Starting phenix.real_space_refine on Mon Jul 6 03:35:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbn_23739/07_2026/7mbn_23739.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbn_23739/07_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_23739/07_2026/7mbn_23739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbn_23739/07_2026/7mbn_23739.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbn_23739/07_2026/7mbn_23739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbn_23739/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 4.12, per 1000 atoms: 0.20 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: 1.79 Conformation dependent library (CDL) restraints added in 588.1 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: 2.87 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: 5.11 Time building geometry restraints manager: 2.32 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' DG P 84 " pdb=" C2' DG P 84 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DC P 111 " pdb=" O3' DC P 111 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" C3' DG O 101 " pdb=" C2' DG O 101 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC O 17 " pdb=" C2' DC O 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT P 57 " pdb=" C2' DT P 57 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 21223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 29647 2.63 - 5.25: 310 5.25 - 7.88: 11 7.88 - 10.51: 0 10.51 - 13.13: 3 Bond angle restraints: 29971 Sorted by residual: angle pdb=" O4' DA P 14 " pdb=" C4' DA P 14 " pdb=" C3' DA P 14 " ideal model delta sigma weight residual 106.00 102.42 3.58 6.00e-01 2.78e+00 3.56e+01 angle pdb=" O4' DG P 130 " pdb=" C4' DG P 130 " pdb=" C3' DG P 130 " ideal model delta sigma weight residual 106.00 102.44 3.56 6.00e-01 2.78e+00 3.52e+01 angle pdb=" O4' DA O 41 " pdb=" C4' DA O 41 " pdb=" C3' DA O 41 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" O5' DG P 112 " pdb=" C5' DG P 112 " pdb=" C4' DG P 112 " ideal model delta sigma weight residual 109.40 113.14 -3.74 8.00e-01 1.56e+00 2.19e+01 angle pdb=" N3 DT P 2 " pdb=" C4 DT P 2 " pdb=" O4 DT P 2 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (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: 2182 0.040 - 0.080: 814 0.080 - 0.121: 316 0.121 - 0.161: 51 0.161 - 0.201: 9 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: 2.980 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.740 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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: 26.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 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 : 0.006 0.051 21228 Z= 0.512 Angle : 0.774 13.134 29971 Z= 0.610 Chirality : 0.049 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/Z covalent geometry : bond 0.00582 / 0.51 (21228) covalent geometry : angle 0.77395 / 0.61 (29971) hydrogen bonds : bond 0.17006 / 11.29 ( 1051) hydrogen bonds : angle 6.20890 / 4.27 ( 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 : 0.597 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: 0.1877 time to fit residues: 135.0687 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 : 0.631 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 1.9990 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: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN A 328 ASN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN B 140 GLN B 265 ASN B 289 GLN B 323 ASN D 354 GLN D 441 GLN I 89 ASN J 79 HIS K 39 HIS K 68 GLN ** L 75 HIS ** 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 = 0.4312 r_free = 0.4312 target = 0.143131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.116637 restraints weight = 65647.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.115743 restraints weight = 107448.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.116612 restraints weight = 91257.