Starting phenix.real_space_refine on Mon Sep 14 18:30:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbn_23739/09_2026/7mbn_23739.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbn_23739/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mbn_23739/09_2026/7mbn_23739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbn_23739/09_2026/7mbn_23739.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mbn_23739/09_2026/7mbn_23739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbn_23739/09_2026/7mbn_23739.map" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15700 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 58 5.16 5 C 11869 2.51 5 N 3645 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 4.33, per 1000 atoms: 0.21 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: 1.60 Conformation dependent library (CDL) restraints added in 580.1 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: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'C' and resid 3815 through 3830 removed outlier: 5.143A pdb=" N LYS C3828 " --> pdb=" O LYS C3824 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLU C3829 " --> pdb=" O LYS C3825 " (cutoff:3.500A) Processing helix chain 'C' and resid 3867 through 3879 Processing helix chain 'C' and resid 3901 through 3905 removed outlier: 3.522A pdb=" N ILE C3905 " --> pdb=" O ALA C3902 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.804A pdb=" N ARG D 294 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 406 Processing helix chain 'D' and resid 499 through 524 removed outlier: 3.572A pdb=" N MET D 503 " --> pdb=" O PRO D 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.664A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.586A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.891A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.923A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.523A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 101 through 120 removed outlier: 3.536A pdb=" N LYS J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.665A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.585A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.892A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.924A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.524A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 88 removed outlier: 3.661A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 98 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.935A pdb=" N THR A 29 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 48 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 50 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 3.779A pdb=" N SER A 71 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 90 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN A 92 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 116 removed outlier: 6.543A pdb=" N CYS A 126 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 113 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 124 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR A 115 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS A 122 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 159 removed outlier: 4.504A pdb=" N LYS A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS A 179 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 185 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.145A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 303 removed outlier: 6.527A pdb=" N ILE A 313 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 301 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA A 311 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA9, first strand: chain 'B' and resid 36 through 42 removed outlier: 5.424A pdb=" N LEU B 37 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS B 331 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 39 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 326 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.542A pdb=" N SER B 64 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLY B 73 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 79 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 90 through 95 removed outlier: 6.945A pdb=" N ASP B 115 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 121 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.438A pdb=" N VAL B 153 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 166 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 155 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.909A pdb=" N