Starting phenix.real_space_refine on Wed Feb 4 00:41:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8p_24900/02_2026/7s8p_24900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8p_24900/02_2026/7s8p_24900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s8p_24900/02_2026/7s8p_24900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8p_24900/02_2026/7s8p_24900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s8p_24900/02_2026/7s8p_24900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8p_24900/02_2026/7s8p_24900.map" } resolution = 2.6 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= 0.002 sd= 0.026 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 54 5.16 5 C 5182 2.51 5 N 1383 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 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: 8093 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1832 Classifications: {'peptide': 247} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'8IX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.54, per 1000 atoms: 0.19 Number of scatterers: 8093 At special positions: 0 Unit cell: (89.18, 117.39, 130.13, 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 54 16.00 O 1474 8.00 N 1383 7.00 C 5182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.04 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: 0.59 Conformation dependent library (CDL) restraints added in 207.7 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 13 sheets defined 37.9% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.680A pdb=" N ALA B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.500A pdb=" N THR B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.903A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.548A pdb=" N LEU B 134 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.740A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.543A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.733A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 195 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.521A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.514A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.859A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.553A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 removed outlier: 4.249A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.866A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.553A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.962A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 52 removed outlier: 3.507A pdb=" N ILE R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL R 40 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU R 42 " --> pdb=" O SER R 38 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 86 removed outlier: 3.620A pdb=" N PHE R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU R 83 " --> pdb=" O GLN R 79 " (cutoff:3.500A) Proline residue: R 84 - end of helix Processing helix chain 'R' and resid 91 through 110 removed outlier: 3.975A pdb=" N LYS R 96 " --> pdb=" O HIS R 92 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL R 99 " --> pdb=" O ARG R 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL R 101 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE R 104 " --> pdb=" O SER R 100 " (cutoff:3.500A) Proline residue: R 105 - end of helix removed outlier: 3.726A pdb=" N THR R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.750A pdb=" N THR R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.544A pdb=" N ARG R 131 " --> pdb=" O PRO R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 155 removed outlier: 3.678A pdb=" N LEU R 151 " --> pdb=" O TRP R 147 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 177 No H-bonds generated for 'chain 'R' and resid 175 through 177' Processing helix chain 'R' and resid 178 through 204 removed outlier: 3.782A pdb=" N ALA R 182 " --> pdb=" O PHE R 178 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP R 183 " --> pdb=" O ILE R 179 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG R 201 " --> pdb=" O VAL R 197 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 210 No H-bonds generated for 'chain 'R' and resid 208 through 210' Processing helix chain 'R' and resid 211 through 229 removed outlier: 3.816A pdb=" N TYR R 215 " --> pdb=" O LEU R 211 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL R 216 " --> pdb=" O THR R 212 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE R 225 " --> pdb=" O THR R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 236 Processing helix chain 'R' and resid 248 through 267 removed outlier: 4.456A pdb=" N HIS R 252 " --> pdb=" O VAL R 248 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR R 254 " --> pdb=" O TYR R 250 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER R 265 " --> pdb=" O SER R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 273 through 280 removed outlier: 