Starting phenix.real_space_refine on Fri Mar 6 16:16:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbn_23739/03_2026/7mbn_23739.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbn_23739/03_2026/7mbn_23739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mbn_23739/03_2026/7mbn_23739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbn_23739/03_2026/7mbn_23739.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbn_23739/03_2026/7mbn_23739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbn_23739/03_2026/7mbn_23739.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15700 atoms to isotropic. 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 292 5.49 5 S 58 5.16 5 C 11869 2.51 5 N 3645 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20222 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 303, 2339 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 303, 2339 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2392 Chain: "C" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1228 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2075 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 5.06, per 1000 atoms: 0.25 Number of scatterers: 20222 At special positions: 0 Unit cell: (131.44, 147.34, 163.24, 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 58 16.00 P 292 15.00 O 4358 8.00 N 3645 7.00 C 11869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 16870 O4' DA O 131 .*. O " rejected from bonding due to valence issues. Atom "ATOM 19511 O4' DG P 112 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 873.6 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 27 sheets defined 34.4% alpha, 20.4% beta 152 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'C' and resid 3815 through 3830 removed outlier: 5.143A pdb=" N LYS C3828 " --> pdb=" O LYS C3824 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLU C3829 " --> pdb=" O LYS C3825 " (cutoff:3.500A) Processing helix chain 'C' and resid 3867 through 3879 Processing helix chain 'C' and resid 3901 through 3905 removed outlier: 3.522A pdb=" N ILE C3905 " --> pdb=" O ALA C3902 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.804A pdb=" N ARG D 294 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 406 Processing helix chain 'D' and resid 499 through 524 removed outlier: 3.572A pdb=" N MET D 503 " --> pdb=" O PRO D 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.664A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.586A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.891A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.923A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.523A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 101 through 120 removed outlier: 3.536A pdb=" N LYS J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.665A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.585A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.892A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.924A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.524A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 88 removed outlier: 3.661A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 98 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.935A pdb=" N THR A 29 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 48 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 50 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 3.779A pdb=" N SER A 71 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 90 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN A 92 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 116 removed outlier: 6.543A pdb=" N CYS A 126 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 113 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 124 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR A 115 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS A 122 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 159 removed outlier: 4.504A pdb=" N LYS A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS A 179 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 185 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.145A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 303 removed outlier: 6.527A pdb=" N ILE A 313 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 301 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA A 311 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA9, first strand: chain 'B' and resid 36 through 42 removed outlier: 5.424A pdb=" N LEU B 37 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS B 331 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 39 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 326 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.542A pdb=" N SER B 64 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLY B 73 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 79 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 90 through 95 removed outlier: 6.945A pdb=" N ASP B 115 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 