CYS B 195 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B 199 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N CYS B 205 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 217 through 222 removed outlier: 3.563A pdb=" N PHE B 219 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 238 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 251 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 240 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.850A pdb=" N VAL B 283 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 296 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 285 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3831 through 3835 Processing sheet with id=AB8, first strand: chain 'C' and resid 3854 through 3857 removed outlier: 7.066A pdb=" N MET C3854 " --> pdb=" O ALA C3930 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C3930 " --> pdb=" O MET C3854 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3906 through 3907 removed outlier: 6.905A pdb=" N ASN C3906 " --> pdb=" O TYR C3942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 298 through 301 Processing sheet with id=AC2, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.930A pdb=" N THR D 372 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 454 through 460 removed outlier: 5.952A pdb=" N PHE D 449 " --> pdb=" O GLN D 456 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL D 458 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE D 447 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR D 479 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 416 through 420 Processing sheet with id=AC5, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.398A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 42 through 43 removed outlier: 6.975A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.403A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.117A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 77 through 78 662 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 389 hydrogen bonds 762 hydrogen bond angles 0 basepair planarities 152 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 1.98 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: 29641 2.63 - 5.25: 316 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.940 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.660 ------------------------------------------------------------------------------- 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 : 0.778 13.134 29971 Z= 0.614 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 0.77832 / 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 : 0.652 Fit side-chains 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: 0.4067 (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: 0.6573 (t) REVERT: B 46 LYS cc_start: 0.2882 (mttt) cc_final: 0.2228 (mmmt) REVERT: B 204 GLN cc_start: 0.4730 (tt0) cc_final: 0.4294 (mt0) REVERT: B 214 ASN cc_start: 0.1776 (t0) cc_final: 0.0699 (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: -0.0828 (m) REVERT: D 360 ASP cc_start: -0.0317 (p0) cc_final: -0.1612 (t0) REVERT: D 368 SER cc_start: 0.0021 (m) cc_final: -0.0285 (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: 0.6936 (mt) REVERT: I 18 SER cc_start: 0.8188 (t) cc_final: 0.7960 (t) REVERT: I 51 LEU cc_start: 0.8587 (pp) cc_final: 0.8211 (tt) REVERT: I 74 LYS cc_start: 0.7855 (mttt) cc_final: 0.7286 (pttp) REVERT: J 29 THR cc_start: 0.5995 (m) cc_final: 0.5742 (t) REVERT: J 76 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7323 (mtm-85) REVERT: K 39 HIS cc_start: 0.5993 (t-90) cc_final: 0.5488 (t-170) REVERT: M 104 GLN cc_start: 0.6594 (mm-40) cc_final: 0.5903 (mm-40) REVERT: N 65 ASP cc_start: 0.7956 (t0) cc_final: 0.7430 (t0) outliers start: 23 outliers final: 1 residues processed: 508 average time/residue: 0.1864 time to fit residues: 134.8669 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 : 0.589 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 G 93 GLN I 89 ASN J 79 HIS K 39 HIS K 68 GLN N 46 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.141324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.114890 restraints weight = 65015.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.113233 restraints weight = 119773.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.113928 restraints weight = 100033.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.114005 restraints weight = 67086.