3.710A pdb=" N GLN R 280 " --> pdb=" O GLY R 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.572A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.663A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.730A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.917A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.891A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.817A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.909A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.700A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.680A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.518A pdb=" N TRP E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG E 98 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN E 113 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N CYS E 96 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.415A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 143 through 148 Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.782A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 942 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: 1.13 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1288 1.31 - 1.44: 2305 1.44 - 1.57: 4591 1.57 - 1.70: 5 1.70 - 1.83: 74 Bond restraints: 8263 Sorted by residual: bond pdb=" C05 8IX R 401 " pdb=" N04 8IX R 401 " ideal model delta sigma weight residual 1.343 1.449 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C14 8IX R 401 " pdb=" C15 8IX R 401 " ideal model delta sigma weight residual 1.532 1.609 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N ILE R 81 " pdb=" CA ILE R 81 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.38e-02 5.25e+03 8.99e+00 bond pdb=" C14 8IX R 401 " pdb=" C16 8IX R 401 " ideal model delta sigma weight residual 1.522 1.462 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" N LEU R 83 " pdb=" CA LEU R 83 " ideal model delta sigma weight residual 1.461 1.487 -0.026 9.20e-03 1.18e+04 7.95e+00 ... (remaining 8258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11001 2.01 - 4.02: 209 4.02 - 6.03: 38 6.03 - 8.04: 12 8.04 - 10.06: 5 Bond angle restraints: 11265 Sorted by residual: angle pdb=" N ILE R 81 " pdb=" CA ILE R 81 " pdb=" C ILE R 81 " ideal model delta sigma weight residual 112.76 108.64 4.12 1.27e+00 6.20e-01 1.05e+01 angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.60e+00 angle pdb=" N ASP C 153 " pdb=" CA ASP C 153 " pdb=" C ASP C 153 " ideal model delta sigma weight residual 110.80 104.41 6.39 2.13e+00 2.20e-01 9.01e+00 angle pdb=" N LEU R 230 " pdb=" CA LEU R 230 " pdb=" C LEU R 230 " ideal model delta sigma weight residual 109.81 116.43 -6.62 2.21e+00 2.05e-01 8.98e+00 angle pdb=" N LEU R 83 " pdb=" CA LEU R 83 " pdb=" C LEU R 83 " ideal model delta sigma weight residual 112.75 108.75 4.00 1.36e+00 5.41e-01 8.64e+00 ... (remaining 11260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 4372 15.19 - 30.37: 375 30.37 - 45.56: 93 45.56 - 60.74: 15 60.74 - 75.93: 7 Dihedral angle restraints: 4862 sinusoidal: 1709 harmonic: 3153 Sorted by residual: dihedral pdb=" CA TYR B 243 " pdb=" C TYR B 243 " pdb=" N ASN B 244 " pdb=" CA ASN B 244 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLU C 130 " pdb=" C GLU C 130 " pdb=" N GLY C 131 " pdb=" CA GLY C 131 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1117 0.062 - 0.125: 197 0.125 - 0.187: 14 0.187 - 0.250: 0 0.250 - 0.312: 2 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C14 8IX R 401 " pdb=" C13 8IX R 401 " pdb=" C15 8IX R 401 " pdb=" C17 8IX R 401 " both_signs ideal model delta sigma weight residual False -2.85 -3.17 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C10 8IX R 401 " pdb=" C09 8IX R 401 " pdb=" C11 8IX R 401 " pdb=" C15 8IX R 401 " both_signs ideal model delta sigma weight residual False 2.70 2.99 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA LEU R 230 " pdb=" N LEU R 230 " pdb=" C LEU R 230 " pdb=" CB LEU R 230 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1327 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO E 107 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 213 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D 49 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.024 5.00e-02 4.00e+02 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 334 2.73 - 3.27: 7462 3.27 - 3.81: 11748 3.81 - 4.36: 14691 4.36 - 4.90: 26319 Nonbonded interactions: 60554 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O GLY R 229 " model vdw 2.183 3.040 nonbonded pdb=" O TYR B 170 " pdb=" NH1 ARG B 188 " model vdw 2.208 3.120 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASP B 20 " pdb=" NZ LYS C 89 " model vdw 2.289 3.120 nonbonded pdb=" NH2 ARG E 67 " pdb=" OD2 ASP E 90 " model vdw 2.305 3.120 ... (remaining 60549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.160 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 8266 Z= 0.236 Angle : 0.749 10.056 