121 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.438A pdb=" N VAL B 153 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 166 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 155 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.909A pdb=" N CYS B 195 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B 199 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N CYS B 205 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 217 through 222 removed outlier: 3.563A pdb=" N PHE B 219 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 238 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 251 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 240 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.850A pdb=" N VAL B 283 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 296 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 285 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3831 through 3835 Processing sheet with id=AB8, first strand: chain 'C' and resid 3854 through 3857 removed outlier: 7.066A pdb=" N MET C3854 " --> pdb=" O ALA C3930 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C3930 " --> pdb=" O MET C3854 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3906 through 3907 removed outlier: 6.905A pdb=" N ASN C3906 " --> pdb=" O TYR C3942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 298 through 301 Processing sheet with id=AC2, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.930A pdb=" N THR D 372 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 454 through 460 removed outlier: 5.952A pdb=" N PHE D 449 " --> pdb=" O GLN D 456 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL D 458 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE D 447 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR D 479 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 416 through 420 Processing sheet with id=AC5, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.398A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 42 through 43 removed outlier: 6.975A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.403A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.117A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 77 through 78 662 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 389 hydrogen bonds 762 hydrogen bond angles 0 basepair planarities 152 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 2.34 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: 4942 1.33 - 1.45: 5597 1.45 - 1.57: 10025 1.57 - 1.69: 582 1.69 - 1.81: 82 Bond restraints: 21228 Sorted by residual: bond pdb=" C3' DT P 15 " pdb=" O3' DT P 15 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.75e+00 bond pdb=" C3' DC P 126 " pdb=" O3' DC P 126 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C PRO D 530 " pdb=" N PRO D 531 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.66e+00 bond pdb=" C4' DG P 112 " pdb=" O4' DG P 112 " ideal model delta sigma weight residual 1.450 1.476 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CB PHE D 488 " pdb=" CG PHE D 488 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.30e-02 1.89e+03 1.39e+00 ... (remaining 21223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 29767 2.63 - 5.25: 190 5.25 - 7.88: 11 7.88 - 10.51: 0 10.51 - 13.13: 3 Bond angle restraints: 29971 Sorted by residual: angle pdb=" C ILE A 66 " pdb=" N HIS A 67 " pdb=" CA HIS A 67 " ideal model delta sigma weight residual 120.69 131.60 -10.91 2.95e+00 1.15e-01 1.37e+01 angle pdb=" CA TRP D 505 " pdb=" CB TRP D 505 " pdb=" CG TRP D 505 " ideal model delta sigma weight residual 113.60 119.14 -5.54 1.90e+00 2.77e-01 8.51e+00 angle pdb=" C3' DT P 15 " pdb=" O3' DT P 15 " pdb=" P DC P 16 " ideal model delta sigma weight residual 120.20 124.31 -4.11 1.50e+00 4.44e-01 7.51e+00 angle pdb=" N GLY D 485 " pdb=" CA GLY D 485 " pdb=" C GLY D 485 " ideal model delta sigma weight residual 112.34 117.89 -5.55 2.04e+00 2.40e-01 7.41e+00 angle pdb=" C3' DC P 126 " pdb=" O3' DC P 126 " pdb=" P DC P 127 " ideal model delta sigma weight residual 120.20 123.91 -3.71 1.50e+00 4.44e-01 6.12e+00 ... (remaining 29966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 10342 35.18 - 70.35: 1552 70.35 - 105.53: 46 105.53 - 140.71: 3 140.71 - 175.88: 2 Dihedral angle restraints: 11945 sinusoidal: 6705 harmonic: 5240 Sorted by residual: dihedral pdb=" CA PRO D 531 " pdb=" C PRO D 531 " pdb=" N TRP D 532 " pdb=" CA TRP D 532 " ideal model delta harmonic sigma weight residual -180.00 -149.82 -30.18 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N TRP A 329 " pdb=" CA TRP A 329 " ideal model delta harmonic sigma weight residual 180.00 149.85 30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA ASN L 64 " pdb=" C ASN L 64 " pdb=" N VAL L 65 " pdb=" CA VAL L 65 " ideal model delta harmonic sigma weight residual -180.00 -155.71 -24.29 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 11942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2379 0.040 - 0.080: 741 0.080 - 