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.114222 restraints weight = 65421.288| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 21228 Z= 0.278 Angle : 0.956 15.731 29971 Z= 0.504 Chirality : 0.058 0.406 3372 Planarity : 0.008 0.107 2787 Dihedral : 29.649 179.761 5164 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 0.33 % Allowed : 6.67 % Favored : 93.00 % 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: -1.65 (0.18), residues: 1778 helix: 0.20 (0.20), residues: 601 sheet: -1.54 (0.26), residues: 359 loop : -1.84 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 498 TYR 0.029 0.003 TYR D 364 PHE 0.040 0.003 PHE D 374 TRP 0.034 0.003 TRP D 505 HIS 0.017 0.003 HIS C3925 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.28 (21228) covalent geometry : angle 0.95575 / 0.50 (29971) hydrogen bonds : bond 0.09522 / 6.25 ( 1051) hydrogen bonds : angle 5.07008 / 3.51 ( 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 : 0.607 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: 0.6386 (tp) cc_final: 0.5788 (tt) REVERT: A 93 TRP cc_start: 0.1135 (m100) cc_final: 0.0735 (m100) REVERT: A 209 LYS cc_start: 0.6314 (ptmm) cc_final: 0.6077 (mmtt) REVERT: B 46 LYS cc_start: 0.2960 (mttt) cc_final: 0.1947 (mmmt) REVERT: B 156 TRP cc_start: 0.4285 (m100) cc_final: 0.3884 (m100) REVERT: C 3896 THR cc_start: 0.3690 (m) cc_final: 0.3414 (m) REVERT: C 3931 MET cc_start: 0.4276 (mtp) cc_final: 0.3130 (tpt) REVERT: C 3965 ARG cc_start: 0.4710 (mtm110) cc_final: 0.3495 (ptp90) REVERT: D 340 THR cc_start: -0.0500 (m) cc_final: -0.0914 (m) REVERT: D 394 PHE cc_start: 0.3875 (m-80) cc_final: 0.3450 (m-80) REVERT: D 493 LYS cc_start: 0.1060 (mmmt) cc_final: 0.0729 (mptt) REVERT: G 82 LEU cc_start: 0.7192 (mp) cc_final: 0.6989 (mp) REVERT: H 63 GLU cc_start: 0.7636 (tt0) cc_final: 0.7416 (tt0) REVERT: I 51 LEU cc_start: 0.8876 (pp) cc_final: 0.8588 (tt) REVERT: I 62 ILE cc_start: 0.8496 (pt) cc_final: 0.8154 (mt) REVERT: I 74 LYS cc_start: 0.8312 (mttt) cc_final: 0.7588 (pptt) REVERT: J 52 SER cc_start: 0.8621 (p) cc_final: 0.8382 (p) REVERT: J 73 GLU cc_start: 0.7622 (tp30) cc_final: 0.7261 (tp30) REVERT: J 76 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7175 (mtm110) outliers start: 5 outliers final: 2 residues processed: 278 average time/residue: 0.1793 time to fit residues: 72.2798 Evaluate side-chains 186 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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: 0.0570 chunk 63 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 overall best weight: 0.8502 ------------------------------------------------------------------------------- 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** G 68 GLN G 93 GLN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 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 = 0.4283 r_free = 0.4283 target = 0.140832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.113621 restraints weight = 65027.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.112702 restraints weight = 106196.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.113399 restraints weight = 92872.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.112973 restraints weight = 67809.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113295 restraints weight = 62792.676| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (17 function evaluations) r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21228 Z= 0.161 Angle : 0.700 8.650 29971 Z= 0.386 Chirality : 0.048 0.370 3372 Planarity : 0.005 0.054 2787 Dihedral : 29.196 177.429 5164 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1778 helix: 1.30 (0.20), residues: 603 sheet: -1.31 (0.26), residues: 368 loop : -1.71 (0.20), residues: 807 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 0.023 0.002 PHE D 329 TRP 0.040 0.002 TRP B 330 HIS 0.012 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (21228) covalent geometry : angle 0.70048 / 0.39 (29971) hydrogen bonds : bond 0.07435 / 4.90 ( 1051) hydrogen bonds : angle 4.37006 / 3.04 ( 2670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3869 (t) cc_final: 0.3601 (t) REVERT: A 95 VAL cc_start: 0.4925 (m) cc_final: 0.4507 (t) REVERT: A 209 LYS cc_start: 0.6376 (ptmm) cc_final: 0.6084 (mmtt) REVERT: B 46 LYS cc_start: 0.2823 (mttt) cc_final: 0.1843 (mmmt) REVERT: B 156 TRP cc_start: 0.4349 (m100) cc_final: 0.3894 (m100) REVERT: B 221 LYS cc_start: 0.5648 (pttt) cc_final: 0.4638 (mttt) REVERT: C 3838 ILE cc_start: 0.2355 (mt) cc_final: 0.1989 (mt) REVERT: C 3931 MET cc_start: 0.4312 (mtp) cc_final: 0.3363 (tpt) REVERT: C 3965 ARG cc_start: 0.4798 (mtm110) cc_final: 0.3468 (ptt-90) REVERT: D 461 LYS cc_start: 0.1571 (tptt) cc_final: 0.1362 (tppt) REVERT: H 63 GLU cc_start: 0.7647 (tt0) cc_final: 0.7356 (tt0) REVERT: I 17 ARG cc_start: 0.8189 (mpp80) cc_final: 0.7989 (mtt180) REVERT: I 51 LEU cc_start: 0.9067 (pp) cc_final: 0.8828 (tt) REVERT: I 62 ILE cc_start: 0.8537 (pt) cc_final: 0.8313 (mt) REVERT: I 74 LYS cc_start: 0.8357 (mttt) cc_final: 0.7686 (pptt) REVERT: J 76 ARG cc_start: 0.7523 (ttm110) cc_final: 0.6980 (mtm180) REVERT: N 48 ASP cc_start: 0.5634 (p0) cc_final: 0.5432 (p0) REVERT: N 73 GLU cc_start: 0.7001 (tp30) cc_final: 0.6685 (tp30) REVERT: N 90 GLU cc_start: 0.6787 (mp0) cc_final: 0.6479 (mp0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1665 time to fit residues: 59.3530 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 : 0.607 ------------------------------------------------------------------------------- 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: 8.9990 chunk 160 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN G 108 ASN H 93 GLN J 92 GLN K 68 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.136304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.107931 restraints weight = 64306.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106828 restraints weight = 103924.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107581 restraints weight = 86493.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.107220 restraints weight = 61596.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.107503 restraints weight = 58973.613| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 21228 Z= 0.206 Angle : 0.753 14.974 29971 Z= 0.411 Chirality : 0.051 0.382 3372 Planarity : 0.006 0.077 2787 Dihedral : 29.014 179.186 5164 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % 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: -0.92 (0.19), residues: 1778 helix: 1.17 (0.21), residues: 603 sheet: -1.26 (0.25), residues: 379 loop : -1.67 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG M 20 TYR 0.050 0.003 TYR J 80 PHE 0.018 0.002 PHE D 484 TRP 0.024 0.002 TRP B 330 HIS 0.015 0.002 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (21228) covalent geometry : angle 0.75276 / 0.41 (29971) hydrogen bonds : bond 0.08179 / 5.32 ( 1051) hydrogen bonds : angle 4.41009 / 3.05 ( 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 235 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6379 (tp) cc_final: 0.6055 (tt) REVERT: B 46 LYS cc_start: 0.2767 (mttt) cc_final: 0.1751 (mmmt) REVERT: B 156 TRP cc_start: 0.4386 (m100) cc_final: 0.3893 (m100) REVERT: C 3931 MET cc_start: 0.4372 (mtp) cc_final: 0.3273 (tpt) REVERT: D 461 LYS cc_start: 0.1752 (tptt) cc_final: 0.1503 (tppt) REVERT: H 63 GLU cc_start: 0.7626 (tt0) cc_final: 0.7386 (tt0) REVERT: I 51 LEU cc_start: 0.9108 (pp) cc_final: 0.8842 (tt) REVERT: I 62 ILE cc_start: 0.8712 (pt) cc_final: 0.8234 (mt) REVERT: I 74 LYS cc_start: 0.8487 (mttt) cc_final: 0.7812 (pptt) REVERT: J 32 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7454 (pt0) REVERT: J 76 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7242 (ttm110) REVERT: K 110 CYS cc_start: 0.6564 (m) cc_final: 0.6309 (m) REVERT: M 90 ASP cc_start: 0.7892 (t0) cc_final: 0.7638 (t0) REVERT: N 73 GLU cc_start: 0.7137 (tp30) cc_final: 0.6748 (tp30) REVERT: N 87 THR cc_start: 0.8809 (p) cc_final: 0.8560 (p) outliers start: 2 outliers final: 1 residues processed: 234 average time/residue: 0.1619 time to fit residues: 56.2706 Evaluate side-chains 169 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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: 0.0470 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 I 24 GLN K 93 GLN M 24 GLN ** 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 = 0.4224 r_free = 0.4224 target = 0.136598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.108661 restraints weight = 63911.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107676 restraints weight = 91812.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.107820 restraints weight = 79248.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107652 restraints weight = 55512.