-chains 276 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 260 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 68 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 635 HIS M 696 HIS ** M 800 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5011 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= 0.210 Angle : 0.607 8.623 22627 Z= 0.345 Chirality : 0.037 0.167 2587 Planarity : 0.004 0.047 1848 Dihedral : 29.546 174.481 4448 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.95 % Allowed : 19.16 % 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: 1.30 (0.25), residues: 1101 helix: 1.34 (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 0.008 0.003 TRP M 793 HIS 0.015 0.001 HIS M 635 PHE 0.011 0.001 PHE M 716 TYR 0.023 0.002 TYR D 83 ARG 0.007 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 293 time to evaluate : 1.290 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 325 LYS cc_start: 0.8411 (pptt) cc_final: 0.8172 (pttp) REVERT: M 635 HIS cc_start: 0.3527 (OUTLIER) cc_final: 0.2490 (t-90) REVERT: M 643 ASN cc_start: 0.6922 (t0) cc_final: 0.6693 (t0) REVERT: M 714 ILE cc_start: 0.6261 (tp) cc_final: 0.5901 (tp) REVERT: M 718 GLU cc_start: 0.7163 (pm20) cc_final: 0.6574 (tm-30) REVERT: M 744 LEU cc_start: 0.5854 (tp) cc_final: 0.5217 (tp) REVERT: M 820 GLU cc_start: 0.7827 (tp30) cc_final: 0.7266 (mm-30) REVERT: A 73 GLU cc_start: 0.7516 (tt0) cc_final: 0.7215 (tt0) REVERT: A 123 ASP cc_start: 0.8878 (m-30) cc_final: 0.8566 (m-30) REVERT: B 26 ILE cc_start: 0.8524 (mp) cc_final: 0.8243 (tp) REVERT: B 31 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7908 (ttpp) REVERT: B 45 ARG cc_start: 0.8694 (ttt-90) cc_final: 0.8474 (ttt-90) REVERT: B 84 MET cc_start: 0.8376 (tpp) cc_final: 0.8144 (tpt) REVERT: C 23 LEU cc_start: 0.8281 (mt) cc_final: 0.8009 (mp) REVERT: C 56 GLU cc_start: 0.8228 (tt0) cc_final: 0.7650 (tt0) REVERT: C 61 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8356 (mm-30) REVERT: C 64 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7868 (tt0) REVERT: C 95 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8633 (ptmm) REVERT: C 104 GLN cc_start: 0.9016 (mp10) cc_final: 0.8173 (mp10) REVERT: D 59 MET cc_start: 0.8890 (tpp) cc_final: 0.8470 (tpp) REVERT: D 68 ASP cc_start: 0.8857 (t70) cc_final: 0.8527 (t0) REVERT: D 108 LYS cc_start: 0.8760 (tmtt) cc_final: 0.8505 (tmtt) REVERT: E 73 GLU cc_start: 0.8776 (tt0) cc_final: 0.8224 (tt0) REVERT: E 94 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8031 (mm-30) REVERT: E 125 GLN cc_start: 0.8745 (mp10) cc_final: 0.8515 (mp10) REVERT: G 33 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8917 (mm) REVERT: G 95 LYS cc_start: 0.9086 (tppt) cc_final: 0.8873 (tptt) REVERT: H 42 TYR cc_start: 0.7489 (t80) cc_final: 0.7208 (t80) REVERT: H 105 GLU cc_start: 0.8570 (tp30) cc_final: 0.8368 (tp30) REVERT: H 108 LYS cc_start: 0.8943 (pptt) cc_final: 0.8654 (ptpp) REVERT: H 113 GLU cc_start: 0.8995 (tp30) cc_final: 0.8756 (tp30) outliers start: 28 outliers final: 14 residues processed: 309 average time/residue: 0.3448 time to fit residues: 143.4114 Evaluate side-chains 277 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 259 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 C residue 95 LYS 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 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 121 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 212 GLN M 635 HIS ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN E 55 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15825 Z= 0.235 Angle : 0.606 8.968 22627 Z= 0.346 Chirality : 0.037 0.173 2587 Planarity : 0.004 0.051 1848 Dihedral : 29.479 174.193 4448 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.11 % Allowed : 19.37 % 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: 1.42 (0.25), residues: 1101 helix: 1.50 (0.20), residues: 677 sheet: 1.09 (0.60), residues: 78 loop : -0.09 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.018 0.001 HIS M 635 PHE 0.010 0.001 PHE A 67 TYR 0.027 0.002 TYR H 83 ARG 0.007 0.001 ARG H 33 *********************** 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 309 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 270 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 198 LEU cc_start: 0.7429 (tp) cc_final: 0.7195 (tp) REVERT: M 263 GLN cc_start: 0.9563 (OUTLIER) cc_final: 0.9324 (mp10) REVERT: M 284 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7623 (mt0) REVERT: M 303 LEU cc_start: 0.8721 (tp) cc_final: 0.8354 (tt) REVERT: M 684 MET cc_start: 0.8030 (mmm) cc_final: 0.7290 (tpp) REVERT: M 718 GLU cc_start: 0.7290 (pm20) cc_final: 0.6451 (tm-30) REVERT: M 719 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7795 (mp) REVERT: M 744 LEU cc_start: 0.5873 (tp) cc_final: 0.5250 (tp) REVERT: A 73 GLU cc_start: 0.8089 (tt0) cc_final: 0.7677 (tt0) REVERT: B 31 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8161 (ttpp) REVERT: B 84 MET cc_start: 0.8502 (tpp) cc_final: 0.8271 (tpt) REVERT: B 88 TYR cc_start: 0.7696 (m-10) cc_final: 0.7262 (m-10) REVERT: C 57 TYR cc_start: 0.8847 (t80) cc_final: 0.8585 (t80) REVERT: C 61 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8620 (mm-30) REVERT: C 64 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: C 104 GLN cc_start: 0.8979 (mp10) cc_final: 0.8717 (mm-40) REVERT: D 59 MET cc_start: 0.9086 (tpp) cc_final: 0.8820 (tpp) REVERT: D 68 ASP cc_start: 0.9006 (t70) cc_final: 0.8802 (t0) REVERT: D 108 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8723 (tmtt) REVERT: E 79 LYS cc_start: 0.8329 (ttmm) cc_final: 0.8001 (ttmm) REVERT: E 125 GLN cc_start: 0.8698 (mp10) cc_final: 0.8372 (mp10) REVERT: G 33 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.8985 (mm) REVERT: G 92 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: H 34 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8390 (mptt) REVERT: H 108 LYS cc_start: 0.8941 (pptt) cc_final: 0.8716 (ptpp) REVERT: U 6 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.6592 (pttp) REVERT: U 76 CYS cc_start: 0.8157 (t) cc_final: 0.7819 (t) outliers start: 39 outliers final: 19 residues processed: 292 average time/residue: 0.3416 time to fit residues: 135.2799 Evaluate side-chains 277 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 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 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 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain 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 108 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 93 GLN E 55 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.7265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15825 Z= 0.302 Angle : 0.644 9.290 22627 Z= 0.366 Chirality : 0.039 0.210 2587 Planarity : 0.005 0.052 1848 Dihedral : 29.653 174.464 4448 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.84 % Allowed : 20.21 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.25), residues: 1101 helix: 1.45 (0.20), residues: 674 sheet: 0.86 (0.58), residues: 80 loop : -0.23 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 793 HIS 0.023 0.002 HIS M 635 PHE 0.011 0.001 PHE A 67 TYR 0.028 0.002 TYR H 83 ARG 0.006 0.001 ARG B 78 *********************** 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 298 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 252 time to evaluate : 1.290 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: 0.7610 (tp) cc_final: 0.7369 (tp) REVERT: M 303 LEU cc_start: 0.8835 (tp) cc_final: 0.8633 (tt) REVERT: M 351 MET cc_start: 0.5122 (tmm) cc_final: 0.4784 (tmm) REVERT: M 718 GLU cc_start: 0.7420 (pm20) cc_final: 0.7061 (pm20) REVERT: A 73 GLU cc_start: 0.8466 (tt0) cc_final: 0.7909 (tt0) REVERT: A 106 ASP cc_start: 0.8587 (m-30) cc_final: 0.8384 (m-30) REVERT: B 44 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9185 (tttp) REVERT: B 77 LYS cc_start: 0.9412 (mttt) cc_final: 0.9155 (mttm) REVERT: D 51 ASP cc_start: 0.8716 (m-30) cc_final: 0.8406 (p0) REVERT: D 59 MET cc_start: 0.9202 (tpp) cc_final: 0.8736 (tpp) REVERT: D 108 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8725 (tmtt) REVERT: E 79 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8438 (ttmm) REVERT: E 125 GLN cc_start: 0.8817 (mp10) cc_final: 0.7701 (mp10) REVERT: G 33 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9019 (mm) REVERT: G 41 GLU cc_start: 0.8668 (pm20) cc_final: 0.8450 (mp0) REVERT: G 72 ASP cc_start: 0.8556 (m-30) cc_final: 0.8309 (m-30) REVERT: G 90 ASP cc_start: 0.8976 (t0) cc_final: 0.8728 (t0) REVERT: H 68 ASP cc_start: 0.9073 (t0) cc_final: 0.8641 (t0) REVERT: H 86 ARG cc_start: 0.8396 (tpp80) cc_final: 0.8189 (tpp80) REVERT: H 93 GLU cc_start: 0.8398 (mp0) cc_final: 0.8092 (mp0) REVERT: H 105 GLU cc_start: 0.8673 (tp30) cc_final: 0.8087 (tp30) REVERT: H 108 LYS cc_start: 0.8946 (pptt) cc_final: 0.8683 (ptpp) REVERT: U 6 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7231 (pptt) REVERT: U 76 CYS cc_start: 0.8081 (t) cc_final: 0.7733 (t) outliers start: 46 outliers final: 25 residues processed: 281 average time/residue: 0.3324 time to fit residues: 127.2609 Evaluate side-chains 267 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 385 LEU Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 THR 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 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR 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 43 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.7628 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= 0.222 Angle : 0.615 11.658 22627 Z= 0.345 Chirality : 0.036 0.185 2587 Planarity : 0.004 0.050 1848 Dihedral : 29.599 175.460 4448 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.26 % Allowed : 22.84 % Favored : 73.89 % 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: 1.53 (0.25), residues: 1101 helix: 1.67 (0.20), residues: 675 sheet: 0.76 (0.62), residues: 71 loop : -0.12 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.005 0.001 HIS M 635 PHE 0.013 0.001 PHE U 45 TYR 0.024 0.002 TYR H 83 ARG 0.009 0.001 ARG M 305 *********************** 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 288 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 257 time to evaluate : 1.216 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: 0.7650 (tp) cc_final: 0.7394 (tp) REVERT: M 284 GLN cc_start: 0.8799 (mm110) cc_final: 0.8470 (mm110) REVERT: M 684 MET cc_start: 0.8059 (mmm) cc_final: 0.7569 (tpp) REVERT: M 821 ARG cc_start: 0.6874 (tpt90) cc_final: 0.5455 (mmm160) REVERT: A 73 GLU cc_start: 0.8590 (tt0) cc_final: 0.8350 (tt0) REVERT: A 125 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8611 (mp10) REVERT: B 44 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9122 (mmmt) REVERT: C 56 GLU cc_start: 0.8629 (tt0) cc_final: 0.8351 (tt0) REVERT: C 73 ASN cc_start: 0.9300 (t0) cc_final: 0.9013 (t0) REVERT: D 59 MET cc_start: 0.9181 (tpp) cc_final: 0.8781 (tpp) REVERT: D 99 ARG cc_start: 0.8845 (mmt90) cc_final: 0.8596 (mtt-85) REVERT: D 108 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8725 (tmtt) REVERT: E 79 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8486 (ttmm) REVERT: E 125 GLN cc_start: 0.8766 (mp10) cc_final: 0.7562 (mp10) REVERT: G 61 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7828 (mm-30) REVERT: G 72 ASP cc_start: 0.8657 (m-30) cc_final: 0.8330 (m-30) REVERT: H 34 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8628 (mptt) REVERT: H 68 ASP cc_start: 0.9091 (t0) cc_final: 0.8725 (t0) REVERT: H 86 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8234 (tpp80) REVERT: H 105 GLU cc_start: 0.8579 (tp30) cc_final: 0.7895 (tp30) REVERT: H 108 LYS cc_start: 0.8935 (pptt) cc_final: 0.8684 (ptpp) REVERT: U 6 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7221 (pptt) outliers start: 31 outliers final: 21 residues processed: 277 average time/residue: 0.3489 time to fit residues: 130.5824 Evaluate side-chains 269 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 268 MET Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 71 VAL 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 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 82 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 284 GLN M 297 GLN ** M 