Starting phenix.real_space_refine on Fri Feb 16 09:13:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/02_2024/8wg5_37503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/02_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_37503/02_2024/8wg5_37503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/02_2024/8wg5_37503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/02_2024/8wg5_37503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg5_37503/02_2024/8wg5_37503.pdb" } 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-5238/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: 8.20, per 1000 atoms: 0.55 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: 8.35 Conformation dependent library (CDL) restraints added in 1.4 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: 7.16 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: 7.34 Time building geometry restraints manager: 8.56 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 2.440 nonbonded pdb=" OE1 GLU M 362 " pdb=" OG SER M 687 " model vdw 2.103 2.440 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 2.440 nonbonded pdb=" NZ LYS M 288 " pdb=" O TYR M 306 " model vdw 2.141 2.520 ... (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 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.190 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 49.510 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.460 ------------------------------------------------------------------------------- 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 : 1.238 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: 0.3536 time to fit residues: 196.9737 Evaluate side-chains 275 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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: 0.0870 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- 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 635 HIS M 683 GLN C 68 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7525 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15825 Z= 0.228 Angle : 0.651 8.645 22627 Z= 0.366 Chirality : 0.038 0.186 2587 Planarity : 0.005 0.048 1848 Dihedral : 29.377 173.545 4452 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.05 % Allowed : 17.16 % Favored : 79.79 % 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: 1.37 (0.25), residues: 1101 helix: 1.44 (0.20), residues: 672 sheet: 1.39 (0.58), residues: 79 loop : -0.13 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.004 TRP M 793 HIS 0.010 0.002 HIS H 49 PHE 0.014 0.002 PHE A 78 TYR 0.035 0.002 TYR D 83 ARG 0.008 0.001 ARG A 129 *********************** 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 335 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 306 time to evaluate : 1.239 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 221 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8172 (mmm-85) REVERT: M 284 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8025 (mt0) REVERT: M 643 ASN cc_start: 0.6828 (t0) cc_final: 0.6590 (t0) REVERT: M 741 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7880 (mm) REVERT: M 820 GLU cc_start: 0.7778 (tp30) cc_final: 0.7253 (mm-30) REVERT: A 99 TYR cc_start: 0.6460 (t80) cc_final: 0.6225 (t80) REVERT: A 123 ASP cc_start: 0.8164 (m-30) cc_final: 0.7603 (m-30) REVERT: B 26 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7817 (mp) REVERT: B 45 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7868 (ttt-90) REVERT: C 25 PHE cc_start: 0.8051 (m-80) cc_final: 0.7489 (m-80) REVERT: C 56 GLU cc_start: 0.7455 (tt0) cc_final: 0.7092 (tt0) REVERT: C 61 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8272 (mm-30) REVERT: C 64 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7296 (tt0) REVERT: D 79 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7783 (mtm-85) REVERT: D 106 LEU cc_start: 0.8734 (tp) cc_final: 0.8359 (tp) REVERT: D 108 LYS cc_start: 0.8359 (tmtt) cc_final: 0.8099 (tmtt) REVERT: F 31 LYS cc_start: 0.8710 (tttm) cc_final: 0.8425 (tttp) REVERT: F 90 LEU cc_start: 0.9402 (mt) cc_final: 0.9189 (mt) REVERT: G 33 