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.116048 restraints weight = 67757.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.116314 restraints weight = 63338.471| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 21228 Z= 0.253 Angle : 0.863 11.871 29971 Z= 0.465 Chirality : 0.055 0.378 3372 Planarity : 0.007 0.095 2787 Dihedral : 29.696 178.631 5164 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 0.33 % Allowed : 5.82 % Favored : 93.85 % 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: -1.57 (0.19), residues: 1778 helix: 0.31 (0.20), residues: 601 sheet: -1.56 (0.25), residues: 362 loop : -1.81 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 498 TYR 0.024 0.003 TYR M 50 PHE 0.026 0.003 PHE C3929 TRP 0.031 0.003 TRP D 505 HIS 0.017 0.002 HIS C3925 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (21228) covalent geometry : angle 0.86302 / 0.46 (29971) hydrogen bonds : bond 0.08851 / 5.80 ( 1051) hydrogen bonds : angle 4.94266 / 3.42 ( 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 281 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 276 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6471 (tp) cc_final: 0.5868 (tt) REVERT: B 46 LYS cc_start: 0.2869 (mttt) cc_final: 0.1897 (mmmt) REVERT: B 156 TRP cc_start: 0.4302 (m100) cc_final: 0.3877 (m100) REVERT: B 214 ASN cc_start: 0.1551 (t0) cc_final: 0.0480 (p0) REVERT: B 249 LEU cc_start: 0.3236 (mt) cc_final: 0.2709 (mm) REVERT: C 3931 MET cc_start: 0.4250 (mtp) cc_final: 0.3123 (tpt) REVERT: C 3965 ARG cc_start: 0.4650 (mtm110) cc_final: 0.3548 (ptt-90) REVERT: D 340 THR cc_start: -0.0553 (m) cc_final: -0.0904 (m) REVERT: D 394 PHE cc_start: 0.3792 (m-80) cc_final: 0.3391 (m-80) REVERT: D 493 LYS cc_start: 0.1112 (mmmt) cc_final: 0.0801 (mptt) REVERT: G 82 LEU cc_start: 0.7153 (mp) cc_final: 0.6933 (mp) REVERT: I 51 LEU cc_start: 0.8879 (pp) cc_final: 0.8520 (tt) REVERT: I 74 LYS cc_start: 0.8210 (mttt) cc_final: 0.7495 (pptt) REVERT: J 73 GLU cc_start: 0.7654 (tp30) cc_final: 0.7256 (tp30) REVERT: J 76 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7013 (mtm180) REVERT: K 39 HIS cc_start: 0.6086 (t70) cc_final: 0.5557 (t70) REVERT: N 90 GLU cc_start: 0.6622 (mp0) cc_final: 0.6386 (mp0) outliers start: 5 outliers final: 3 residues processed: 278 average time/residue: 0.1613 time to fit residues: 66.3278 Evaluate side-chains 190 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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: 5.9990 chunk 63 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN K 68 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.140913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.112067 restraints weight = 64116.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.111245 restraints weight = 92709.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.112029 restraints weight = 76725.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.111244 restraints weight = 60837.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.111689 restraints weight = 54208.116| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (8 function evaluations) r_final: 0.3789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21228 Z= 0.178 Angle : 0.697 9.219 29971 Z= 0.388 Chirality : 0.049 0.341 3372 Planarity : 0.005 0.054 2787 Dihedral : 29.280 176.656 5164 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.07 % Allowed : 3.92 % Favored : 96.01 % 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: -0.87 (0.19), residues: 1778 helix: 1.31 (0.20), residues: 603 sheet: -1.29 (0.26), residues: 367 loop : -1.70 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 498 TYR 0.022 0.002 TYR D 460 PHE 0.019 0.002 PHE C3929 TRP 0.051 0.003 TRP B 330 HIS 0.011 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (21228) covalent geometry : angle 0.69688 / 0.39 (29971) hydrogen bonds : bond 0.07444 / 4.88 ( 1051) hydrogen bonds : angle 4.38906 / 