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.107861 restraints weight = 52377.860| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21228 Z= 0.146 Angle : 0.663 8.804 29971 Z= 0.368 Chirality : 0.047 0.382 3372 Planarity : 0.005 0.062 2787 Dihedral : 28.815 179.472 5164 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % 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: -0.63 (0.19), residues: 1778 helix: 1.59 (0.21), residues: 601 sheet: -1.21 (0.26), residues: 377 loop : -1.59 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C3965 TYR 0.031 0.002 TYR N 37 PHE 0.014 0.002 PHE B 266 TRP 0.061 0.002 TRP B 330 HIS 0.011 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (21228) covalent geometry : angle 0.66294 / 0.37 (29971) hydrogen bonds : bond 0.07110 / 4.64 ( 1051) hydrogen bonds : angle 4.14268 / 2.88 ( 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 226 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6336 (tp) cc_final: 0.5712 (pp) REVERT: A 43 CYS cc_start: 0.3957 (t) cc_final: 0.3749 (t) REVERT: B 46 LYS cc_start: 0.2748 (mttt) cc_final: 0.1570 (mmmt) REVERT: B 111 LEU cc_start: 0.2780 (mp) cc_final: 0.2537 (mp) REVERT: B 156 TRP cc_start: 0.4353 (m100) cc_final: 0.3881 (m100) REVERT: C 3931 MET cc_start: 0.4411 (mtp) cc_final: 0.3568 (tpt) REVERT: C 3965 ARG cc_start: 0.4452 (mtm110) cc_final: 0.3381 (ptt-90) REVERT: D 315 MET cc_start: 0.1536 (ttp) cc_final: 0.1189 (ttt) REVERT: D 336 MET cc_start: 0.1119 (mmp) cc_final: -0.1394 (ppp) REVERT: D 461 LYS cc_start: 0.1780 (tptt) cc_final: 0.1428 (tppt) REVERT: H 63 GLU cc_start: 0.7698 (tt0) cc_final: 0.7421 (tt0) REVERT: H 84 MET cc_start: 0.7858 (tpt) cc_final: 0.7489 (tpt) REVERT: I 62 ILE cc_start: 0.8619 (pt) cc_final: 0.8205 (mt) REVERT: I 74 LYS cc_start: 0.8486 (mttt) cc_final: 0.7653 (pptt) REVERT: J 32 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7226 (pt0) REVERT: J 76 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7466 (ttm110) REVERT: M 90 ASP cc_start: 0.7858 (t0) cc_final: 0.7634 (t0) REVERT: N 51 ILE cc_start: 0.8289 (pt) cc_final: 0.7953 (pt) REVERT: N 73 GLU cc_start: 0.7123 (tp30) cc_final: 0.6823 (tp30) REVERT: N 87 THR cc_start: 0.8742 (p) cc_final: 0.8326 (p) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.1597 time to fit residues: 54.4178 Evaluate side-chains 169 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 0.3980 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 204 GLN ** D 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN H 93 GLN J 81 ASN K 39 HIS ** 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 = 0.4166 r_free = 0.4166 target = 0.132658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.104016 restraints weight = 63220.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103104 restraints weight = 106059.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.103538 restraints weight = 92571.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.102993 restraints weight = 68526.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103323 restraints weight = 62226.375| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 21228 Z= 0.209 Angle : 0.734 8.914 29971 Z= 0.401 Chirality : 0.050 0.370 3372 Planarity : 0.006 0.083 2787 Dihedral : 28.700 179.750 5164 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.26 % Allowed : 3.34 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 1778 helix: 1.39 (0.21), residues: 600 sheet: -1.31 (0.26), residues: 362 loop : -1.61 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 83 TYR 0.051 0.003 TYR D 364 PHE 0.025 0.002 PHE K 67 TRP 0.026 0.002 TRP D 505 HIS 0.023 0.003 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (21228) covalent geometry : angle 0.73412 / 0.40 (29971) hydrogen bonds : bond 0.08082 / 5.19 ( 1051) hydrogen bonds : angle 4.22819 / 2.94 ( 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 216 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 212 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3977 (t) cc_final: 0.3742 (t) REVERT: A 290 LEU cc_start: 0.6845 (mt) cc_final: 0.4456 (mt) REVERT: A 321 TRP cc_start: 0.5872 (m100) cc_final: 0.4265 (t-100) REVERT: B 46 LYS cc_start: 0.2527 (mttt) cc_final: 0.1586 (mmtt) REVERT: B 126 LYS cc_start: 0.4164 (mmmm) cc_final: 0.3611 (tttt) REVERT: B 156 TRP cc_start: 0.4482 (m100) cc_final: 0.3924 (m100) REVERT: B 316 ILE cc_start: 0.5250 (pt) cc_final: 0.5022 (pt) REVERT: B 330 TRP cc_start: 0.1795 (m100) cc_final: 0.1409 (m100) REVERT: C 3931 MET cc_start: 0.4476 (mtp) cc_final: 0.3580 (tpt) REVERT: C 3965 ARG cc_start: 0.4549 (mtm110) cc_final: 0.3386 (ptt-90) REVERT: D 315 MET cc_start: 0.1678 (ttp) cc_final: 0.1340 (ttt) REVERT: D 461 LYS cc_start: 0.1889 (tptt) cc_final: 0.1531 (tppt) REVERT: H 63 GLU cc_start: 0.7583 (tt0) cc_final: 0.7369 (tt0) REVERT: I 62 ILE cc_start: 0.8779 (pt) cc_final: 0.8217 (mt) REVERT: I 74 LYS cc_start: 0.8510 (mttt) cc_final: 0.7588 (pptt) REVERT: J 76 ARG cc_start: 0.7738 (ttm110) cc_final: 0.7181 (ttm110) REVERT: N 73 GLU cc_start: 0.7166 (tp30) cc_final: 0.6879 (tp30) outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.1504 time to fit residues: 49.7868 Evaluate side-chains 171 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 55 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN G 68 GLN G 76 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN K 39 HIS K 68 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.130971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102529 restraints weight = 63479.