Starting phenix.real_space_refine on Wed Feb 4 05:50:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o40_70088/02_2026/9o40_70088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o40_70088/02_2026/9o40_70088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o40_70088/02_2026/9o40_70088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o40_70088/02_2026/9o40_70088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o40_70088/02_2026/9o40_70088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o40_70088/02_2026/9o40_70088.map" } resolution = 2.92 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= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 5815 2.51 5 N 1535 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8967 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1721 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1721 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1721 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1721 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1721 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 181 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 181 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 2.37, per 1000 atoms: 0.26 Number of scatterers: 8967 At special positions: 0 Unit cell: (89.1, 92.4, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1580 8.00 N 1535 7.00 C 5815 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 382.9 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 90.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 14 through 59 removed outlier: 3.795A pdb=" N LEU A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 78 through 97 removed outlier: 3.678A pdb=" N ILE A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 124 removed outlier: 3.518A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 157 removed outlier: 3.888A pdb=" N GLY A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 167 through 222 removed outlier: 4.084A pdb=" N ILE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Proline residue: A 187 - end of helix removed outlier: 4.182A pdb=" N MET A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 222 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 57 removed outlier: 3.865A pdb=" N MET B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.892A pdb=" N LYS B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 removed outlier: 4.126A pdb=" N ALA B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.565A pdb=" N ARG B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 159 removed outlier: 4.309A pdb=" N LEU B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Proline residue: B 138 - end of helix removed outlier: 3.830A pdb=" N ALA B 158 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.968A pdb=" N VAL B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 175 through 222 Proline residue: B 187 - end of helix removed outlier: 3.551A pdb=" N TYR B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 14 through 59 removed outlier: 3.566A pdb=" N LYS C 18 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.537A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 95 removed outlier: 3.506A pdb=" N ILE C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 95 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 124 removed outlier: 3.608A pdb=" N VAL C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 159 removed outlier: 3.785A pdb=" N GLY C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 3.933A pdb=" N VAL C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 222 removed outlier: 3.641A pdb=" N VAL C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.628A pdb=" N LEU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Proline residue: C 187 - end of helix removed outlier: 3.907A pdb=" N ASN C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 222 " --> pdb=" O HIS C 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 12 Processing helix chain 'D' and resid 14 through 58 removed outlier: 3.745A pdb=" N LEU D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 41 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.793A pdb=" N GLY D 71 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 97 removed outlier: 3.729A pdb=" N ILE D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 123 removed outlier: 4.286A pdb=" N VAL D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 159 removed outlier: 3.995A pdb=" N LEU D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 3.623A pdb=" N ALA D 158 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 175 through 222 removed outlier: 4.274A pdb=" N ALA D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Proline residue: D 187 - end of helix removed outlier: 3.524A pdb=" N