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 55 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.7887 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= 0.201 Angle : 0.611 11.207 22627 Z= 0.343 Chirality : 0.036 0.183 2587 Planarity : 0.004 0.049 1848 Dihedral : 29.505 175.566 4448 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.26 % Allowed : 22.95 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.25), residues: 1101 helix: 1.68 (0.20), residues: 675 sheet: 0.82 (0.64), residues: 71 loop : -0.09 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 PHE 0.016 0.001 PHE U 45 TYR 0.027 0.002 TYR H 83 ARG 0.006 0.000 ARG D 33 *********************** 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 289 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 258 time to evaluate : 1.220 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 198 LEU cc_start: 0.7699 (tp) cc_final: 0.7428 (tp) REVERT: M 221 ARG cc_start: 0.8331 (mmt180) cc_final: 0.8113 (mmt180) REVERT: M 718 GLU cc_start: 0.6799 (pm20) cc_final: 0.6542 (tp30) REVERT: M 821 ARG cc_start: 0.6907 (tpt90) cc_final: 0.5651 (mmp-170) REVERT: A 125 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8658 (mp10) REVERT: B 44 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9124 (mmmt) REVERT: C 56 GLU cc_start: 0.8681 (tt0) cc_final: 0.8396 (tt0) REVERT: C 73 ASN cc_start: 0.9310 (t0) cc_final: 0.8965 (t0) REVERT: D 59 MET cc_start: 0.9188 (tpp) cc_final: 0.8987 (tpp) REVERT: D 79 ARG cc_start: 0.8640 (mtm-85) cc_final: 0.8375 (mtm110) REVERT: D 83 TYR cc_start: 0.7850 (m-80) cc_final: 0.6923 (m-80) REVERT: D 108 LYS cc_start: 0.9176 (tmtt) cc_final: 0.8732 (tmtt) REVERT: E 79 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8505 (ttmm) REVERT: E 125 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8504 (mm-40) REVERT: G 61 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7840 (mm-30) REVERT: G 72 ASP cc_start: 0.8720 (m-30) cc_final: 0.8498 (m-30) REVERT: G 104 GLN cc_start: 0.9055 (mp10) cc_final: 0.8813 (mm-40) REVERT: H 34 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8581 (mptt) REVERT: H 68 ASP cc_start: 0.9086 (t0) cc_final: 0.8728 (t0) REVERT: H 105 GLU cc_start: 0.8533 (tp30) cc_final: 0.7816 (tp30) REVERT: U 6 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7211 (pptt) outliers start: 31 outliers final: 20 residues processed: 276 average time/residue: 0.3584 time to fit residues: 133.2021 Evaluate side-chains 271 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 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 263 GLN Chi-restraints excluded: chain M residue 385 LEU Chi-restraints excluded: chain M residue 686 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 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 125 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.8030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15825 Z= 0.199 Angle : 0.617 12.484 22627 Z= 0.344 Chirality : 0.036 0.188 2587 Planarity : 0.004 0.048 1848 Dihedral : 29.454 175.699 4448 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.47 % Allowed : 22.53 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.20), residues: 675 sheet: 1.06 (0.63), residues: 69 loop : -0.05 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 PHE 0.013 0.001 PHE U 45 TYR 0.028 0.002 TYR D 83 ARG 0.005 0.000 ARG D 33 *********************** 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 279 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 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: 0.7726 (tp) cc_final: 0.7459 (tp) REVERT: M 821 ARG cc_start: 0.6957 (tpt90) cc_final: 0.5692 (mmp-170) REVERT: A 125 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8635 (mp10) REVERT: A 129 ARG cc_start: 0.8705 (mmm160) cc_final: 0.8503 (mmm160) REVERT: B 44 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9055 (mmmt) REVERT: B 88 TYR cc_start: 0.8084 (m-80) cc_final: 0.7317 (m-80) REVERT: B 97 LEU cc_start: 0.8976 (pt) cc_final: 0.8734 (pt) REVERT: C 15 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8541 (mmmm) REVERT: C 56 