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101508 restraints weight = 112328.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101931 restraints weight = 97443.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101584 restraints weight = 69408.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101899 restraints weight = 62328.177| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.7046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21228 Z= 0.205 Angle : 0.713 12.100 29971 Z= 0.393 Chirality : 0.049 0.358 3372 Planarity : 0.005 0.059 2787 Dihedral : 28.557 177.583 5164 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1778 helix: 1.41 (0.21), residues: 606 sheet: -1.18 (0.27), residues: 333 loop : -1.69 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 20 TYR 0.029 0.002 TYR D 450 PHE 0.027 0.002 PHE D 449 TRP 0.026 0.002 TRP D 505 HIS 0.008 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (21228) covalent geometry : angle 0.71329 / 0.39 (29971) hydrogen bonds : bond 0.07749 / 4.95 ( 1051) hydrogen bonds : angle 4.22619 / 2.94 ( 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 230 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3898 (t) cc_final: 0.3691 (t) REVERT: B 46 LYS cc_start: 0.2558 (mttt) cc_final: 0.1515 (mmtm) REVERT: B 126 LYS cc_start: 0.4314 (mmmm) cc_final: 0.3771 (mttt) REVERT: B 156 TRP cc_start: 0.4428 (m100) cc_final: 0.4002 (m100) REVERT: B 316 ILE cc_start: 0.5221 (pt) cc_final: 0.4758 (pt) REVERT: B 330 TRP cc_start: 0.1890 (m100) cc_final: 0.1530 (m100) REVERT: C 3931 MET cc_start: 0.4450 (mtp) cc_final: 0.3558 (tpt) REVERT: C 3965 ARG cc_start: 0.4463 (mtm110) cc_final: 0.3196 (ptt-90) REVERT: D 315 MET cc_start: 0.1807 (ttp) cc_final: 0.1433 (ttt) REVERT: D 334 ASP cc_start: 0.3292 (m-30) cc_final: 0.2677 (t70) REVERT: D 373 LYS cc_start: 0.4122 (mmmt) cc_final: 0.3604 (ptmt) REVERT: D 461 LYS cc_start: 0.2049 (tptt) cc_final: 0.1671 (tppt) REVERT: H 63 GLU cc_start: 0.7684 (tt0) cc_final: 0.7419 (tt0) REVERT: I 62 ILE cc_start: 0.8834 (pt) cc_final: 0.8234 (mt) REVERT: I 74 LYS cc_start: 0.8587 (mttt) cc_final: 0.7617 (pptt) REVERT: I 101 THR cc_start: 0.8871 (t) cc_final: 0.8663 (m) REVERT: J 76 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7565 (ttp-110) REVERT: N 73 GLU cc_start: 0.7253 (tp30) cc_final: 0.6922 (tp30) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1641 time to fit residues: 56.9319 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 : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 90 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 23 optimal weight: 0.0020 chunk 121 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- 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** D 320 HIS D 483 ASN G 39 HIS G 76 GLN H 93 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 HIS K 39 HIS K 68 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.131157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.102231 restraints weight = 63714.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.100984 restraints weight = 117301.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101993 restraints weight = 99647.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101446 restraints weight = 70348.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101952 restraints weight = 64435.436| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21228 Z= 0.159 Angle : 0.671 13.367 29971 Z= 0.370 Chirality : 0.047 0.366 3372 Planarity : 0.005 0.075 2787 Dihedral : 28.347 177.408 5164 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.07 % Allowed : 0.72 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1778 helix: 1.66 (0.21), residues: 606 sheet: -1.29 (0.26), residues: 363 loop : -1.62 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 83 TYR 0.037 0.002 TYR D 450 PHE 0.024 0.002 PHE D 394 TRP 0.023 0.002 TRP B 330 HIS 0.011 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (21228) covalent geometry : angle 0.67140 / 0.37 (29971) hydrogen bonds : bond 0.07478 / 4.78 ( 1051) hydrogen bonds : angle 4.10924 / 2.86 ( 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 215 