0.121: 220 0.121 - 0.161: 25 0.161 - 0.201: 7 Chirality restraints: 3372 Sorted by residual: chirality pdb=" CG LEU G 100 " pdb=" CB LEU G 100 " pdb=" CD1 LEU G 100 " pdb=" CD2 LEU G 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CG LEU L 58 " pdb=" CB LEU L 58 " pdb=" CD1 LEU L 58 " pdb=" CD2 LEU L 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CG LEU K 100 " pdb=" CB LEU K 100 " pdb=" CD1 LEU K 100 " pdb=" CD2 LEU K 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 3369 not shown) Planarity restraints: 2787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 485 " -0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO D 486 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 486 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 486 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 531 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C PRO D 531 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO D 531 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP D 532 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 54 " 0.003 2.00e-02 2.50e+03 1.52e-02 5.21e+00 pdb=" N1 DC O 54 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DC O 54 " 0.038 2.00e-02 2.50e+03 pdb=" O2 DC O 54 " -0.020 2.00e-02 2.50e+03 pdb=" N3 DC O 54 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC O 54 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC O 54 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC O 54 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC O 54 " -0.002 2.00e-02 2.50e+03 ... (remaining 2784 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 77 2.26 - 2.92: 9080 2.92 - 3.58: 36722 3.58 - 4.24: 57181 4.24 - 4.90: 83176 Nonbonded interactions: 186236 Sorted by model distance: nonbonded pdb=" NH1 ARG G 69 " pdb=" OP2 DA O 91 " model vdw 1.598 3.120 nonbonded pdb=" NH2 ARG G 42 " pdb=" OP2 DG P 145 " model vdw 1.780 3.120 nonbonded pdb=" NH2 ARG H 36 " pdb=" OP1 DA P 61 " model vdw 1.802 3.120 nonbonded pdb=" OD1 ASN A 342 " pdb=" O GLY C3860 " model vdw 1.813 3.040 nonbonded pdb=" NH2 ARG I 77 " pdb=" O4' DA O 131 " model vdw 1.819 3.120 ... (remaining 186231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'M' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.500 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21228 Z= 0.258 Angle : 0.679 13.134 29971 Z= 0.396 Chirality : 0.043 0.201 3372 Planarity : 0.005 0.077 2787 Dihedral : 25.181 175.885 8571 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 37.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.50 % Allowed : 6.54 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.17), residues: 1778 helix: -1.60 (0.18), residues: 584 sheet: -1.88 (0.24), residues: 385 loop : -2.35 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 42 TYR 0.016 0.002 TYR J 118 PHE 0.017 0.002 PHE D 484 TRP 0.022 0.002 TRP D 505 HIS 0.006 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00536 (21228) covalent geometry : angle 0.67851 (29971) hydrogen bonds : bond 0.17006 ( 1051) hydrogen bonds : angle 6.20890 ( 2670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 499 time to evaluate : 0.608 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: A 20 THR cc_start: 0.4285 (t) cc_final: 0.4070 (p) REVERT: A 58 ILE cc_start: 0.2457 (mt) cc_final: 0.2138 (mt) REVERT: A 287 VAL cc_start: 0.6925 (t) cc_final: 0.6566 (t) REVERT: B 46 LYS cc_start: 0.2882 (mttt) cc_final: 0.2227 (mmmt) REVERT: B 204 GLN cc_start: 0.4730 (tt0) cc_final: 0.4299 (mt0) REVERT: B 214 ASN cc_start: 0.1776 (t0) cc_final: 0.0700 (p0) REVERT: C 3931 MET cc_start: 0.4370 (mtp) cc_final: 0.3054 (tpt) REVERT: D 340 THR cc_start: 0.0105 (m) cc_final: -0.0830 (m) REVERT: D 360 ASP cc_start: -0.0317 (p0) cc_final: -0.1616 (t0) REVERT: D 368 SER cc_start: 0.0021 (m) cc_final: -0.0281 (m) REVERT: D 424 LEU cc_start: 0.1967 (pt) cc_final: 0.1518 (tp) REVERT: H 90 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6933 (mt) REVERT: I 18 SER cc_start: 0.8188 (t) cc_final: 0.7958 (t) REVERT: I 51 LEU cc_start: 0.8587 (pp) cc_final: 0.8217 (tt) REVERT: I 74 LYS cc_start: 0.7855 (mttt) cc_final: 0.7282 (pttp) REVERT: J 29 THR cc_start: 0.5995 (m) cc_final: 0.5729 (t) REVERT: J 76 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7312 (mtm-85) REVERT: K 39 HIS cc_start: 0.5993 (t-90) cc_final: 0.5254 (t-170) REVERT: M 104 GLN cc_start: 0.6594 (mm-40) cc_final: 0.5911 (mm-40) REVERT: N 65 ASP cc_start: 0.7956 (t0) cc_final: 0.7435 (t0) outliers start: 23 outliers final: 1 residues processed: 508 average time/residue: 0.1997 time to fit residues: 142.1403 Evaluate side-chains 230 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN B 140 GLN B 170 HIS B 265 ASN B 289 GLN D 354 GLN H 93 GLN I 89 ASN J 79 HIS K 39 HIS K 68 GLN L 25 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 HIS ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.137375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.109221 restraints weight = 64317.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.107627 restraints weight = 112867.