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8723 (mm) REVERT: G 61 GLU cc_start: 0.6115 (mp0) cc_final: 0.5915 (mp0) REVERT: G 74 LYS cc_start: 0.8402 (ptmt) cc_final: 0.8140 (ptmm) REVERT: H 68 ASP cc_start: 0.8372 (t0) cc_final: 0.8117 (t0) REVERT: H 83 TYR cc_start: 0.7509 (m-10) cc_final: 0.7279 (m-10) REVERT: U 6 LYS cc_start: 0.7473 (pttp) cc_final: 0.6660 (tmtt) REVERT: U 27 LYS cc_start: 0.8210 (ptpp) cc_final: 0.7873 (ptpt) REVERT: U 76 CYS cc_start: 0.7868 (t) cc_final: 0.7595 (t) outliers start: 29 outliers final: 13 residues processed: 325 average time/residue: 0.3263 time to fit residues: 145.0032 Evaluate side-chains 290 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 274 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 286 CYS Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 719 ILE Chi-restraints excluded: chain M residue 741 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN B 25 ASN D 95 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 15825 Z= 0.357 Angle : 0.734 10.778 22627 Z= 0.410 Chirality : 0.043 0.338 2587 Planarity : 0.006 0.055 1848 Dihedral : 29.776 172.618 4448 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.11 % Allowed : 17.79 % Favored : 78.11 % 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: 0.94 (0.25), residues: 1101 helix: 1.06 (0.20), residues: 675 sheet: 1.21 (0.56), residues: 76 loop : -0.21 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP M 793 HIS 0.051 0.003 HIS M 635 PHE 0.012 0.002 PHE M 354 TYR 0.031 0.003 TYR F 88 ARG 0.019 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 337 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 298 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 684 MET cc_start: 0.7995 (mmm) cc_final: 0.7261 (tpp) REVERT: M 820 GLU cc_start: 0.7863 (tp30) cc_final: 0.7421 (mm-30) REVERT: B 78 ARG cc_start: 0.7221 (ptt90) cc_final: 0.6432 (ptt90) REVERT: C 56 GLU cc_start: 0.8462 (tt0) cc_final: 0.8051 (tt0) REVERT: C 57 TYR cc_start: 0.8747 (t80) cc_final: 0.8468 (t80) REVERT: C 61 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8537 (mm-30) REVERT: C 64 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: C 95 LYS cc_start: 0.8893 (ptpt) cc_final: 0.8635 (ptmm) REVERT: C 104 GLN cc_start: 0.9081 (mp10) cc_final: 0.8781 (mm110) REVERT: D 59 MET cc_start: 0.9295 (tpp) cc_final: 0.8974 (tpp) REVERT: D 105 GLU cc_start: 0.8219 (pm20) cc_final: 0.7892 (pm20) REVERT: D 108 LYS cc_start: 0.9059 (tmtt) cc_final: 0.8700 (tmtt) REVERT: D 111 VAL cc_start: 0.9223 (m) cc_final: 0.9012 (t) REVERT: E 96 CYS cc_start: 0.8467 (m) cc_final: 0.7980 (m) REVERT: F 88 TYR cc_start: 0.8092 (m-10) cc_final: 0.7465 (m-10) REVERT: G 33 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.8955 (mm) REVERT: G 92 GLU cc_start: 0.8580 (tt0) cc_final: 0.8095 (tt0) REVERT: H 34 LYS cc_start: 0.8633 (mppt) cc_final: 0.8319 (mptt) REVERT: H 42 TYR cc_start: 0.7891 (t80) cc_final: 0.7646 (t80) REVERT: H 68 ASP cc_start: 0.9058 (t0) cc_final: 0.8383 (t0) REVERT: H 71 GLU cc_start: 0.8502 (tp30) cc_final: 0.7761 (mp0) REVERT: H 72 ARG cc_start: 0.9063 (mtt180) cc_final: 0.8760 (mtt180) REVERT: U 6 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7015 (pttp) REVERT: U 76 CYS cc_start: 0.7977 (t) cc_final: 0.7662 (t) outliers start: 39 outliers final: 19 residues processed: 319 average time/residue: 0.3616 time to fit residues: 155.3871 Evaluate side-chains 280 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 258 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 57 VAL 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 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 122 THR 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: 2.