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3908 (t) cc_final: 0.3643 (t) REVERT: B 46 LYS cc_start: 0.2405 (mttt) cc_final: 0.1533 (mmtm) REVERT: B 69 ILE cc_start: 0.4214 (tp) cc_final: 0.3807 (mp) REVERT: B 156 TRP cc_start: 0.4526 (m100) cc_final: 0.3844 (m100) REVERT: B 178 HIS cc_start: 0.5367 (t-170) cc_final: 0.5134 (t70) REVERT: B 316 ILE cc_start: 0.5284 (pt) cc_final: 0.4896 (pt) REVERT: B 330 TRP cc_start: 0.1706 (m100) cc_final: 0.1474 (m100) REVERT: C 3931 MET cc_start: 0.4302 (mtp) cc_final: 0.3487 (tpt) REVERT: C 3965 ARG cc_start: 0.4618 (mtm110) cc_final: 0.3328 (ptt-90) REVERT: D 315 MET cc_start: 0.1889 (ttp) cc_final: 0.1478 (ttt) REVERT: D 334 ASP cc_start: 0.3220 (m-30) cc_final: 0.2630 (t70) REVERT: D 373 LYS cc_start: 0.4395 (mmmt) cc_final: 0.4089 (mmmt) REVERT: D 460 TYR cc_start: -0.0169 (m-80) cc_final: -0.0631 (m-80) REVERT: D 500 MET cc_start: 0.5360 (tmm) cc_final: 0.4964 (mmt) REVERT: G 129 ARG cc_start: 0.7298 (tpt90) cc_final: 0.6982 (tpt90) REVERT: H 63 GLU cc_start: 0.7597 (tt0) cc_final: 0.7395 (tt0) REVERT: I 62 ILE cc_start: 0.8822 (pt) cc_final: 0.8270 (mt) REVERT: I 74 LYS cc_start: 0.8645 (mttt) cc_final: 0.7699 (pptt) REVERT: J 76 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7334 (ttp-110) REVERT: K 42 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7489 (mmm-85) REVERT: N 73 GLU cc_start: 0.7295 (tp30) cc_final: 0.6926 (tp30) outliers start: 1 outliers final: 1 residues processed: 214 average time/residue: 0.1606 time to fit residues: 52.4140 Evaluate side-chains 175 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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: 9.9990 chunk 93 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- 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** B 204 GLN B 214 ASN ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** C3907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN K 113 HIS L 75 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.124365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100500 restraints weight = 64468.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101108 restraints weight = 103769.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.099448 restraints weight = 81900.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099050 restraints weight = 83191.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.099001 restraints weight = 66045.379| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.8654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.115 21228 Z= 0.500 Angle : 1.131 15.027 29971 Z= 0.585 Chirality : 0.068 0.390 3372 Planarity : 0.010 0.106 2787 Dihedral : 28.854 169.180 5164 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 0.07 % Allowed : 1.57 % Favored : 98.36 % 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: -2.02 (0.18), residues: 1778 helix: -0.05 (0.19), residues: 612 sheet: -1.45 (0.26), residues: 334 loop : -2.30 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG M 17 TYR 0.066 0.005 TYR I 50 PHE 0.044 0.005 PHE I 25 TRP 0.042 0.005 TRP D 505 HIS 0.021 0.003 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.01128 / 0.50 (21228) covalent geometry : angle 1.13054 / 0.58 (29971) hydrogen bonds : bond 0.12266 / 7.89 ( 1051) hydrogen bonds : angle 5.33934 / 3.68 ( 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 189 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 43 CYS cc_start: 0.3779 (t) cc_final: 0.3512 (t) REVERT: B 46 LYS cc_start: 0.2407 (mttt) cc_final: 0.1327 (mmtm) REVERT: B 69 ILE cc_start: 0.3858 (tp) cc_final: 0.3408 (mp) REVERT: B 156 TRP cc_start: 0.4413 (m100) cc_final: 0.3673 (m100) REVERT: B 330 TRP cc_start: 0.2174 (m100) cc_final: 0.1937 (m100) REVERT: C 3931 MET cc_start: 0.3938 (mtp) cc_final: 0.3278 (tpt) REVERT: D 334 ASP cc_start: 0.4030 (m-30) cc_final: 0.3053 (t70) REVERT: D 449 PHE cc_start: 0.1103 (m-80) cc_final: 0.0867 (m-80) REVERT: D 460 TYR cc_start: -0.0888 (m-80) cc_final: -0.1106 (m-80) REVERT: H 63 GLU cc_start: 0.7894 (tt0) cc_final: 0.7666 (tt0) REVERT: I 74 LYS cc_start: 0.8707 (mttt) cc_final: 0.8237 (pptt) REVERT: J 76 ARG cc_start: 0.7771 (ttm110) cc_final: 0.6867 (ttm110) REVERT: K 42 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7275 (mmm-85) REVERT: L 25 ASN cc_start: 0.7993 (m-40) cc_final: 0.7626 (m-40) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1382 time to fit residues: 40.8456 Evaluate side-chains 158 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 0.9990 chunk 73 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B 257 ASN ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.127790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100416 restraints weight = 64146.