3.05 ( 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 237 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.4185 (tpt) cc_final: 0.3635 (tpt) REVERT: B 46 LYS cc_start: 0.2773 (mttt) cc_final: 0.1820 (mmmt) REVERT: B 156 TRP cc_start: 0.4362 (m100) cc_final: 0.3875 (m100) REVERT: B 221 LYS cc_start: 0.5711 (pttt) cc_final: 0.4650 (mttp) REVERT: C 3838 ILE cc_start: 0.2438 (mt) cc_final: 0.2041 (mt) REVERT: C 3931 MET cc_start: 0.4386 (mtp) cc_final: 0.3339 (tpt) REVERT: C 3965 ARG cc_start: 0.4626 (mtm110) cc_final: 0.3383 (ptt-90) REVERT: D 384 SER cc_start: 0.4240 (p) cc_final: 0.3786 (t) REVERT: D 461 LYS cc_start: 0.1117 (tptt) cc_final: 0.0879 (tppt) REVERT: D 500 MET cc_start: 0.5473 (mmt) cc_final: 0.5258 (ttp) REVERT: H 63 GLU cc_start: 0.7811 (tt0) cc_final: 0.7500 (tt0) REVERT: I 62 ILE cc_start: 0.8511 (pt) cc_final: 0.8277 (mt) REVERT: I 74 LYS cc_start: 0.8390 (mttt) cc_final: 0.7688 (pptt) REVERT: J 73 GLU cc_start: 0.7585 (tp30) cc_final: 0.7121 (tp30) REVERT: J 76 ARG cc_start: 0.7598 (ttm110) cc_final: 0.6569 (mtm180) REVERT: N 48 ASP cc_start: 0.5682 (p0) cc_final: 0.5481 (p0) REVERT: N 73 GLU cc_start: 0.7053 (tp30) cc_final: 0.6659 (tp30) REVERT: N 90 GLU cc_start: 0.6697 (mp0) cc_final: 0.6425 (mp0) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.1710 time to fit residues: 59.2159 Evaluate side-chains 174 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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: 0.0010 chunk 160 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN D 441 GLN G 39 HIS G 68 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.139880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.111166 restraints weight = 64171.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.109570 restraints weight = 102237.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.110539 restraints weight = 86027.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.109905 restraints weight = 63775.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.110370 restraints weight = 56879.494| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21228 Z= 0.151 Angle : 0.670 11.671 29971 Z= 0.373 Chirality : 0.048 0.361 3372 Planarity : 0.005 0.058 2787 Dihedral : 29.073 178.717 5164 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.60 % 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: -0.69 (0.19), residues: 1778 helix: 1.49 (0.21), residues: 603 sheet: -1.20 (0.25), residues: 373 loop : -1.62 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 42 TYR 0.035 0.002 TYR A 167 PHE 0.020 0.002 PHE D 329 TRP 0.021 0.002 TRP D 505 HIS 0.017 0.002 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (21228) covalent geometry : angle 0.67019 / 0.37 (29971) hydrogen bonds : bond 0.07261 / 4.76 ( 1051) hydrogen bonds : angle 4.28011 / 2.97 ( 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 228 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.4430 (tpt) cc_final: 0.4031 (tpt) REVERT: A 39 LEU cc_start: 0.6343 (tp) cc_final: 0.5967 (tt) REVERT: B 46 LYS cc_start: 0.2545 (mttt) cc_final: 0.1658 (mmmt) REVERT: B 156 TRP cc_start: 0.4403 (m100) cc_final: 0.3816 (m100) REVERT: B 221 LYS cc_start: 0.5576 (pttt) cc_final: 0.4642 (mttt) REVERT: C 3931 MET cc_start: 0.4325 (mtp) cc_final: 0.3298 (tpt) REVERT: C 3965 ARG cc_start: 0.4630 (mtm110) cc_final: 0.3453 (ptt-90) REVERT: D 315 MET cc_start: 0.1063 (ttp) cc_final: 0.0816 (ttt) REVERT: D 329 PHE cc_start: 0.1000 (p90) cc_final: 0.0484 (p90) REVERT: D 384 SER cc_start: 0.3793 (p) cc_final: 0.3564 (t) REVERT: D 500 MET cc_start: 0.5539 (mmt) cc_final: 0.5048 (tmm) REVERT: H 63 GLU cc_start: 0.7815 (tt0) cc_final: 0.7543 (tt0) REVERT: I 62 ILE cc_start: 0.8551 (pt) cc_final: 0.8278 (mt) REVERT: I 64 GLU cc_start: 0.6443 (tt0) cc_final: 0.6218 (tt0) REVERT: I 74 LYS cc_start: 0.8397 (mttt) cc_final: 0.7711 (pptt) REVERT: J 32 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6914 (pt0) REVERT: J 73 GLU cc_start: 0.7614 (tp30) cc_final: 0.7229 (tp30) REVERT: J 76 ARG cc_start: 0.7654 (ttm110) cc_final: 0.6653 (mtm180) REVERT: K 42 ARG cc_start: 0.7022 (mmm160) cc_final: 0.6747 (mmp-170) REVERT: K 108 ASN cc_start: 0.8413 (t0) cc_final: 0.8133 (t0) REVERT: K 112 ILE cc_start: 0.8753 (mm) cc_final: 0.8542 (mm) REVERT: M 90 ASP cc_start: 0.8168 (t0) cc_final: 0.7956 (t0) REVERT: N 73 GLU cc_start: 0.7080 (tp30) cc_final: 0.6738 (tp30) REVERT: N 90 GLU cc_start: 0.6535 (mp0) cc_final: 0.6323 (mp0) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1454 time to fit residues: 50.4585 Evaluate side-chains 171 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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: 0.0570 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 183 GLN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN G 93 GLN G 108 ASN H 93 GLN K 93 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.137408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.110050 restraints weight = 64405.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.109681 restraints weight = 96495.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.109283 restraints weight = 87146.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.109033 restraints weight = 60830.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.109298 restraints weight = 53144.906| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21228 Z= 0.166 Angle : 0.669 9.569 29971 Z= 0.372 Chirality : 0.048 0.351 3372 Planarity : 0.005 0.071 2787 Dihedral : 28.913 178.248 5164 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: -0.66 (0.19), residues: 1778 helix: 1.55 (0.20), residues: 603 sheet: -1.23 (0.25), residues: 381 loop : -1.60 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 29 TYR 0.050 0.002 TYR J 80 PHE 0.015 0.002 PHE D 329 TRP 0.067 0.003 TRP B 330 HIS 0.009 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (21228) covalent geometry : angle 0.66851 / 0.37 (29971) hydrogen bonds : bond 0.07232 / 4.70 ( 1051) hydrogen bonds : angle 4.15108 / 2.89 ( 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 228 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.4871 (tpt) cc_final: 0.4542 (tpt) REVERT: A 39 LEU cc_start: 0.6224 (tp) cc_final: 0.5832 (tt) REVERT: B 46 LYS cc_start: 0.2668 (mttt) cc_final: 0.1540 (mmmt) REVERT: B 156 TRP cc_start: 0.4348 (m100) cc_final: 0.3837 (m100) REVERT: B 221 LYS cc_start: 0.5525 (pttt) cc_final: 0.4521 (mttt) REVERT: B 330 TRP cc_start: 0.3034 (m100) cc_final: 0.1968 (m100) REVERT: C 3931 MET cc_start: 0.4425 (mtp) cc_final: 0.3602 (tpt) REVERT: D 315 MET cc_start: 0.1237 (ttp) cc_final: 0.0992 (ttt) REVERT: D 329 PHE cc_start: 0.0984 (p90) cc_final: 0.0343 (p90) REVERT: D 336 MET cc_start: 0.0851 (mmp) cc_final: -0.1169 (ppp) REVERT: D 500 MET cc_start: 0.5567 (mmt) cc_final: 0.5182 (ttp) REVERT: H 63 GLU cc_start: 0.7934 (tt0) cc_final: 0.7574 (tt0) REVERT: H 67 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7392 (ttp80) REVERT: I 62 ILE cc_start: 0.8594 (pt) cc_final: 0.8260 (mt) REVERT: I 74 LYS cc_start: 0.8463 (mttt) cc_final: 0.7811 (pptt) REVERT: J 32 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7212 (pt0) REVERT: J 73 GLU cc_start: 0.7637 (tp30) cc_final: 0.7345 (tp30) REVERT: J 76 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7233 (ttm110) REVERT: K 42 ARG cc_start: 0.7209 (mmm160) cc_final: 0.6980 (mmp-170) REVERT: K 73 GLU cc_start: 0.7094 (tt0) cc_final: 0.6843 (tt0) REVERT: K 110 CYS cc_start: 0.6552 (m) cc_final: 0.6158 (m) REVERT: L 84 MET cc_start: 0.7706 (mmm) cc_final: 0.7493 (mmm) REVERT: N 51 ILE cc_start: 0.8110 (pt) cc_final: 0.7754 (pt) REVERT: N 73 GLU cc_start: 0.7061 (tp30) cc_final: 0.6674 (tp30) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1428 time to fit residues: 48.7885 Evaluate side-chains 176 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 0.9980 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 204 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN J 81 ASN ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.132345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.104070 restraints weight = 63176.