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 85 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 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: 0.8210 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15825 Z= 0.231 Angle : 0.609 9.050 22627 Z= 0.345 Chirality : 0.037 0.164 2587 Planarity : 0.004 0.048 1848 Dihedral : 29.679 174.734 4448 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.89 % Allowed : 19.47 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.25), residues: 1101 helix: 1.52 (0.20), residues: 676 sheet: 1.25 (0.62), residues: 69 loop : -0.12 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.011 0.001 HIS M 635 PHE 0.015 0.001 PHE M 282 TYR 0.028 0.002 TYR H 83 ARG 0.008 0.001 ARG B 35 *********************** 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 302 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 1.389 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 284 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8115 (mt0) REVERT: M 714 ILE cc_start: 0.5985 (tp) cc_final: 0.5670 (tp) REVERT: M 741 LEU cc_start: 0.8420 (pt) cc_final: 0.7968 (mm) REVERT: M 820 GLU cc_start: 0.8036 (tp30) cc_final: 0.7461 (mm-30) REVERT: A 73 GLU cc_start: 0.8418 (tt0) cc_final: 0.8194 (tt0) REVERT: B 35 ARG cc_start: 0.9056 (mtp85) cc_final: 0.8684 (mtp-110) REVERT: B 77 LYS cc_start: 0.9359 (mttt) cc_final: 0.9082 (mttm) REVERT: B 88 TYR cc_start: 0.7893 (m-80) cc_final: 0.7335 (m-10) REVERT: D 51 ASP cc_start: 0.8682 (m-30) cc_final: 0.8302 (p0) REVERT: D 59 MET cc_start: 0.9243 (tpp) cc_final: 0.9002 (tpp) REVERT: D 90 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8220 (p) REVERT: D 108 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8906 (tmtt) REVERT: E 59 GLU cc_start: 0.7911 (pm20) cc_final: 0.7658 (pm20) REVERT: E 96 CYS cc_start: 0.8705 (m) cc_final: 0.8353 (m) REVERT: F 88 TYR cc_start: 0.8106 (m-10) cc_final: 0.7303 (m-10) REVERT: G 33 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9322 (mt) REVERT: G 72 ASP cc_start: 0.8242 (m-30) cc_final: 0.8031 (m-30) REVERT: G 90 ASP cc_start: 0.8878 (t0) cc_final: 0.8574 (t0) REVERT: H 34 LYS cc_start: 0.8703 (mppt) cc_final: 0.8414 (mptt) REVERT: H 68 ASP cc_start: 0.9092 (t0) cc_final: 0.8570 (t0) REVERT: H 71 GLU cc_start: 0.8554 (tp30) cc_final: 0.7774 (mp0) REVERT: H 76 GLU cc_start: 0.8950 (tp30) cc_final: 0.8491 (tp30) REVERT: H 79 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8308 (ttp-110) REVERT: H 105 GLU cc_start: 0.8642 (tp30) cc_final: 0.8025 (tp30) REVERT: H 108 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8567 (ptpp) REVERT: U 6 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6932 (pttp) REVERT: U 76 CYS cc_start: 0.7981 (t) cc_final: 0.7699 (t) outliers start: 37 outliers final: 22 residues processed: 282 average time/residue: 0.3543 time to fit residues: 134.6140 Evaluate side-chains 274 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 248 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 311 MET Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE 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 43 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 61 ILE 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: 0.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.0170 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 32 optimal weight: 0.0870 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 696 HIS ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15825 Z= 0.187 Angle : 0.581 9.324 22627 Z= 0.330 Chirality : 0.036 0.178 2587 Planarity : 0.004 0.046 1848 Dihedral : 29.504 175.193 4448 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.37 % Allowed : 20.11 % 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: 1.66 (0.25), residues: 1101 helix: 1.75 (0.20), residues: 676 sheet: 1.47 (0.63), residues: 67 loop : -0.14 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP M 793 HIS 0.010 0.001 HIS M 635 PHE 0.010 0.001 PHE M 282 TYR 0.039 0.002 TYR D 83 ARG 0.005 0.000 ARG D 33 *********************** 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 306 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 274 time to evaluate : 1.401 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: 0.7423 (tp) cc_final: 0.7138 (tp) REVERT: M 284 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8021 (mt0) REVERT: M 351 MET cc_start: 0.4953 (tmm) cc_final: 0.4469 (tmm) REVERT: M 684 MET cc_start: 0.8057 (mmm) cc_final: 0.7213 (tpp) REVERT: M 695 LEU cc_start: 0.7835 (mm) cc_final: 0.7376 (mt) REVERT: M 741 LEU cc_start: 0.8467 (pt) cc_final: 0.7976 (mm) REVERT: M 820 GLU cc_start: 0.7921 (tp30) cc_final: 0.7360 (mm-30) REVERT: B 35 ARG cc_start: 0.9051 (mtp85) cc_final: 0.8770 (mtp-110) REVERT: B 77 LYS cc_start: 0.9408 (mttt) cc_final: 0.9119 (mttm) REVERT: C 73 ASN cc_start: 0.9065 (t0) cc_final: 0.8766 (t0) REVERT: C 92 GLU cc_start: 0.7568 (tp30) cc_final: 0.7279 (tp30) REVERT: D 51 ASP cc_start: 0.8720 (m-30) cc_final: 0.8385 (p0) REVERT: D 59 MET cc_start: 0.9238 (tpp) cc_final: 0.9022 (tpp) REVERT: D 90 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8250 (p) REVERT: D 101 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9031 (mm) REVERT: D 108 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8617 (tmtt) REVERT: E 96 CYS cc_start: 0.8714 (m) cc_final: 0.8498 (m) REVERT: G 33 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9290 (mt) REVERT: G 90 ASP cc_start: 0.8859 (t0) cc_final: 0.8583 (t0) REVERT: H 34 LYS cc_start: 0.8699 (mppt) cc_final: 0.8419 (mptt) REVERT: H 68 ASP cc_start: 0.9085 (t0) cc_final: 0.8620 (t0) REVERT: H 71 GLU cc_start: 0.8545 (tp30) cc_final: 0.7772 (mp0) REVERT: H 79 ARG cc_start: 0.8865 (ttp-110) cc_final: 0.8576 (mtm-85) REVERT: H 86 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7914 (tpp80) REVERT: H 105 GLU cc_start: 0.8541 (tp30) cc_final: 0.7818 (tp30) REVERT: H 108 LYS cc_start: 0.8903 (pptt) cc_final: 0.8661 (ptpp) REVERT: U 76 CYS cc_start: 0.7947 (t) cc_final: 0.7672 (t) outliers start: 32 outliers final: 22 residues processed: 289 average time/residue: 0.3658 time to fit residues: 143.1855 Evaluate side-chains 282 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 257 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain M residue 822 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN 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: 0.9980 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 73 ASN D 84 ASN G 104 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.7995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15825 Z= 0.347 Angle : 0.641 8.743 22627 Z= 0.364 Chirality : 0.039 0.190 2587 Planarity : 0.005 0.058 1848 Dihedral : 29.677 174.790 4448 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.11 % Allowed : 21.16 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1101 helix: 1.65 (0.20), residues: 675 sheet: 1.31 (0.62), residues: 67 loop : -0.29 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.009 0.001 HIS M 635 PHE 0.014 0.002 PHE U 45 TYR 0.032 0.003 TYR H 83 ARG 0.006 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 1.344 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 311 MET cc_start: 0.7549 (mmm) cc_final: 0.7196 (mmm) REVERT: M 684 MET cc_start: 0.8000 (mmm) cc_final: 0.7413 (tpp) REVERT: M 820 GLU cc_start: 0.8031 (tp30) cc_final: 0.7416 (mm-30) REVERT: B 97 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8967 (pt) REVERT: C 73 ASN cc_start: 0.9164 (t160) cc_final: 0.8825 (t0) REVERT: D 59 MET cc_start: 0.9295 (tpp) cc_final: 0.8866 (tpp) REVERT: D 90 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8381 (p) REVERT: D 101 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9221 (mm) REVERT: D 105 GLU cc_start: 0.8216 (pm20) cc_final: 0.7943 (pm20) REVERT: D 108 LYS cc_start: 0.9182 (tmtt) cc_final: 0.8784 (tmtt) REVERT: E 59 GLU cc_start: 0.7972 (pm20) cc_final: 0.7761 (pm20) REVERT: E 96 CYS cc_start: 0.8703 (m) cc_final: 0.8385 (m) REVERT: G 90 ASP cc_start: 0.9002 (t0) cc_final: 0.8714 (t0) REVERT: H 34 LYS cc_start: 0.8881 (mppt) cc_final: 0.8612 (mmtm) REVERT: H 68 ASP cc_start: 0.9084 (t0) cc_final: 0.8653 (t0) REVERT: H 71 GLU cc_start: 0.8583 (tp30) cc_final: 0.7803 (mp0) REVERT: H 79 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.8595 (mtm-85) REVERT: H 83 TYR cc_start: 0.8645 (m-80) cc_final: 0.8427 (m-80) REVERT: H 105 GLU cc_start: 0.8657 (tp30) cc_final: 0.7950 (tp30) REVERT: H 108 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8492 (tttm) REVERT: U 6 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7248 (pptt) REVERT: U 76 CYS cc_start: 0.8006 (t) cc_final: 0.7682 (t) outliers start: 39 outliers final: 24 residues processed: 265 average time/residue: 0.3496 time to fit residues: 124.3277 Evaluate side-chains 258 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 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 D residue 84 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 43 VAL 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 G residue 102 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 108 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 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 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 696 HIS ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN G 104 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15825 Z= 0.188 Angle : 0.590 11.314 22627 Z= 0.332 Chirality : 0.036 0.196 2587 Planarity : 0.004 0.044 1848 Dihedral : 29.597 176.292 4448 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.37 % Allowed : 22.11 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.25), residues: 1101 helix: 1.78 (0.20), residues: 670 sheet: 1.39 (0.63), residues: 67 loop : -0.21 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.003 0.001 HIS D 82 PHE 0.011 0.001 PHE M 716 TYR 0.048 0.002 TYR D 83 ARG 0.005 0.000 ARG B 35 *********************** 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 291 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 259 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 311 MET cc_start: 0.7624 (mmm) cc_final: 0.7263 (mmm) REVERT: M 684 MET cc_start: 0.8080 (mmm) cc_final: 0.7431 (tpp) REVERT: M 820 GLU cc_start: 0.8012 (tp30) cc_final: 0.7402 (mm-30) REVERT: B 97 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8802 (pt) REVERT: C 73 ASN cc_start: 0.9163 (t160) cc_final: 0.8769 (t0) REVERT: D 90 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8544 (p) REVERT: D 101 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9232 (mm) REVERT: D 108 LYS cc_start: 0.9154 (tmtt) cc_final: 0.8799 (ttpp) REVERT: E 59 GLU cc_start: 0.7971 (pm20) cc_final: 0.7761 (pm20) REVERT: E 96 CYS cc_start: 0.8748 (m) cc_final: 0.8412 (m) REVERT: G 90 ASP cc_start: 0.9056 (t0) cc_final: 0.8764 (t0) REVERT: G 92 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8386 (mm-30) REVERT: H 34 LYS cc_start: 0.8836 (mppt) cc_final: 0.8549 (mptt) REVERT: H 68 ASP cc_start: 0.9088 (t0) cc_final: 0.8656 (t0) REVERT: H 71 GLU cc_start: 0.8580 (tp30) cc_final: 0.7819 (mp0) REVERT: H 79 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.8679 (mtm-85) REVERT: H 105 GLU cc_start: 0.8529 (tp30) cc_final: 0.7835 (tp30) REVERT: H 108 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8603 (tttm) REVERT: U 6 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7148 (pptt) REVERT: U 76 CYS cc_start: 0.8032 (t) cc_final: 0.7714 (t) outliers start: 32 outliers final: 21 residues processed: 276 average time/residue: 0.3703 time to fit residues: 136.3730 Evaluate side-chains 268 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 108 LYS 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: 1.9990 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN D 49 HIS E 76 GLN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.8442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15825 Z= 0.228 Angle : 0.606 12.975 22627 Z= 0.339 Chirality : 0.036 0.199 2587 Planarity : 0.004 0.050 1848 Dihedral : 29.516 175.708 4448 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.37 % Allowed : 22.53 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.25), residues: 1101 helix: 1.81 (0.20), residues: 675 sheet: 1.12 (0.63), residues: 69 loop : -0.21 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.002 0.001 HIS M 795 PHE 0.019 0.001 PHE U 45 TYR 0.024 0.002 TYR D 83 ARG 0.009 0.001 ARG M 312 *********************** 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 282 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 1.411 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 306 TYR cc_start: 0.8909 (m-80) cc_final: 0.8675 (m-80) REVERT: M 311 MET cc_start: 0.7630 (mmm) cc_final: 0.7271 (mmm) REVERT: M 684 MET