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.108705 restraints weight = 95899.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108130 restraints weight = 70683.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108648 restraints weight = 64068.206| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 21228 Z= 0.239 Angle : 0.789 11.231 29971 Z= 0.429 Chirality : 0.048 0.177 3372 Planarity : 0.007 0.091 2787 Dihedral : 29.154 179.401 5164 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.39 % Allowed : 5.69 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 1778 helix: 0.64 (0.20), residues: 603 sheet: -1.34 (0.26), residues: 369 loop : -1.74 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 67 TYR 0.027 0.003 TYR N 39 PHE 0.032 0.003 PHE G 67 TRP 0.037 0.003 TRP D 505 HIS 0.014 0.003 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00541 (21228) covalent geometry : angle 0.78889 (29971) hydrogen bonds : bond 0.08288 ( 1051) hydrogen bonds : angle 4.61360 ( 2670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 289 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TRP cc_start: 0.1349 (m100) cc_final: 0.0922 (m-90) REVERT: A 95 VAL cc_start: 0.4924 (m) cc_final: 0.4589 (t) REVERT: B 46 LYS cc_start: 0.2799 (mttt) cc_final: 0.1755 (mmmt) REVERT: B 156 TRP cc_start: 0.4144 (m100) cc_final: 0.3651 (m100) REVERT: B 221 LYS cc_start: 0.5310 (pttt) cc_final: 0.4993 (mmtm) REVERT: B 250 LYS cc_start: 0.1094 (mttm) cc_final: 0.0825 (mtmm) REVERT: C 3838 ILE cc_start: 0.2212 (mt) cc_final: 0.1826 (mt) REVERT: C 3884 MET cc_start: 0.0687 (ppp) cc_final: 0.0486 (ppp) REVERT: C 3896 THR cc_start: 0.3718 (m) cc_final: 0.3301 (m) REVERT: C 3931 MET cc_start: 0.4401 (mtp) cc_final: 0.3243 (tpt) REVERT: C 3965 ARG cc_start: 0.4732 (mtm110) cc_final: 0.3444 (ptt-90) REVERT: D 340 THR cc_start: -0.0442 (m) cc_final: -0.0658 (m) REVERT: D 449 PHE cc_start: 0.1106 (t80) cc_final: 0.0789 (t80) REVERT: D 493 LYS cc_start: 0.1810 (mmmt) cc_final: 0.1366 (mptt) REVERT: G 39 HIS cc_start: 0.6260 (t-90) cc_final: 0.5894 (t-90) REVERT: G 50 GLU cc_start: 0.7665 (tp30) cc_final: 0.7414 (tp30) REVERT: H 59 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8159 (ttmt) REVERT: I 62 ILE cc_start: 0.8548 (pt) cc_final: 0.8246 (mt) REVERT: I 74 LYS cc_start: 0.8475 (mttt) cc_final: 0.7717 (pptt) REVERT: J 76 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7126 (mtm180) outliers start: 6 outliers final: 2 residues processed: 290 average time/residue: 0.1907 time to fit residues: 79.0785 Evaluate side-chains 184 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 120 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 127 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN B 323 ASN G 76 GLN G 93 GLN H 93 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN L 25 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.136567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.108440 restraints weight = 64931.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.107181 restraints weight = 109104.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.108223 restraints weight = 89251.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.107795 restraints weight = 63019.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.108213 restraints weight = 60133.330| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21228 Z= 0.155 Angle : 0.603 7.516 29971 Z= 0.340 Chirality : 0.041 0.176 3372 Planarity : 0.004 0.060 2787 Dihedral : 28.512 178.848 5164 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 1778 helix: 1.86 (0.20), residues: 603 sheet: -1.16 (0.26), residues: 370 loop : -1.55 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 77 TYR 0.013 0.002 TYR D 328 PHE 0.016 0.002 PHE C3929 TRP 0.036 0.002 TRP D 366 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00335 (21228) covalent geometry : angle 0.60317 (29971) hydrogen bonds : bond 0.06611 ( 1051) hydrogen bonds : angle 3.97027 ( 2670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.4645 (tpt) cc_final: 0.4261 (tpt) REVERT: A 95 VAL cc_start: 0.4948 (m) cc_final: 0.4625 (t) REVERT: A 321 TRP cc_start: 0.5324 (m100) cc_final: 0.5111 (m100) REVERT: B 46 LYS cc_start: 0.2827 (mttt) cc_final: 0.1657 (mmmt) REVERT: B 156 TRP cc_start: 0.4241 (m100) cc_final: 0.3648 (m100) REVERT: B 219 PHE cc_start: 0.1175 (t80) cc_final: 0.0946 (t80) REVERT: B 221 LYS cc_start: 0.5590 (pttt) cc_final: 0.4627 (mttp) REVERT: C 3884 MET cc_start: 0.0576 (ppp) cc_final: 0.0353 (ppp) REVERT: C 3897 MET cc_start: 0.4508 (mpp) cc_final: 0.3033 (tpp) REVERT: C 3931 MET cc_start: 0.4190 (mtp) cc_final: 0.3330 (tpt) REVERT: C 3965 ARG cc_start: 0.4617 (mtm110) cc_final: 0.3385 (ptt-90) REVERT: D 315 MET cc_start: 0.1199 (ttp) cc_final: 0.0892 (ttt) REVERT: D 336 MET cc_start: 0.0897 (mmp) cc_final: -0.0887 (ppp) REVERT: H 59 LYS cc_start: 0.8333 (ttpt) cc_final: 0.8101 (ttmt) REVERT: I 74 LYS cc_start: 0.8432 (mttt) cc_final: 0.7675 (pptt) REVERT: J 32 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7166 (pt0) REVERT: J 76 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7050 (mtm-85) REVERT: L 84 MET cc_start: 0.7927 (mmm) cc_final: 0.7710 (mmm) REVERT: M 79 ILE cc_start: 0.8441 (tp) cc_final: 0.8159 (tt) REVERT: N 73 GLU cc_start: 0.6923 (tp30) cc_final: 0.6692 (tp30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1850 time to fit residues: 64.7001 Evaluate side-chains 178 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 33 optimal weight: 0.0670 chunk 160 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 76 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN L 25 ASN M 24 GLN M 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.133626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.106294 restraints weight = 64472.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.105526 restraints weight = 116770.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.105903 restraints weight = 99839.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105644 restraints weight = 69425.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106305 restraints weight = 59281.293| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21228 Z= 0.164 Angle : 0.602 8.094 29971 Z= 0.338 Chirality : 0.041 0.155 3372 Planarity : 0.005 0.056 2787 Dihedral : 28.171 177.036 5164 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1778 helix: 1.84 (0.20), residues: 608 sheet: -1.02 (0.26), residues: 368 loop : -1.43 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 77 TYR 0.049 0.002 TYR J 80 PHE 0.016 0.002 PHE C3929 TRP 0.026 0.002 TRP D 366 HIS 0.008 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00366 (21228) covalent geometry : angle 0.60219 (29971) hydrogen bonds : bond 0.06773 ( 1051) hydrogen bonds : angle 3.91701 ( 2670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3717 (t) cc_final: 0.3450 (t) REVERT: A 95 VAL cc_start: 0.4667 (m) cc_final: 0.4324 (t) REVERT: B 46 LYS cc_start: 0.2869 (mttt) cc_final: 0.1922 (mmtt) REVERT: B 156 TRP cc_start: 0.4185 (m100) cc_final: 0.3646 (m100) REVERT: B 219 PHE cc_start: 0.1208 (t80) cc_final: 0.0817 (t80) REVERT: B 221 LYS cc_start: 0.5468 (pttt) cc_final: 0.4431 (mttt) REVERT: C 3856 ILE cc_start: 0.1994 (tp) cc_final: 0.1666 (mm) REVERT: C 3884 MET cc_start: 0.0678 (ppp) cc_final: 0.0401 (ppp) REVERT: C 3931 MET cc_start: 0.4346 (mtp) cc_final: 0.3460 (tpt) REVERT: C 3933 LYS cc_start: 0.5575 (mmmt) cc_final: 0.3654 (pttp) REVERT: C 3965 ARG cc_start: 0.4588 (mtm110) cc_final: 0.3372 (ptt-90) REVERT: D 315 MET cc_start: 0.1496 (ttp) cc_final: 0.1139 (ttt) REVERT: D 336 MET cc_start: 0.0942 (mmp) cc_final: -0.0831 (ppp) REVERT: D 375 HIS cc_start: 0.2866 (t70) cc_final: 0.2367 (t70) REVERT: D 500 MET cc_start: 0.5714 (mmm) cc_final: 0.4344 (tmm) REVERT: G 56 LYS cc_start: 0.7919 (ttmm) cc_final: 0.7698 (ttmm) REVERT: J 76 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7289 (ttm110) REVERT: J 113 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7822 (ttmm) REVERT: K 73 GLU cc_start: 0.7160 (tt0) cc_final: 0.6801 (tt0) REVERT: N 73 GLU cc_start: 0.7265 (tp30) cc_final: 0.7015 (tp30) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.1667 time to fit residues: 58.5193 Evaluate side-chains 179 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 165 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 295 GLN G 76 GLN H 93 GLN ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN K 39 HIS K 68 GLN K 108 ASN L 25 ASN M 38 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.129201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.102295 restraints weight = 64258.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.101780 restraints weight = 122825.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101861 restraints weight = 109178.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101555 restraints weight = 76474.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101867 restraints weight = 66733.956| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21228 Z= 0.223 Angle : 0.682 11.437 29971 Z= 0.378 Chirality : 0.044 0.211 3372 Planarity : 0.005 0.052 2787 Dihedral : 28.006 174.152 5164 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.19), residues: 1778 helix: 1.34 (0.20), residues: 613 sheet: -0.92 (0.26), residues: 362 loop : -1.50 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 77 TYR 0.027 0.002 TYR N 39 PHE 0.027 0.002 PHE D 484 TRP 0.028 0.003 TRP D 505 HIS 0.011 0.002 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00508 (21228) covalent geometry : angle 0.68238 (29971) hydrogen bonds : bond 0.07727 ( 1051) hydrogen bonds : angle 4.19619 ( 2670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3527 (t) cc_final: 0.3209 (t) REVERT: A 95 VAL cc_start: 0.4136 (m) cc_final: 0.3871 (t) REVERT: A 290 LEU cc_start: 0.6619 (mt) cc_final: 0.6318 (mp) REVERT: B 46 LYS cc_start: 0.2609 (mttt) cc_final: 0.1551 (mmtm) REVERT: B 69 ILE cc_start: 0.3919 (tp) cc_final: 0.3553 (mp) REVERT: B 156 TRP cc_start: 0.4086 (m100) cc_final: 0.3619 (m100) REVERT: C 3856 ILE cc_start: 0.1463 (tp) cc_final: 0.1196 (mm) REVERT: C 3931 MET cc_start: 0.4298 (mtp) cc_final: 0.3684 (tpt) REVERT: D 336 MET cc_start: 0.1041 (mmp) cc_final: -0.0866 (ppp) REVERT: D 373 LYS cc_start: 0.4293 (mmmt) cc_final: 0.3899 (pttt) REVERT: D 375 HIS cc_start: 0.3101 (t70) cc_final: 0.2409 (t70) REVERT: D 500 MET cc_start: 0.5667 (mmm) cc_final: 0.4771 (tmm) REVERT: H 88 TYR cc_start: 0.7988 (m-10) cc_final: 0.7547 (m-10) REVERT: I 74 LYS cc_start: 0.8342 (mttm) cc_final: 0.8136 (mttm) REVERT: J 76 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7271 (mtm-85) REVERT: J 79 HIS cc_start: 0.7423 (t-90) cc_final: 0.7216 (t70) REVERT: K 73 GLU cc_start: 0.7397 (tt0) cc_final: 0.6893 (tt0) REVERT: M 90 ASP cc_start: 0.7693 (t0) cc_final: 0.7475 (t0) REVERT: N 57 SER cc_start: 0.8605 (p) cc_final: 0.8280 (m) REVERT: N 73 GLU cc_start: 0.7085 (tp30) cc_final: 0.6823 (tp30) outliers start: 1 outliers final: 1 residues processed: 230 average time/residue: 0.1609 time to fit residues: 55.5123 Evaluate side-chains 185 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN G 76 GLN K 68 GLN L 25 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.130153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102596 restraints weight = 63754.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101503 restraints weight = 117010.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102162 restraints weight = 99462.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101669 restraints weight = 72260.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.102003 restraints weight = 65321.217| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21228 Z= 0.161 Angle : 0.601 9.475 29971 Z= 0.337 Chirality : 0.041 0.221 3372 Planarity : 0.005 0.055 2787 Dihedral : 27.669 174.924 5164 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1778 helix: 1.72 (0.21), residues: 612 sheet: -0.73 (0.27), residues: 361 loop : -1.43 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C3965 TYR 0.022 0.002 TYR J 80 PHE 0.022 0.002 PHE B 219 TRP 0.019 0.002 TRP D 505 HIS 0.010 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00356 (21228) covalent geometry : angle 0.60072 (29971) hydrogen bonds : bond 0.06890 ( 1051) hydrogen bonds : angle 3.92670 ( 2670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 CYS cc_start: 0.4059 (t) cc_final: 0.3660 (t) REVERT: A 99 ASP cc_start: 0.1442 (p0) cc_final: 0.0654 (t70) REVERT: A 242 MET cc_start: 0.3757 (mtt) cc_final: 0.3096 (mmm) REVERT: A 290 LEU cc_start: 0.6676 (mt) cc_final: 0.3983 (mp) REVERT: B 46 LYS cc_start: 0.2756 (mttt) cc_final: 0.1919 (mmtm) REVERT: B 156 TRP cc_start: 0.4027 (m100) cc_final: 0.3609 (m100) REVERT: C 3931 MET cc_start: 0.4103 (mtp) cc_final: 0.3482 (tpt) REVERT: C 3933 LYS cc_start: 0.6002 (mmpt) cc_final: 0.4104 (pttp) REVERT: C 3965 ARG cc_start: 0.4187 (mtm110) cc_final: 0.3131 (ptt-90) REVERT: D 334 ASP cc_start: 0.3004 (m-30) cc_final: 0.2509 (t0) REVERT: D 336 MET cc_start: 0.0845 (mmp) cc_final: -0.0910 (ppp) REVERT: D 375 HIS cc_start: 0.2959 (t70) cc_final: 0.2355 (t70) REVERT: D 500 MET cc_start: 0.5044 (mmm) cc_final: 0.4494 (tmm) REVERT: J 76 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7493 (ttp-170) REVERT: J 80 TYR cc_start: 0.7890 (m-10) cc_final: 0.7684 (m-80) REVERT: M 92 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7269 (mm-30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1822 time to fit residues: 64.1484 Evaluate side-chains 182 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 55 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN G 39 HIS G 68 GLN G 76 GLN H 93 GLN ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN K 108 ASN L 25 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.129944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.103167 restraints weight = 64484.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102704 restraints weight = 112812.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.103045 restraints weight = 100714.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102628 restraints weight = 77296.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102914 restraints weight = 67780.936| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.8496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21228 Z= 0.160 Angle : 0.603 9.711 29971 Z= 0.337 Chirality : 0.041 0.227 3372 Planarity : 0.005 0.061 2787 Dihedral : 27.512 174.247 5164 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1778 helix: 1.83 (0.21), residues: 612 sheet: -0.61 (0.27), residues: 371 loop : -1.43 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C3965 TYR 0.015 0.002 TYR A 167 PHE 0.017 0.002 PHE B 149 TRP 0.019 0.002 TRP D 505 HIS 0.008 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00355 (21228) covalent geometry : angle 0.60261 (29971) hydrogen bonds : bond 0.06929 ( 1051) hydrogen bonds : angle 3.86831 ( 2670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.1614 (p0) cc_final: 0.1041 (t70) REVERT: A 