GLN D 197 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE D 222 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 14 through 58 removed outlier: 4.033A pdb=" N ARG E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE E 41 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 70 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 78 through 97 removed outlier: 3.534A pdb=" N GLY E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 95 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 96 " --> pdb=" O ARG E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 124 removed outlier: 3.577A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 137 removed outlier: 4.144A pdb=" N LEU E 130 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 159 removed outlier: 3.656A pdb=" N GLY E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 143 " --> pdb=" O TYR E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 166 removed outlier: 3.934A pdb=" N MET E 166 " --> pdb=" O THR E 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 163 through 166' Processing helix chain 'E' and resid 167 through 223 removed outlier: 3.736A pdb=" N LEU E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Proline residue: E 187 - end of helix removed outlier: 3.849A pdb=" N ASN E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 201 " --> pdb=" O GLN E 197 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE E 222 " --> pdb=" O HIS E 218 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 36 removed outlier: 4.265A pdb=" N LEU F 22 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 36 711 hydrogen bonds defined for protein. 2133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2917 1.34 - 1.46: 1381 1.46 - 1.57: 4769 1.57 - 1.69: 0 1.69 - 1.80: 74 Bond restraints: 9141 Sorted by residual: bond pdb=" CA SER D 137 " pdb=" C SER D 137 " ideal model delta sigma weight residual 1.521 1.535 -0.014 1.17e-02 7.31e+03 1.40e+00 bond pdb=" CA SER C 137 " pdb=" C SER C 137 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.29e+00 bond pdb=" C GLN C 37 " pdb=" O GLN C 37 " ideal model delta sigma weight residual 1.237 1.250 -0.013 1.19e-02 7.06e+03 1.23e+00 bond pdb=" CA SER B 137 " pdb=" C SER B 137 " ideal model delta sigma weight residual 1.520 1.533 -0.012 1.23e-02 6.61e+03 9.85e-01 bond pdb=" C ILE C 186 " pdb=" O ILE C 186 " ideal model delta sigma weight residual 1.240 1.252 -0.012 1.26e-02 6.30e+03 9.70e-01 ... (remaining 9136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 12038 1.21 - 2.42: 265 2.42 - 3.63: 33 3.63 - 4.84: 30 4.84 - 6.04: 3 Bond angle restraints: 12369 Sorted by residual: angle pdb=" N THR C 125 " pdb=" CA THR C 125 " pdb=" C THR C 125 " ideal model delta sigma weight residual 111.03 115.64 -4.61 1.11e+00 8.12e-01 1.72e+01 angle pdb=" N VAL E 167 " pdb=" CA VAL E 167 " pdb=" C VAL E 167 " ideal model delta sigma weight residual 113.42 108.97 4.45 1.17e+00 7.31e-01 1.44e+01 angle pdb=" C ILE A 186 " pdb=" CA ILE A 186 " pdb=" CB ILE A 186 " ideal model delta sigma weight residual 114.00 110.18 3.82 1.31e+00 5.83e-01 8.49e+00 angle pdb=" N GLU A 119 " pdb=" CA GLU A 119 " pdb=" CB GLU A 119 " ideal model delta sigma weight residual 110.16 114.43 -4.27 1.48e+00 4.57e-01 8.32e+00 angle pdb=" N ILE C 186 " pdb=" CA ILE C 186 " pdb=" C ILE C 186 " ideal model delta sigma weight residual 108.88 114.92 -6.04 2.16e+00 2.14e-01 7.83e+00 ... (remaining 12364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 5018 17.69 - 35.38: 338 35.38 - 53.08: 52 53.08 - 70.77: 22 70.77 - 88.46: 18 Dihedral angle restraints: 5448 sinusoidal: 2141 harmonic: 3307 Sorted by residual: dihedral pdb=" CA ILE E 136 " pdb=" C ILE E 136 " pdb=" N SER E 137 " pdb=" CA SER E 137 " ideal model delta harmonic sigma weight residual 180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU B 53 " pdb=" CG GLU B 53 " pdb=" CD GLU B 53 " pdb=" OE1 GLU B 53 " ideal model delta sinusoidal sigma weight residual 0.00 87.09 -87.09 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 211 " pdb=" CG GLU A 211 " pdb=" CD GLU A 211 " pdb=" OE1 GLU A 211 " ideal model delta sinusoidal sigma weight residual 0.00 86.38 -86.38 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 5445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1007 0.033 - 0.065: 300 0.065 - 0.098: 86 0.098 - 0.130: 36 0.130 - 0.163: 2 Chirality restraints: 1431 Sorted by residual: chirality pdb=" CA ILE D 60 " pdb=" N ILE D 60 " pdb=" C ILE D 60 " pdb=" CB ILE D 60 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CB ILE F 18 " pdb=" CA ILE F 18 " pdb=" CG1 ILE F 18 " pdb=" CG2 ILE F 18 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA HIS D 126 " pdb=" N HIS D 126 " pdb=" C HIS D 126 " pdb=" CB HIS D 126 