cc_start: 0.7982 (mmm) cc_final: 0.7412 (tpp) REVERT: M 820 GLU cc_start: 0.8090 (tp30) cc_final: 0.7458 (mm-30) REVERT: B 97 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8810 (pt) REVERT: C 73 ASN cc_start: 0.9213 (t160) cc_final: 0.8779 (t0) REVERT: C 104 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8584 (mm-40) REVERT: D 90 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8443 (p) REVERT: D 101 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9278 (mm) REVERT: E 96 CYS cc_start: 0.8740 (m) cc_final: 0.8399 (m) REVERT: G 90 ASP cc_start: 0.9114 (t0) cc_final: 0.8791 (t0) REVERT: H 34 LYS cc_start: 0.8866 (mppt) cc_final: 0.8601 (mmtm) REVERT: H 68 ASP cc_start: 0.9107 (t0) cc_final: 0.8678 (t0) REVERT: H 71 GLU cc_start: 0.8592 (tp30) cc_final: 0.7829 (mp0) REVERT: H 79 ARG cc_start: 0.8875 (ttp-110) cc_final: 0.8585 (mtm-85) REVERT: H 108 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8678 (tttm) REVERT: U 6 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7197 (pptt) REVERT: U 76 CYS cc_start: 0.7994 (t) cc_final: 0.7688 (t) outliers start: 32 outliers final: 22 residues processed: 268 average time/residue: 0.3748 time to fit residues: 134.6969 Evaluate side-chains 268 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 241 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 268 MET Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 LEU 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 D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain U residue 6 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 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: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 263 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN D 84 ASN G 104 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.8983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15825 Z= 0.268 Angle : 0.633 12.891 22627 Z= 0.351 Chirality : 0.038 0.244 2587 Planarity : 0.004 0.048 1848 Dihedral : 29.606 176.162 4448 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.58 % Allowed : 22.63 % 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: 1.63 (0.26), residues: 1101 helix: 1.78 (0.20), residues: 671 sheet: 1.31 (0.59), residues: 76 loop : -0.27 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 793 HIS 0.003 0.001 HIS E 113 PHE 0.011 0.001 PHE M 716 TYR 0.029 0.002 TYR D 83 ARG 0.010 0.001 ARG M 305 *********************** 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 282 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 248 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 684 MET cc_start: 0.8067 (mmm) cc_final: 0.7490 (tpp) REVERT: M 820 GLU cc_start: 0.8163 (tp30) cc_final: 0.7553 (mm-30) REVERT: B 77 LYS cc_start: 0.9519 (mttm) cc_final: 0.9110 (mttm) REVERT: B 88 TYR cc_start: 0.8957 (m-10) cc_final: 0.8385 (m-80) REVERT: B 97 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8875 (pt) REVERT: C 72 ASP cc_start: 0.8721 (m-30) cc_final: 0.8478 (m-30) REVERT: C 73 ASN cc_start: 0.9187 (t160) cc_final: 0.8698 (t0) REVERT: C 104 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8578 (mm-40) REVERT: D 90 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8465 (p) REVERT: D 101 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9304 (mm) REVERT: E 96 CYS cc_start: 0.8553 (m) cc_final: 0.8058 (m) REVERT: H 34 LYS cc_start: 0.8949 (mppt) cc_final: 0.8678 (mmtm) REVERT: H 68 ASP cc_start: 0.9109 (t0) cc_final: 0.8671 (t0) REVERT: H 71 GLU cc_start: 0.8608 (tp30) cc_final: 0.7842 (mp0) REVERT: U 1 MET cc_start: 0.4865 (ttt) cc_final: 0.4646 (ttt) REVERT: U 27 LYS cc_start: 0.8558 (ptpp) cc_final: 0.8258 (ptpt) REVERT: U 76 CYS cc_start: 0.8007 (t) cc_final: 0.7721 (t) outliers start: 34 outliers final: 22 residues processed: 267 average time/residue: 0.3602 time to fit residues: 129.0058 Evaluate side-chains 266 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 241 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 LEU 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 108 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 112 SER 