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099754 restraints weight = 113236.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100175 restraints weight = 101766.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099783 restraints weight = 75147.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100013 restraints weight = 69683.112| |-----------------------------------------------------------------------------| 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: 3 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.8648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 21228 Z= 0.171 Angle : 0.744 12.031 29971 Z= 0.405 Chirality : 0.050 0.304 3372 Planarity : 0.006 0.082 2787 Dihedral : 28.211 172.880 5164 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.13 % Allowed : 0.07 % Favored : 99.80 % 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: -1.25 (0.19), residues: 1778 helix: 1.05 (0.21), residues: 609 sheet: -1.49 (0.26), residues: 332 loop : -2.00 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 83 TYR 0.029 0.002 TYR N 37 PHE 0.052 0.002 PHE D 469 TRP 0.038 0.003 TRP D 366 HIS 0.010 0.002 HIS C3925 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (21228) covalent geometry : angle 0.74352 / 0.41 (29971) hydrogen bonds : bond 0.08168 / 5.19 ( 1051) hydrogen bonds : angle 4.52444 / 3.12 ( 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 205 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 53 PHE cc_start: 0.5620 (t80) cc_final: 0.5242 (t80) REVERT: B 46 LYS cc_start: 0.2525 (mttt) cc_final: 0.1469 (mmtm) REVERT: B 69 ILE cc_start: 0.3895 (tp) cc_final: 0.3445 (mp) REVERT: B 154 ARG cc_start: 0.4746 (mpt90) cc_final: 0.4304 (mmt180) REVERT: B 156 TRP cc_start: 0.4279 (m100) cc_final: 0.3424 (m100) REVERT: B 316 ILE cc_start: 0.4928 (pt) cc_final: 0.4627 (pt) REVERT: C 3931 MET cc_start: 0.4183 (mtp) cc_final: 0.3510 (tpt) REVERT: D 334 ASP cc_start: 0.3112 (m-30) cc_final: 0.2629 (t70) REVERT: D 336 MET cc_start: 0.1674 (mmp) cc_final: -0.1200 (mtm) REVERT: D 500 MET cc_start: 0.5356 (tmm) cc_final: 0.4909 (mmt) REVERT: H 52 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6275 (mp0) REVERT: H 63 GLU cc_start: 0.7813 (tt0) cc_final: 0.7501 (tt0) REVERT: I 62 ILE cc_start: 0.8676 (pt) cc_final: 0.8341 (mt) REVERT: J 30 ARG cc_start: 0.5887 (ttm-80) cc_final: 0.5473 (ttm-80) REVERT: J 76 ARG cc_start: 0.7553 (ttm110) cc_final: 0.6917 (ttm170) REVERT: J 80 TYR cc_start: 0.7836 (m-10) cc_final: 0.7618 (m-80) REVERT: K 42 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7292 (mmm-85) REVERT: N 73 GLU cc_start: 0.7079 (tp30) cc_final: 0.6769 (tp30) outliers start: 2 outliers final: 2 residues processed: 204 average time/residue: 0.1599 time to fit residues: 49.0259 Evaluate side-chains 174 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 0.9990 chunk 112 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 21 optimal weight: 0.0020 chunk 12 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 13 optimal weight: 0.0970 chunk 73 optimal weight: 5.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.128320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099405 restraints weight = 63944.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098470 restraints weight = 101025.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.099023 restraints weight = 90105.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098846 restraints weight = 61664.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099233 restraints weight = 56777.220| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.8647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21228 Z= 0.147 Angle : 0.683 11.610 29971 Z= 0.376 Chirality : 0.047 0.361 3372 Planarity : 0.005 0.076 2787 Dihedral : 27.839 173.150 5164 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.78 (0.19), residues: 1778 helix: 1.60 (0.21), residues: 612 sheet: -1.40 (0.26), residues: 348 loop : -1.79 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C3965 TYR 0.026 0.002 TYR N 37 PHE 0.030 0.002 PHE B 149 TRP 0.033 0.002 TRP B 198 HIS 0.019 0.002 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (21228) covalent geometry : angle 0.68281 / 0.38 (29971) hydrogen bonds : bond 0.07546 / 4.83 ( 1051) hydrogen bonds : angle 4.19730 / 2.91 ( 2670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.76 seconds wall clock time: 58 minutes 7.27 seconds (3487.27 seconds total)