242 MET cc_start: 0.3976 (mtt) cc_final: 0.3082 (mmm) REVERT: B 46 LYS cc_start: 0.2763 (mttt) cc_final: 0.1866 (mmtm) REVERT: B 156 TRP cc_start: 0.3903 (m100) cc_final: 0.3598 (m100) REVERT: B 219 PHE cc_start: 0.1170 (t80) cc_final: 0.0912 (t80) REVERT: C 3931 MET cc_start: 0.4054 (mtp) cc_final: 0.3408 (tpt) REVERT: C 3933 LYS cc_start: 0.5894 (mmpt) cc_final: 0.4149 (pttp) REVERT: C 3965 ARG cc_start: 0.4238 (mtm110) cc_final: 0.3117 (ptt-90) REVERT: D 334 ASP cc_start: 0.3122 (m-30) cc_final: 0.2542 (t0) REVERT: D 336 MET cc_start: 0.0733 (mmp) cc_final: -0.0912 (mtp) REVERT: D 373 LYS cc_start: 0.4105 (mmmt) cc_final: 0.3865 (mmmm) REVERT: D 375 HIS cc_start: 0.3244 (t70) cc_final: 0.2721 (t70) REVERT: D 500 MET cc_start: 0.4828 (mmm) cc_final: 0.4372 (tmm) REVERT: J 76 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7495 (ttp-170) REVERT: J 80 TYR cc_start: 0.7802 (m-10) cc_final: 0.7582 (m-80) REVERT: N 73 GLU cc_start: 0.7305 (tp30) cc_final: 0.6978 (tp30) outliers start: 1 outliers final: 1 residues processed: 231 average time/residue: 0.1739 time to fit residues: 59.2224 Evaluate side-chains 184 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 90 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 159 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 99 optimal weight: 0.0020 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN G 39 HIS G 68 GLN G 76 GLN K 68 GLN K 108 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.130086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.102004 restraints weight = 64671.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100527 restraints weight = 114812.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101179 restraints weight = 97444.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101209 restraints weight = 61788.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101461 restraints weight = 60465.984| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21228 Z= 0.150 Angle : 0.593 9.480 29971 Z= 0.332 Chirality : 0.040 0.178 3372 Planarity : 0.005 0.058 2787 Dihedral : 27.349 174.581 5164 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1778 helix: 1.86 (0.21), residues: 612 sheet: -0.83 (0.26), residues: 380 loop : -1.39 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 105 TYR 0.018 0.002 TYR N 80 PHE 0.013 0.001 PHE B 53 TRP 0.029 0.002 TRP A 51 HIS 0.013 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00329 (21228) covalent geometry : angle 0.59306 (29971) hydrogen bonds : bond 0.06741 ( 1051) hydrogen bonds : angle 3.82890 ( 2670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3826 (t) cc_final: 0.3343 (t) REVERT: A 242 MET cc_start: 0.4129 (mtt) cc_final: 0.3324 (mmm) REVERT: A 294 ARG cc_start: 0.4693 (mmm160) cc_final: 0.3558 (mmt-90) REVERT: B 46 LYS cc_start: 0.2432 (mttt) cc_final: 0.1307 (mmmt) REVERT: B 156 TRP cc_start: 0.3954 (m100) cc_final: 0.3571 (m100) REVERT: C 3931 MET cc_start: 0.4059 (mtp) cc_final: 0.3425 (tpt) REVERT: C 3933 LYS cc_start: 0.5956 (mmpt) cc_final: 0.4209 (pttp) REVERT: C 3965 ARG cc_start: 0.4173 (mtm110) cc_final: 0.3059 (ptt-90) REVERT: D 334 ASP cc_start: 0.3207 (m-30) cc_final: 0.2627 (t0) REVERT: D 336 MET cc_start: 0.0690 (mmp) cc_final: -0.0951 (ppp) REVERT: D 375 HIS cc_start: 0.3270 (t70) cc_final: 0.2591 (t70) REVERT: D 500 MET cc_start: 0.4846 (mmm) cc_final: 0.4499 (tmm) REVERT: J 56 MET cc_start: 0.8350 (tpt) cc_final: 0.8036 (tpp) REVERT: J 76 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7423 (ttp-170) REVERT: N 73 GLU cc_start: 0.7367 (tp30) cc_final: 0.6943 (tp30) REVERT: N 87 THR cc_start: 0.8730 (p) cc_final: 0.8371 (p) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1623 time to fit residues: 55.4556 Evaluate side-chains 186 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 177 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 185 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 76 GLN H 93 GLN ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.127672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.100647 restraints weight = 64254.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099434 restraints weight = 117657.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100039 restraints weight = 100848.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099611 restraints weight = 71388.