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 1428 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 36 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO F 37 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 37 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 37 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 19 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.30e+00 pdb=" N PRO G 20 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO G 20 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 20 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 127 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO D 128 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " -0.016 5.00e-02 4.00e+02 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2656 2.84 - 3.35: 9206 3.35 - 3.87: 13714 3.87 - 4.38: 13912 4.38 - 4.90: 26108 Nonbonded interactions: 65596 Sorted by model distance: nonbonded pdb=" O PHE A 222 " pdb=" ND2 ASN B 97 " model vdw 2.319 3.120 nonbonded pdb=" O THR C 39 " pdb=" ND2 ASN C 43 " model vdw 2.353 3.120 nonbonded pdb=" O SER A 115 " pdb=" OE1 GLU A 119 " model vdw 2.404 3.040 nonbonded pdb=" OE2 GLU B 212 " pdb=" NH2 ARG C 118 " model vdw 2.415 3.120 nonbonded pdb=" OD1 ASN D 43 " pdb=" NH2 ARG D 198 " model vdw 2.430 3.120 ... (remaining 65591 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9141 Z= 0.160 Angle : 0.473 6.044 12369 Z= 0.271 Chirality : 0.037 0.163 1431 Planarity : 0.003 0.034 1568 Dihedral : 13.779 88.459 3302 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 3.39 (0.25), residues: 1129 helix: 2.93 (0.16), residues: 966 sheet: None (None), residues: 0 loop : -2.43 (0.43), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.014 0.001 TYR D 192 PHE 0.013 0.001 PHE C 52 TRP 0.008 0.001 TRP D 57 HIS 0.002 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9141) covalent geometry : angle 0.47251 (12369) hydrogen bonds : bond 0.13721 ( 711) hydrogen bonds : angle 4.17866 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.350 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6956 (mt-10) REVERT: C 106 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6679 (mt-10) REVERT: C 112 MET cc_start: 0.8739 (mtm) cc_final: 0.8515 (mtm) REVERT: D 48 GLU cc_start: 0.7315 (tt0) cc_final: 0.7097 (tt0) REVERT: D 76 LEU cc_start: 0.8627 (mt) cc_final: 0.8416 (mp) REVERT: D 119 GLU cc_start: 0.7224 (mp0) cc_final: 0.6465 (mp0) REVERT: E 53 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7426 (mm-30) REVERT: E 112 MET cc_start: 0.8566 (mtm) cc_final: 0.8364 (mtp) REVERT: G 30 LEU cc_start: 0.8650 (mt) cc_final: 0.8431 (mt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.7175 time to fit residues: 162.8304 Evaluate side-chains 199 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0270 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.152685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132042 restraints weight = 11929.417| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.01 r_work: 0.3574 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9141 Z= 0.171 Angle : 0.508 7.048 12369 Z= 0.276 Chirality : 0.037 0.141 1431 Planarity : 0.003 0.033 1568 Dihedral : 3.563 18.879 1226 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.80 % Allowed : 10.87 % Favored : 86.33 % 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: 3.72 (0.25), residues: 1129 helix: 3.17 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -2.51 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 219 TYR 0.014 0.001 TYR D 192 PHE 0.014 0.001 PHE C 52 TRP 0.006 0.001 TRP A 147 HIS 0.004 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9141) covalent geometry : angle 0.50812 (12369) hydrogen bonds : bond 0.08148 ( 711) hydrogen bonds : angle 3.27799 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.348 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 89 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7167 (tm-30) REVERT: C 106 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7134 (mt-10) REVERT: D 48 GLU cc_start: 0.7769 (tt0) cc_final: 0.7559 (tt0) REVERT: D 60 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7778 (tp) REVERT: D 76 LEU cc_start: 0.8687 (mt) cc_final: 0.8456 (mp) REVERT: D 119 GLU cc_start: 0.7324 (mp0) cc_final: 0.7122 (mt-10) REVERT: E 53 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7650 (mm-30) REVERT: E 66 TYR cc_start: 0.8907 (t80) cc_final: 0.8682 (t80) REVERT: E 85 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8296 (m) REVERT: F 33 MET cc_start: 0.8322 (mmm) cc_final: 0.7857 (mpp) REVERT: G 30 LEU cc_start: 0.8676 (mt) cc_final: 0.8476 (mt) outliers start: 26 outliers final: 13 residues processed: 216 average time/residue: 0.7634 time to fit residues: 173.1066 Evaluate side-chains 213 