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103154 restraints weight = 105475.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.103505 restraints weight = 94283.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.103242 restraints weight = 66684.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.103645 restraints weight = 58647.736| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 21228 Z= 0.209 Angle : 0.747 11.788 29971 Z= 0.412 Chirality : 0.051 0.492 3372 Planarity : 0.006 0.061 2787 Dihedral : 28.801 179.143 5164 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % 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: -0.95 (0.19), residues: 1778 helix: 1.15 (0.21), residues: 601 sheet: -1.31 (0.26), residues: 360 loop : -1.67 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C3965 TYR 0.027 0.002 TYR N 37 PHE 0.056 0.003 PHE K 67 TRP 0.029 0.002 TRP B 330 HIS 0.009 0.002 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (21228) covalent geometry : angle 0.74734 / 0.41 (29971) hydrogen bonds : bond 0.08186 / 5.24 ( 1051) hydrogen bonds : angle 4.34709 / 3.02 ( 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 240 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6149 (tp) cc_final: 0.5865 (tt) REVERT: A 43 CYS cc_start: 0.3791 (t) cc_final: 0.3577 (t) REVERT: A 290 LEU cc_start: 0.6863 (mt) cc_final: 0.4583 (mt) REVERT: A 320 ILE cc_start: 0.6601 (tp) cc_final: 0.6271 (tp) REVERT: A 321 TRP cc_start: 0.5936 (m100) cc_final: 0.4288 (t-100) REVERT: B 46 LYS cc_start: 0.2521 (mttt) cc_final: 0.1566 (mmtt) REVERT: B 156 TRP cc_start: 0.4387 (m100) cc_final: 0.3929 (m100) REVERT: C 3931 MET cc_start: 0.4323 (mtp) cc_final: 0.3565 (tpt) REVERT: C 3933 LYS cc_start: 0.5760 (mmmt) cc_final: 0.4262 (pttp) REVERT: C 3965 ARG cc_start: 0.4534 (mtm110) cc_final: 0.3577 (ptt-90) REVERT: D 315 MET cc_start: 0.1728 (ttp) cc_final: 0.1361 (ttt) REVERT: D 375 HIS cc_start: 0.3047 (t70) cc_final: 0.1716 (t-90) REVERT: D 500 MET cc_start: 0.5865 (mmt) cc_final: 0.4906 (tmm) REVERT: H 63 GLU cc_start: 0.7975 (tt0) cc_final: 0.7635 (tt0) REVERT: H 67 ARG cc_start: 0.7847 (ttp-110) cc_final: 0.7638 (ttp-110) REVERT: I 62 ILE cc_start: 0.8781 (pt) cc_final: 0.8264 (mt) REVERT: I 74 LYS cc_start: 0.8501 (mttt) cc_final: 0.7989 (pptt) REVERT: I 92 GLU cc_start: 0.7557 (tp30) cc_final: 0.7286 (tp30) REVERT: J 76 ARG cc_start: 0.7806 (ttm110) cc_final: 0.6847 (mtm180) REVERT: J 90 GLU cc_start: 0.7480 (mp0) cc_final: 0.7259 (mp0) REVERT: K 119 ILE cc_start: 0.9195 (mm) cc_final: 0.8944 (mt) REVERT: N 73 GLU cc_start: 0.7133 (tp30) cc_final: 0.6767 (tp30) outliers start: 2 outliers final: 0 residues processed: 240 average time/residue: 0.1484 time to fit residues: 53.5748 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 : 0.635 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN G 108 ASN H 93 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.131725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103651 restraints weight = 64056.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.102091 restraints weight = 119052.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.103007 restraints weight = 99544.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.102353 restraints weight = 72831.