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 128 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 134 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 266 ASN ** M 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 702 GLN ** M 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 76 GLN G 104 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: 0.8348 moved from start: 0.9106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15825 Z= 0.209 Angle : 0.637 11.687 22627 Z= 0.350 Chirality : 0.037 0.229 2587 Planarity : 0.004 0.068 1848 Dihedral : 29.530 176.669 4448 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.63 % Allowed : 23.68 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.26), residues: 1101 helix: 1.81 (0.21), residues: 669 sheet: 1.35 (0.59), residues: 76 loop : -0.31 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP M 793 HIS 0.004 0.001 HIS U 68 PHE 0.012 0.001 PHE U 45 TYR 0.020 0.001 TYR D 83 ARG 0.010 0.000 ARG M 305 ********************** 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 281 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 256 time to evaluate : 1.464 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 684 MET cc_start: 0.8063 (mmm) cc_final: 0.7491 (tpp) REVERT: M 820 GLU cc_start: 0.8149 (tp30) cc_final: 0.7915 (tp30) REVERT: B 88 TYR cc_start: 0.8915 (m-10) cc_final: 0.8531 (m-80) REVERT: B 97 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8813 (pt) REVERT: C 72 ASP cc_start: 0.8694 (m-30) cc_final: 0.8456 (m-30) REVERT: C 73 ASN cc_start: 0.9180 (t160) cc_final: 0.8694 (t0) REVERT: C 104 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8515 (mm-40) REVERT: D 33 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8613 (mmm-85) REVERT: D 34 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8607 (mppt) REVERT: D 90 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8402 (p) REVERT: D 101 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9265 (mm) REVERT: E 96 CYS cc_start: 0.8699 (m) cc_final: 0.8357 (m) REVERT: F 35 ARG cc_start: 0.8874 (mtp-110) cc_final: 0.8592 (mtp85) REVERT: F 88 TYR cc_start: 0.9005 (m-10) cc_final: 0.8796 (m-10) REVERT: G 13 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8668 (mmmt) REVERT: H 34 LYS cc_start: 0.8933 (mppt) cc_final: 0.8685 (mmtm) REVERT: H 68 ASP cc_start: 0.9117 (t0) cc_final: 0.8696 (t0) REVERT: H 71 GLU cc_start: 0.8618 (tp30) cc_final: 0.7845 (mp0) REVERT: H 105 GLU cc_start: 0.8734 (tp30) cc_final: 0.8483 (tp30) REVERT: U 76 CYS cc_start: 0.7916 (t) cc_final: 0.7632 (t) outliers start: 25 outliers final: 20 residues processed: 271 average time/residue: 0.3691 time to fit residues: 134.4647 Evaluate side-chains 274 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 251 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 635 HIS Chi-restraints excluded: chain M residue 686 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 112 SER 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: 0.5980 chunk 98 optimal weight: 0.0050 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 702 GLN D 84 ASN D 95 GLN G 104 GLN G 112 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.080647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.051183 restraints weight = 56128.769| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.42 r_work: 0.2718 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.9182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15825 Z= 0.199 Angle : 0.635 11.904 22627 Z= 0.348 Chirality : 0.036 0.243 2587 Planarity : 0.004 0.057 1848 Dihedral : 29.445 176.702 4448 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.32 % Allowed : 23.79 % 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: 1.67 (0.26), residues: 1101 helix: 1.82 (0.21), residues: 669 sheet: 1.36 (0.59), residues: 76 loop : -0.27 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP M 793 HIS 0.004 0.001 HIS D 82 PHE 0.010 0.001 PHE M 716 TYR 0.019 0.001 TYR D 83 ARG 0.010 0.000 ARG M 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3691.14 seconds wall clock time: 66 minutes 59.66 seconds (4019.66 seconds total)