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.099932 restraints weight = 65754.634| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.9202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21228 Z= 0.203 Angle : 0.649 10.702 29971 Z= 0.360 Chirality : 0.043 0.420 3372 Planarity : 0.005 0.057 2787 Dihedral : 27.417 172.715 5164 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1778 helix: 1.60 (0.21), residues: 612 sheet: -0.88 (0.26), residues: 373 loop : -1.46 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C3965 TYR 0.057 0.002 TYR J 80 PHE 0.022 0.002 PHE D 469 TRP 0.032 0.003 TRP B 330 HIS 0.009 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00460 (21228) covalent geometry : angle 0.64871 (29971) hydrogen bonds : bond 0.07483 ( 1051) hydrogen bonds : angle 4.10382 ( 2670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3931 (t) cc_final: 0.3462 (t) REVERT: A 242 MET cc_start: 0.4275 (mtt) cc_final: 0.3657 (mmm) REVERT: B 46 LYS cc_start: 0.2456 (mttt) cc_final: 0.1429 (mmtm) REVERT: B 156 TRP cc_start: 0.3930 (m100) cc_final: 0.3465 (m100) REVERT: C 3931 MET cc_start: 0.4149 (mtp) cc_final: 0.3453 (tpt) REVERT: C 3933 LYS cc_start: 0.6248 (mmpt) cc_final: 0.4384 (pttp) REVERT: D 336 MET cc_start: 0.0657 (mmp) cc_final: -0.0923 (mtp) REVERT: D 373 LYS cc_start: 0.3905 (mmmt) cc_final: 0.3686 (pttt) REVERT: D 375 HIS cc_start: 0.3072 (t70) cc_final: 0.2756 (t70) REVERT: D 500 MET cc_start: 0.4901 (mmm) cc_final: 0.4525 (tmm) REVERT: N 73 GLU cc_start: 0.7298 (tp30) cc_final: 0.6893 (tp30) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1605 time to fit residues: 50.7365 Evaluate side-chains 168 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 129 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 91 optimal weight: 0.3980 chunk 68 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN K 68 GLN K 108 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.128991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101235 restraints weight = 65094.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100174 restraints weight = 108120.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100935 restraints weight = 95454.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100367 restraints weight = 72411.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.100758 restraints weight = 66688.827| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.9308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21228 Z= 0.152 Angle : 0.599 9.415 29971 Z= 0.335 Chirality : 0.040 0.234 3372 Planarity : 0.005 0.055 2787 Dihedral : 27.117 174.187 5164 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1778 helix: 1.75 (0.21), residues: 612 sheet: -0.74 (0.27), residues: 363 loop : -1.42 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C3965 TYR 0.059 0.002 TYR J 80 PHE 0.027 0.002 PHE D 469 TRP 0.023 0.002 TRP D 505 HIS 0.012 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00335 (21228) covalent geometry : angle 0.59923 (29971) hydrogen bonds : bond 0.06914 ( 1051) hydrogen bonds : angle 3.91068 ( 2670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.616 Fit side-chains REVERT: A 43 CYS cc_start: 0.3815 (t) cc_final: 0.3300 (t) REVERT: A 99 ASP cc_start: 0.1093 (p0) cc_final: 0.0616 (t70) REVERT: A 242 MET cc_start: 0.4368 (mtt) cc_final: 0.3721 (mmm) REVERT: A 294 ARG cc_start: 0.4783 (mmm160) cc_final: 0.3577 (mmt-90) REVERT: B 46 LYS cc_start: 0.2541 (mttt) cc_final: 0.1629 (mmtm) REVERT: B 156 TRP cc_start: 0.3820 (m100) cc_final: 0.3380 (m100) REVERT: B 219 PHE cc_start: 0.1258 (t80) cc_final: 0.1026 (t80) REVERT: C 3931 MET cc_start: 0.3970 (mtp) cc_final: 0.3446 (tpt) REVERT: C 3933 LYS cc_start: 0.6108 (mmpt) cc_final: 0.4359 (pttp) REVERT: C 3945 LYS cc_start: 0.3069 (mttt) cc_final: 0.2605 (mptt) REVERT: C 3965 ARG cc_start: 0.4174 (mtm110) cc_final: 0.3087 (ptt-90) REVERT: D 336 MET cc_start: 0.0560 (mmp) cc_final: -0.0924 (mtp) REVERT: D 500 MET cc_start: 0.4831 (mmm) cc_final: 0.4521 (tmm) REVERT: N 73 GLU cc_start: 0.7272 (tp30) cc_final: 0.6907 (tp30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1562 time to fit residues: 50.5070 Evaluate side-chains 177 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 84 optimal weight: 5.9990 chunk 112 optimal weight: 0.0040 chunk 67 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 76 GLN H 93 GLN ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.127090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.100011 restraints weight = 64798.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.098878 restraints weight = 124989.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.099482 restraints weight = 100309.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.099408 restraints weight = 66889.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.099826 restraints weight = 60874.052| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.9674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21228 Z= 0.215 Angle : 0.666 12.196 29971 Z= 0.367 Chirality : 0.043 0.186 3372 Planarity : 0.005 0.068 2787 Dihedral : 27.352 172.662 5164 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 1778 helix: 1.48 (0.21), residues: 606 sheet: -0.83 (0.27), residues: 364 loop : -1.57 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C3965 TYR 0.025 0.002 TYR N 37 PHE 0.039 0.002 PHE B 149 TRP 0.035 0.003 TRP A 321 HIS 0.011 0.002 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00490 (21228) covalent geometry : angle 0.66604 (29971) hydrogen bonds : bond 0.07807 ( 1051) hydrogen bonds : angle 4.19961 ( 2670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.75 seconds wall clock time: 60 minutes 18.80 seconds (3618.80 seconds total)