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.102861 restraints weight = 64210.087| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21228 Z= 0.188 Angle : 0.699 14.307 29971 Z= 0.384 Chirality : 0.048 0.350 3372 Planarity : 0.006 0.078 2787 Dihedral : 28.634 178.671 5164 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -0.80 (0.19), residues: 1778 helix: 1.37 (0.21), residues: 606 sheet: -1.40 (0.26), residues: 357 loop : -1.60 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 40 TYR 0.058 0.003 TYR J 80 PHE 0.022 0.002 PHE D 329 TRP 0.029 0.002 TRP B 330 HIS 0.012 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (21228) covalent geometry : angle 0.69898 / 0.38 (29971) hydrogen bonds : bond 0.07596 / 4.86 ( 1051) hydrogen bonds : angle 4.25117 / 2.95 ( 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 232 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 79 HIS cc_start: 0.3895 (m-70) cc_final: 0.3597 (m-70) REVERT: B 46 LYS cc_start: 0.2346 (mttt) cc_final: 0.1456 (mmtm) REVERT: B 156 TRP cc_start: 0.4478 (m100) cc_final: 0.3904 (m100) REVERT: C 3931 MET cc_start: 0.4197 (mtp) cc_final: 0.3465 (tpt) REVERT: C 3965 ARG cc_start: 0.4536 (mtm110) cc_final: 0.3454 (ptt-90) REVERT: D 334 ASP cc_start: 0.3279 (m-30) cc_final: 0.2643 (t0) REVERT: D 336 MET cc_start: 0.1252 (mmp) cc_final: -0.1077 (mtt) REVERT: D 394 PHE cc_start: 0.3907 (m-80) cc_final: 0.3577 (m-80) REVERT: D 500 MET cc_start: 0.5929 (mmt) cc_final: 0.4960 (tmm) REVERT: H 63 GLU cc_start: 0.7917 (tt0) cc_final: 0.7601 (tt0) REVERT: I 62 ILE cc_start: 0.8726 (pt) cc_final: 0.8268 (mt) REVERT: I 74 LYS cc_start: 0.8583 (mttt) cc_final: 0.7561 (pptt) REVERT: J 76 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7681 (ttp-110) REVERT: N 73 GLU cc_start: 0.6870 (tp30) cc_final: 0.6508 (tp30) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1516 time to fit residues: 52.9817 Evaluate side-chains 181 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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: 8.9990 chunk 109 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 76 GLN G 108 ASN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN K 39 HIS K 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.132333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.105404 restraints weight = 64247.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.104328 restraints weight = 112357.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.104758 restraints weight = 98563.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.104408 restraints weight = 69986.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.104649 restraints weight = 63921.322| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21228 Z= 0.144 Angle : 0.653 10.850 29971 Z= 0.362 Chirality : 0.046 0.359 3372 Planarity : 0.005 0.064 2787 Dihedral : 28.441 178.231 5164 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.07 % Allowed : 0.92 % Favored : 99.02 % 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: -0.57 (0.19), residues: 1778 helix: 1.69 (0.21), residues: 605 sheet: -1.32 (0.26), residues: 364 loop : -1.54 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 131 TYR 0.026 0.002 TYR N 37 PHE 0.030 0.002 PHE D 449 TRP 0.026 0.002 TRP B 330 HIS 0.013 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (21228) covalent geometry : angle 0.65291 / 0.36 (29971) hydrogen bonds : bond 0.07252 / 4.63 ( 1051) hydrogen bonds : angle 4.14550 / 2.85 ( 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 235 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.4158 (mtt) cc_final: 0.3235 (mmm) REVERT: B 46 LYS cc_start: 0.2539 (mttt) cc_final: 0.1614 (mmtm) REVERT: B 156 TRP cc_start: 0.4232 (m100) cc_final: 0.3778 (m100) REVERT: C 3931 MET cc_start: 0.3936 (mtp) cc_final: 0.3295 (tpt) REVERT: C 3933 LYS cc_start: 0.5632 (mmmt) cc_final: 0.3784 (pttp) REVERT: C 3965 ARG cc_start: 0.4492 (mtm110) cc_final: 0.3367 (ptt-90) REVERT: D 334 ASP cc_start: 0.2967 (m-30) cc_final: 0.2445 (t0) REVERT: D 336 MET cc_start: 0.1098 (mmp) cc_final: -0.1017 (mtt) REVERT: D 375 HIS cc_start: 0.3142 (t70) cc_final: 0.1722 (t-90) REVERT: D 500 MET cc_start: 0.5822 (mmt) cc_final: 0.4888 (tmm) REVERT: H 63 GLU cc_start: 0.7955 (tt0) cc_final: 0.7645 (tt0) REVERT: I 62 ILE cc_start: 0.8666 (pt) cc_final: 0.8295 (mt) REVERT: I 64 GLU cc_start: 0.6430 (tt0) cc_final: 0.6222 (tt0) REVERT: N 73 GLU cc_start: 0.7116 (tp30) cc_final: 0.6720 (tp30) REVERT: N 87 THR cc_start: 0.8592 (p) cc_final: 0.8218 (p) outliers start: 1 outliers final: 1 residues processed: 234 average time/residue: 0.1472 time to fit residues: 51.5539 Evaluate side-chains 180 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 10.0000 chunk 199 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 5 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 185 optimal weight: 9.9990 overall best weight: 5.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 HIS ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C3906 ASN H 93 GLN J 81 ASN K 68 GLN K 113 HIS L 25 ASN L 75 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.124926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.095630 restraints weight = 63799.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.094361 restraints weight = 119562.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095212 restraints weight = 98924.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.094722 restraints weight = 68643.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095183 restraints weight = 61913.535| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.8578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.160 21228 Z= 0.431 Angle : 1.104 15.099 29971 Z= 0.578 Chirality : 0.066 0.487 3372 Planarity : 0.010 0.108 2787 Dihedral : 28.951 170.909 5164 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.81 % 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 : 0.06 % 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: -1.95 (0.18), residues: 1778 helix: -0.07 (0.20), residues: 600 sheet: -1.47 (0.26), residues: 340 loop : -2.13 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG G 53 TYR 0.057 0.005 TYR D 328 PHE 0.051 0.005 PHE I 25 TRP 0.048 0.005 TRP D 505 HIS 0.019 0.003 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00963 / 0.43 (21228) covalent geometry : angle 1.10365 / 0.58 (29971) hydrogen bonds : bond 0.12286 / 7.92 ( 1051) hydrogen bonds : angle 5.35544 / 3.70 ( 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 202 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.617 Fit side-chains REVERT: A 43 CYS cc_start: 0.3705 (t) cc_final: 0.3467 (t) REVERT: B 46 LYS cc_start: 0.2150 (mttt) cc_final: 0.1037 (mmtm) REVERT: B 156 TRP cc_start: 0.4491 (m100) cc_final: 0.3582 (m100) REVERT: B 330 TRP cc_start: 0.3389 (m100) cc_final: 0.3176 (m100) REVERT: C 3931 MET cc_start: 0.3937 (mtp) cc_final: 0.3409 (tpt) REVERT: D 334 ASP cc_start: 0.3332 (m-30) cc_final: 0.2719 (t70) REVERT: D 336 MET cc_start: 0.2228 (mmp) cc_final: -0.0562 (mtm) REVERT: D 500 MET cc_start: 0.6723 (mmm) cc_final: 0.5372 (tmm) REVERT: H 63 GLU cc_start: 0.7956 (tt0) cc_final: 0.7610 (tt0) REVERT: L 25 ASN cc_start: 0.7996 (m110) cc_final: 0.7724 (m-40) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1288 time to fit residues: 41.2628 Evaluate side-chains 160 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 0.4980 chunk 73 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 91 optimal weight: 0.0670 chunk 68 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.129291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101578 restraints weight = 63817.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100711 restraints weight = 105982.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101143 restraints weight = 88992.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.100876 restraints weight = 61573.