GLU cc_start: 0.8701 (tt0) cc_final: 0.8417 (tt0) REVERT: C 73 ASN cc_start: 0.9303 (t0) cc_final: 0.8938 (t0) REVERT: D 79 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8340 (mtm-85) REVERT: D 101 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9185 (mm) REVERT: D 108 LYS cc_start: 0.9178 (tmtt) cc_final: 0.8781 (ttpp) REVERT: E 113 HIS cc_start: 0.9044 (OUTLIER) cc_final: 0.8711 (t-90) REVERT: E 125 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8377 (mm-40) REVERT: G 61 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7850 (mm-30) REVERT: G 104 GLN cc_start: 0.9038 (mp10) cc_final: 0.8797 (mm-40) REVERT: H 34 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8598 (mptt) REVERT: H 68 ASP cc_start: 0.9091 (t0) cc_final: 0.8736 (t0) REVERT: U 6 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7218 (pptt) REVERT: U 70 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7240 (m) outliers start: 33 outliers final: 17 residues processed: 267 average time/residue: 0.3544 time to fit residues: 128.2751 Evaluate side-chains 264 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 385 LEU Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 117 VAL 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 C residue 95 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 113 HIS 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 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 113 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 702 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.8292 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= 0.212 Angle : 0.629 11.939 22627 Z= 0.349 Chirality : 0.037 0.318 2587 Planarity : 0.004 0.047 1848 Dihedral : 29.431 175.760 4448 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.58 % Allowed : 22.32 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.26), residues: 1101 helix: 1.62 (0.20), residues: 677 sheet: 0.97 (0.64), residues: 69 loop : -0.06 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 793 HIS 0.003 0.001 HIS M 316 PHE 0.013 0.001 PHE U 45 TYR 0.023 0.002 TYR D 83 ARG 0.005 0.000 ARG D 79 *********************** 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 284 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 1.130 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: 0.7755 (tp) cc_final: 0.7487 (tp) REVERT: M 281 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8584 (tt) REVERT: M 718 GLU cc_start: 0.6677 (pm20) cc_final: 0.6462 (tp30) REVERT: M 821 ARG cc_start: 0.7006 (tpt90) cc_final: 0.6169 (mmm160) REVERT: A 125 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8627 (mp10) REVERT: A 129 ARG cc_start: 0.8708 (mmm160) cc_final: 0.8507 (mmm160) REVERT: B 97 LEU cc_start: 0.8969 (pt) cc_final: 0.8736 (pt) REVERT: C 15 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8605 (mmmm) REVERT: C 56 GLU cc_start: 0.8733 (tt0) cc_final: 0.8422 (tt0) REVERT: C 73 ASN cc_start: 0.9271 (t0) cc_final: 0.8883 (t0) REVERT: D 71 GLU cc_start: 0.8780 (tp30) cc_final: 0.8471 (tp30) REVERT: D 79 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8379 (mtm110) REVERT: D 101 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9202 (mm) REVERT: D 108 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8791 (ttpp) REVERT: E 113 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8740 (t-90) REVERT: E 125 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8392 (mm-40) REVERT: G 36 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8952 (mmmm) REVERT: G 61 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7860 (mm-30) REVERT: G 72 ASP cc_start: 0.8519 (m-30) cc_final: 0.8291 (m-30) REVERT: H 34 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8599 (mmtm) REVERT: H 68 ASP cc_start: 0.9097 (t0) cc_final: 0.8768 (t0) REVERT: U 6 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7202 (pptt) REVERT: U 70 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.7290 (m) outliers start: 34 outliers final: 20 residues processed: 271 average time/residue: 0.3620 time to fit residues: 131.3753 Evaluate side-chains 270 