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 40.0000 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.150778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130403 restraints weight = 11955.950| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.00 r_work: 0.3552 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9141 Z= 0.173 Angle : 0.505 6.737 12369 Z= 0.272 Chirality : 0.036 0.143 1431 Planarity : 0.003 0.033 1568 Dihedral : 3.564 18.342 1226 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.98 % Allowed : 12.16 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.25), residues: 1129 helix: 3.21 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -2.69 (0.42), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 219 TYR 0.014 0.001 TYR D 66 PHE 0.015 0.001 PHE C 52 TRP 0.008 0.001 TRP D 57 HIS 0.004 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9141) covalent geometry : angle 0.50455 (12369) hydrogen bonds : bond 0.08242 ( 711) hydrogen bonds : angle 3.21664 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.376 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7563 (mt-10) REVERT: C 89 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7185 (tm-30) REVERT: C 106 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7101 (mt-10) REVERT: D 48 GLU cc_start: 0.7776 (tt0) cc_final: 0.7554 (tt0) REVERT: D 60 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7804 (tp) REVERT: D 76 LEU cc_start: 0.8664 (mt) cc_final: 0.8439 (mp) REVERT: D 119 GLU cc_start: 0.7193 (mp0) cc_final: 0.6989 (mt-10) REVERT: E 27 PHE cc_start: 0.8621 (m-10) cc_final: 0.8239 (m-10) REVERT: E 53 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 66 TYR cc_start: 0.8936 (t80) cc_final: 0.8653 (t80) REVERT: F 33 MET cc_start: 0.8454 (mmm) cc_final: 0.8074 (mpp) outliers start: 37 outliers final: 23 residues processed: 217 average time/residue: 0.7272 time to fit residues: 165.6360 Evaluate side-chains 229 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 166 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.151743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130870 restraints weight = 11957.340| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.00 r_work: 0.3556 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9141 Z= 0.172 Angle : 0.512 7.126 12369 Z= 0.274 Chirality : 0.036 0.142 1431 Planarity : 0.003 0.033 1568 Dihedral : 3.562 18.435 1226 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.41 % Allowed : 13.02 % Favored : 82.56 % 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: 3.80 (0.25), residues: 1129 helix: 3.26 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -2.78 (0.42), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.018 0.001 TYR D 66 PHE 0.015 0.001 PHE C 52 TRP 0.009 0.001 TRP D 57 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9141) covalent geometry : angle 0.51237 (12369) hydrogen bonds : bond 0.08249 ( 711) hydrogen bonds : angle 3.19636 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.374 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 119 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: B 89 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 89 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7298 (tm-30) REVERT: C 106 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7089 (mt-10) REVERT: D 48 GLU cc_start: 0.7768 (tt0) cc_final: 0.7554 (tt0) REVERT: D 60 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7895 (tp) REVERT: D 76 LEU cc_start: 0.8688 (mt) cc_final: 0.8463 (mp) REVERT: D 119 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7043 (mt-10) REVERT: E 27 PHE cc_start: 0.8634 (m-10) cc_final: 0.8212 (m-10) REVERT: E 53 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7669 (mm-30) REVERT: E 66 TYR cc_start: 0.8937 (t80) cc_final: 0.8613 (t80) REVERT: E 85 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8285 (m) REVERT: F 33 MET cc_start: 0.8466 (mmm) cc_final: 0.8113 (mpp) outliers start: 41 outliers final: 27 residues processed: 219 average time/residue: 0.6973 time to fit residues: 160.5126 Evaluate side-chains 238 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 93 optimal weight: 0.0670 chunk 84 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.150120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129263 restraints weight = 11914.760| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.98 r_work: 0.3597 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9141 Z= 0.157 Angle : 0.499 7.477 12369 Z= 0.266 Chirality : 0.036 0.141 1431 Planarity : 0.003 0.031 1568 Dihedral : 3.533 17.663 1226 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.74 % Allowed : 13.67 % Favored : 81.59 % 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: 3.91 (0.25), residues: 1129 helix: 3.33 (0.16), residues: 971 sheet: None (None), residues: 0 loop : -2.81 (0.42), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.018 0.001 TYR D 66 PHE 0.013 0.001 PHE C 52 TRP 0.010 0.001 TRP D 57 HIS 0.005 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9141) covalent geometry : angle 0.49872 (12369) hydrogen bonds : bond 0.07590 ( 711) hydrogen bonds : angle 3.10537 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.350 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 21 MET cc_start: 0.7043 (mtp) cc_final: 0.6818 (mtp) REVERT: A 50 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 119 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: B 89 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7658 (tm-30) REVERT: C 89 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7285 (tm-30) REVERT: C 106 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7118 (mt-10) REVERT: D 48 GLU cc_start: 0.7794 (tt0) cc_final: 0.7556 (tt0) REVERT: D 60 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7800 (tp) REVERT: D 76 LEU cc_start: 0.8621 (mt) cc_final: 0.8361 (mp) REVERT: D 119 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6896 (mt-10) REVERT: E 27 PHE cc_start: 0.8561 (m-10) cc_final: 0.8198 (m-10) REVERT: E 53 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7621 (mm-30) REVERT: E 66 TYR cc_start: 0.8860 (t80) cc_final: 0.8517 (t80) REVERT: E 85 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8288 (m) REVERT: E 210 MET cc_start: 0.7954 (ttp) cc_final: 0.7719 (mtm) REVERT: F 33 MET cc_start: 0.8429 (mmm) cc_final: 0.8068 (mpp) outliers start: 44 outliers final: 28 residues processed: 221 average time/residue: 0.6900 time to fit residues: 160.4142 Evaluate side-chains 238 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127811 restraints weight = 11901.582| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.99 r_work: 0.3566 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9141 Z= 0.167 Angle : 0.513 7.586 12369 Z= 0.272 Chirality : 0.036 0.142 1431 Planarity : 0.003 0.031 1568 Dihedral : 3.508 18.327 1226 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.20 % Allowed : 14.32 % Favored : 81.49 % 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: 3.86 (0.25), residues: 1129 helix: 3.30 (0.16), residues: 971 sheet: None (None), residues: 0 loop : -2.86 (0.42), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.016 0.001 TYR D 66 PHE 0.015 0.001 PHE C 52 TRP 0.010 0.001 TRP D 57 HIS 0.006 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9141) covalent geometry : angle 0.51273 (12369) hydrogen bonds : bond 0.07961 ( 711) hydrogen bonds : angle 3.11870 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.328 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 119 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: B 89 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 89 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 106 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7224 (mt-10) REVERT: D 48 GLU cc_start: 0.7719 (tt0) cc_final: 0.7500 (tt0) REVERT: D 60 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7851 (tp) REVERT: D 76 LEU cc_start: 0.8685 (mt) cc_final: 0.8441 (mp) REVERT: D 119 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6935 (mt-10) REVERT: E 27 PHE cc_start: 0.8639 (m-10) cc_final: 0.8274 (m-10) REVERT: E 53 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7678 (mm-30) REVERT: E 66 TYR cc_start: 0.8914 (t80) cc_final: 0.8581 (t80) REVERT: E 85 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8263 (m) REVERT: F 33 MET cc_start: 0.8442 (mmm) cc_final: 0.8127 (mpp) outliers start: 39 outliers final: 29 residues processed: 221 average time/residue: 0.7041 time to fit residues: 163.6730 Evaluate side-chains 239 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 GLN E 37 GLN E 218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.147569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126498 restraints weight = 11819.096| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.97 r_work: 0.3546 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9141 Z= 0.183 Angle : 0.540 8.642 12369 Z= 0.287 Chirality : 0.037 0.143 1431 Planarity : 0.003 0.031 1568 Dihedral : 3.551 18.929 1226 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.52 % Allowed : 14.42 % Favored : 81.05 % 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: 3.76 (0.25), residues: 1129 helix: 3.19 (0.16), residues: 977 sheet: None (None), residues: 0 loop : -2.86 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.021 0.002 TYR D 66 PHE 0.015 0.001 PHE D 222 TRP 0.012 0.001 TRP D 57 HIS 0.012 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9141) covalent geometry : angle 0.54044 (12369) hydrogen bonds : bond 0.08452 ( 711) hydrogen bonds : angle 3.19089 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.370 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 119 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: B 89 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7706 (tm-30) REVERT: C 89 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7339 (tm-30) REVERT: C 106 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7267 (mt-10) REVERT: D 48 GLU cc_start: 0.7740 (tt0) cc_final: 0.7523 (tt0) REVERT: D 60 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7900 (tp) REVERT: D 76 LEU cc_start: 0.8684 (mt) cc_final: 0.8442 (mp) REVERT: D 119 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7030 (mt-10) REVERT: E 27 PHE cc_start: 0.8655 (m-10) cc_final: 0.8281 (m-10) REVERT: E 53 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7685 (mm-30) REVERT: E 66 TYR cc_start: 0.8918 (t80) cc_final: 0.8584 (t80) REVERT: E 85 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8266 (m) REVERT: F 33 MET cc_start: 0.8475 (mmm) cc_final: 0.8145 (mpp) outliers start: 42 outliers final: 29 residues processed: 216 average time/residue: 0.7450 time to fit residues: 168.9397 Evaluate side-chains 235 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 60.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 GLN E 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.151222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130484 restraints weight = 11925.593| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.00 r_work: 0.3550 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9141 Z= 0.171 Angle : 0.535 8.289 12369 Z= 0.282 Chirality : 0.037 0.142 1431 Planarity : 0.003 0.031 1568 Dihedral : 3.540 18.812 1226 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.84 % Allowed : 14.64 % Favored : 80.52 % 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: 3.82 (0.25), residues: 1129 helix: 3.23 (0.16), residues: 977 sheet: None (None), residues: 0 loop : -2.87 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.020 0.001 TYR D 66 PHE 0.014 0.001 PHE A 52 TRP 0.012 0.001 TRP D 57 HIS 0.012 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9141) covalent geometry : angle 0.53474 (12369) hydrogen bonds : bond 0.08106 ( 711) hydrogen bonds : angle 3.14921 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.279 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 119 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: B 89 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7675 (tm-30) REVERT: C 106 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7262 (mt-10) REVERT: D 48 GLU cc_start: 0.7742 (tt0) cc_final: 0.7522 (tt0) REVERT: D 60 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7876 (tp) REVERT: D 76 LEU cc_start: 0.8682 (mt) cc_final: 0.8432 (mp) REVERT: D 119 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6943 (mt-10) REVERT: E 27 PHE cc_start: 0.8659 (m-10) cc_final: 0.8211 (m-10) REVERT: E 53 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7694 (mm-30) REVERT: E 66 TYR cc_start: 0.8910 (t80) cc_final: 0.8625 (t80) REVERT: E 85 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8276 (m) REVERT: E 164 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7930 (mt) REVERT: F 33 MET cc_start: 0.8479 (mmm) cc_final: 0.8172 (mpp) outliers start: 45 outliers final: 28 residues processed: 209 average time/residue: 0.6727 time to fit residues: 147.6139 Evaluate side-chains 228 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain F residue 29 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 0.0370 chunk 46 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 GLN E 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.150716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129521 restraints weight = 11926.910| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.99 r_work: 0.3582 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9141 Z= 0.157 Angle : 0.533 8.680 12369 Z= 0.279 Chirality : 0.036 0.141 1431 Planarity : 0.003 0.031 1568 Dihedral : 3.526 18.170 1226 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.88 % Allowed : 15.29 % Favored : 80.84 % 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: 3.91 (0.25), residues: 1129 helix: 3.31 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -2.89 (0.43), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.018 0.001 TYR D 66 PHE 0.012 0.001 PHE C 52 TRP 0.012 0.001 TRP D 57 HIS 0.012 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9141) covalent geometry : angle 0.53317 (12369) hydrogen bonds : bond 0.07517 ( 711) hydrogen bonds : angle 3.07607 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.302 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7556 (mt-10) REVERT: B 89 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7666 (tm-30) REVERT: B 190 MET cc_start: 0.8348 (ttp) cc_final: 0.8134 (mtm) REVERT: C 106 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7297 (mt-10) REVERT: D 48 GLU cc_start: 0.7715 (tt0) cc_final: 0.7489 (tt0) REVERT: D 60 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7815 (tp) REVERT: D 76 LEU cc_start: 0.8664 (mt) cc_final: 0.8416 (mp) REVERT: D 119 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6869 (mt-10) REVERT: E 27 PHE cc_start: 0.8582 (m-10) cc_final: 0.8138 (m-10) REVERT: E 53 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7705 (mm-30) REVERT: E 66 TYR cc_start: 0.8908 (t80) cc_final: 0.8619 (t80) REVERT: E 85 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8278 (m) REVERT: F 33 MET cc_start: 0.8479 (mmm) cc_final: 0.8169 (mpp) outliers start: 36 outliers final: 23 residues processed: 213 average time/residue: 0.7425 time to fit residues: 166.0664 Evaluate side-chains 230 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain F residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.0060 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN E 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130875 restraints weight = 11861.633| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.00 r_work: 0.3560 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9141 Z= 0.173 Angle : 0.558 8.709 12369 Z= 0.291 Chirality : 0.037 0.142 1431 Planarity : 0.003 0.031 1568 Dihedral : 3.503 19.163 1226 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.34 % Allowed : 16.15 % Favored : 80.52 % 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: 3.84 (0.25), residues: 1129 helix: 3.26 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -2.83 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.018 0.001 TYR D 66 PHE 0.015 0.001 PHE C 52 TRP 0.012 0.001 TRP D 57 HIS 0.013 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9141) covalent geometry : angle 0.55770 (12369) hydrogen bonds : bond 0.08030 ( 711) hydrogen bonds : angle 3.12054 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.327 Fit side-chains TARDY: cannot create tardy model for: "THR A 223 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 50 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 89 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 106 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7381 (mt-10) REVERT: D 48 GLU cc_start: 0.7721 (tt0) cc_final: 0.7496 (tt0) REVERT: D 60 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7858 (tp) REVERT: D 76 LEU cc_start: 0.8689 (mt) cc_final: 0.8446 (mp) REVERT: D 119 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6928 (mt-10) REVERT: D 220 GLN cc_start: 0.7693 (tp40) cc_final: 0.7443 (tp-100) REVERT: E 27 PHE cc_start: 0.8573 (m-10) cc_final: 0.8130 (m-10) REVERT: E 53 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7742 (mm-30) REVERT: E 66 TYR cc_start: 0.8915 (t80) cc_final: 0.8619 (t80) REVERT: E 85 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8279 (m) REVERT: E 136 ILE cc_start: 0.7820 (tp) cc_final: 0.7534 (tt) REVERT: F 33 MET cc_start: 0.8481 (mmm) cc_final: 0.8179 (mpp) outliers start: 31 outliers final: 24 residues processed: 213 average time/residue: 0.6886 time to fit residues: 154.0471 Evaluate side-chains 230 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain F residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.4980 chunk 45 optimal weight: 0.0020 chunk 93 optimal weight: 0.4980 chunk 21 optimal weight: 40.0000 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.3546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 218 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.153189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132058 restraints weight = 11709.728| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.98 r_work: 0.3621 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9141 Z= 0.148 Angle : 0.542 9.210 12369 Z= 0.278 Chirality : 0.036 0.140 1431 Planarity : 0.003 0.032 1568 Dihedral : 3.478 18.145 1226 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.48 % Allowed : 17.01 % Favored : 80.52 % 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: 4.02 (0.25), residues: 1129 helix: 3.37 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -2.75 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.016 0.001 TYR D 66 PHE 0.012 0.001 PHE D 153 TRP 0.011 0.001 TRP D 57 HIS 0.013 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9141) covalent geometry : angle 0.54246 (12369) hydrogen bonds : bond 0.06875 ( 711) hydrogen bonds : angle 3.01319 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.68 seconds wall clock time: 64 minutes 25.75 seconds (3865.75 seconds total)