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101350 restraints weight = 55227.042| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 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 = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.8510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 21228 Z= 0.158 Angle : 0.722 9.522 29971 Z= 0.398 Chirality : 0.050 0.396 3372 Planarity : 0.006 0.074 2787 Dihedral : 28.193 174.472 5164 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -1.04 (0.19), residues: 1778 helix: 1.17 (0.21), residues: 609 sheet: -1.36 (0.27), residues: 333 loop : -1.85 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 89 TYR 0.035 0.002 TYR D 328 PHE 0.060 0.002 PHE D 469 TRP 0.033 0.002 TRP B 330 HIS 0.008 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (21228) covalent geometry : angle 0.72156 / 0.40 (29971) hydrogen bonds : bond 0.07948 / 5.07 ( 1051) hydrogen bonds : angle 4.43515 / 3.07 ( 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 226 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.4919 (pp20) cc_final: 0.4367 (pp20) REVERT: B 46 LYS cc_start: 0.2534 (mttt) cc_final: 0.1412 (mmtm) REVERT: B 69 ILE cc_start: 0.3996 (tp) cc_final: 0.3532 (mp) REVERT: B 154 ARG cc_start: 0.4788 (mpt90) cc_final: 0.4345 (mmt180) REVERT: B 156 TRP cc_start: 0.4113 (m100) cc_final: 0.3474 (m100) REVERT: B 330 TRP cc_start: 0.3354 (m100) cc_final: 0.3072 (m100) REVERT: C 3931 MET cc_start: 0.3836 (mtp) cc_final: 0.3387 (tpt) REVERT: C 3933 LYS cc_start: 0.5577 (mmmt) cc_final: 0.3682 (pttp) REVERT: D 330 GLU cc_start: 0.2732 (mt-10) cc_final: 0.1972 (mt-10) REVERT: D 334 ASP cc_start: 0.2904 (m-30) cc_final: 0.2438 (t70) REVERT: D 336 MET cc_start: 0.1371 (mmp) cc_final: -0.1020 (mtm) REVERT: D 500 MET cc_start: 0.6175 (mmm) cc_final: 0.4638 (tmm) REVERT: H 63 GLU cc_start: 0.7972 (tt0) cc_final: 0.7593 (tt0) REVERT: I 62 ILE cc_start: 0.8632 (pt) cc_final: 0.8391 (mt) REVERT: J 80 TYR cc_start: 0.7782 (m-10) cc_final: 0.7473 (m-80) REVERT: N 73 GLU cc_start: 0.7105 (tp30) cc_final: 0.6751 (tp30) REVERT: N 87 THR cc_start: 0.8446 (p) cc_final: 0.8083 (p) REVERT: N 90 GLU cc_start: 0.7160 (mp0) cc_final: 0.6888 (mt-10) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1414 time to fit residues: 48.8000 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 : 0.654 ------------------------------------------------------------------------------- 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: 0.0570 chunk 112 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 21 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN G 76 GLN G 85 GLN G 108 ASN H 93 GLN ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN K 108 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.129374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100020 restraints weight = 63500.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.098945 restraints weight = 99901.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.099834 restraints weight = 87398.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099279 restraints weight = 62889.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099653 restraints weight = 58021.486| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 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 = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.8545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21228 Z= 0.141 Angle : 0.655 9.833 29971 Z= 0.365 Chirality : 0.047 0.296 3372 Planarity : 0.005 0.065 2787 Dihedral : 27.877 174.248 5164 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.72 (0.19), residues: 1778 helix: 1.52 (0.21), residues: 613 sheet: -1.30 (0.26), residues: 352 loop : -1.68 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C3965 TYR 0.032 0.002 TYR N 37 PHE 0.026 0.002 PHE B 149 TRP 0.031 0.003 TRP B 198 HIS 0.021 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (21228) covalent geometry : angle 0.65526 / 0.36 (29971) hydrogen bonds : bond 0.07452 / 4.78 ( 1051) hydrogen bonds : angle 4.15674 / 2.89 ( 2670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.72 seconds wall clock time: 55 minutes 2.97 seconds (3302.97 seconds total)