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 385 LEU Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 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 33 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 301 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** C 112 GLN D 49 HIS D 84 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.8846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15825 Z= 0.238 Angle : 0.642 12.029 22627 Z= 0.356 Chirality : 0.037 0.197 2587 Planarity : 0.004 0.046 1848 Dihedral : 29.479 176.071 4448 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.74 % Allowed : 23.37 % Favored : 73.89 % 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: 1.50 (0.26), residues: 1101 helix: 1.61 (0.21), residues: 675 sheet: 0.95 (0.64), residues: 69 loop : -0.10 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 793 HIS 0.003 0.001 HIS D 49 PHE 0.015 0.001 PHE U 45 TYR 0.032 0.002 TYR H 83 ARG 0.009 0.001 ARG D 33 ********************** 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 267 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 241 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 198 LEU cc_start: 0.7838 (tp) cc_final: 0.7547 (tp) REVERT: M 309 ASP cc_start: 0.8145 (p0) cc_final: 0.7530 (p0) REVERT: M 708 ARG cc_start: 0.8260 (tmt170) cc_final: 0.7172 (ptm-80) REVERT: M 821 ARG cc_start: 0.7025 (tpt90) cc_final: 0.5712 (mmp-170) REVERT: A 125 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8651 (mp10) REVERT: B 77 LYS cc_start: 0.9522 (mttm) cc_final: 0.9119 (mttm) REVERT: B 97 LEU cc_start: 0.8988 (pt) cc_final: 0.8781 (pt) REVERT: C 56 GLU cc_start: 0.8761 (tt0) cc_final: 0.8477 (tt0) REVERT: C 72 ASP cc_start: 0.8730 (m-30) cc_final: 0.8476 (m-30) REVERT: C 73 ASN cc_start: 0.9335 (t0) cc_final: 0.8878 (t0) REVERT: D 79 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8383 (mtm180) REVERT: D 101 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9317 (mm) REVERT: D 108 LYS cc_start: 0.9197 (tmtt) cc_final: 0.8811 (ttpp) REVERT: E 113 HIS cc_start: 0.9094 (OUTLIER) cc_final: 0.8822 (t-90) REVERT: E 125 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8516 (mp10) REVERT: G 61 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7966 (mm-30) REVERT: H 34 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8678 (mmtm) REVERT: H 68 ASP cc_start: 0.9107 (t0) cc_final: 0.8761 (t0) REVERT: U 6 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7177 (pptt) outliers start: 26 outliers final: 17 residues processed: 257 average time/residue: 0.3558 time to fit residues: 122.2766 Evaluate side-chains 253 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 385 LEU Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 113 HIS 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 U residue 6 LYS Chi-restraints excluded: chain U residue 27 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 114 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 297 GLN M 758 HIS ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS D 84 ASN ** 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 = 0.3744 r_free = 0.3744 target = 0.080036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.049902 restraints weight = 54988.382| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.47 r_work: 0.2692 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.9235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15825 Z= 0.271 Angle : 0.674 13.487 22627 Z= 0.366 Chirality : 0.038 0.333 2587 Planarity : 0.005 0.053 1848 Dihedral : 29.547 176.386 4448 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.42 % Allowed : 23.68 % Favored : 73.89 % 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: 1.47 (0.26), residues: 1101 helix: 1.62 (0.21), residues: 675 sheet: 0.60 (0.61), residues: 76 loop : -0.10 (0.33), residues: 350 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 0.010 0.001 PHE A 67 TYR 0.028 0.002 TYR H 83 ARG 0.014 0.001 ARG U 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.27 seconds wall clock time: 66 minutes 8.09 seconds (3968.09 seconds total)