11271 Z= 0.389 Chirality : 0.049 0.312 1330 Planarity : 0.004 0.045 1417 Dihedral : 12.741 75.928 2817 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.23), residues: 1071 helix: -1.79 (0.24), residues: 350 sheet: 0.15 (0.32), residues: 253 loop : -1.72 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 131 TYR 0.013 0.002 TYR C 105 PHE 0.014 0.002 PHE R 225 TRP 0.018 0.002 TRP C 63 HIS 0.007 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 8263) covalent geometry : angle 0.74860 (11265) SS BOND : bond 0.01232 ( 3) SS BOND : angle 1.38203 ( 6) hydrogen bonds : bond 0.30277 ( 337) hydrogen bonds : angle 8.33105 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.265 Fit side-chains REVERT: B 223 ASN cc_start: 0.7663 (m-40) cc_final: 0.7419 (m110) REVERT: B 230 ASP cc_start: 0.7601 (m-30) cc_final: 0.7286 (m-30) REVERT: C 135 VAL cc_start: 0.8325 (t) cc_final: 0.8062 (p) REVERT: R 67 ASN cc_start: 0.6652 (m110) cc_final: 0.6383 (m-40) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.4987 time to fit residues: 95.3312 Evaluate side-chains 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0030 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN C 156 GLN C 340 ASN E 39 GLN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097746 restraints weight = 11656.828| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.70 r_work: 0.3175 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8266 Z= 0.152 Angle : 0.649 10.413 11271 Z= 0.339 Chirality : 0.045 0.160 1330 Planarity : 0.004 0.040 1417 Dihedral : 5.004 29.167 1217 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.99 % Allowed : 9.08 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.24), residues: 1071 helix: 0.06 (0.27), residues: 357 sheet: 0.39 (0.31), residues: 273 loop : -1.61 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 201 TYR 0.017 0.002 TYR R 106 PHE 0.015 0.002 PHE R 225 TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8263) covalent geometry : angle 0.64864 (11265) SS BOND : bond 0.01141 ( 3) SS BOND : angle 1.37503 ( 6) hydrogen bonds : bond 0.06222 ( 337) hydrogen bonds : angle 4.80520 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.306 Fit side-chains REVERT: B 239 ASN cc_start: 0.8456 (m-40) cc_final: 0.8197 (m110) REVERT: C 146 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8732 (mp) REVERT: C 262 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8422 (mmm) REVERT: R 226 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8000 (mp) REVERT: R 241 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6235 (mpp-170) outliers start: 16 outliers final: 6 residues processed: 165 average time/residue: 0.5610 time to fit residues: 97.6554 Evaluate side-chains 158 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 144 ASN C 340 ASN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096921 restraints weight = 11490.839| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.70 r_work: 0.3170 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8266 Z= 0.149 Angle : 0.621 10.252 11271 Z= 0.324 Chirality : 0.044 0.160 1330 Planarity : 0.004 0.038 1417 Dihedral : 4.840 27.538 1217 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.99 % Allowed : 12.56 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1071 helix: 0.79 (0.28), residues: 360 sheet: 0.44 (0.31), residues: 279 loop : -1.54 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 201 TYR 0.014 0.002 TYR R 106 PHE 0.015 0.001 PHE B 228 TRP 0.013 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8263) covalent geometry : angle 0.62056 (11265) SS BOND : bond 0.01155 ( 3) SS BOND : angle 1.52842 ( 6) hydrogen bonds : bond 0.05622 ( 337) hydrogen bonds : angle 4.47312 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.320 Fit side-chains REVERT: B 194 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7848 (ttm-80) REVERT: B 239 ASN cc_start: 0.8342 (m-40) cc_final: 0.7941 (m110) REVERT: C 146 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8760 (mp) outliers start: 24 outliers final: 12 residues processed: 170 average time/residue: 0.6151 time to fit residues: 110.1859 Evaluate side-chains 171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 239 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 66 optimal weight: 0.2980 chunk 47 optimal weight: 0.0020 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 144 ASN C 340 ASN E 77 ASN E 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099828 restraints weight = 11711.362| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.72 r_work: 0.3210 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8266 Z= 0.109 Angle : 0.546 9.265 11271 Z= 0.286 Chirality : 0.042 0.148 1330 Planarity : 0.004 0.034 1417 Dihedral : 4.406 29.207 1217 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.11 % Allowed : 13.56 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1071 helix: 1.24 (0.29), residues: 360 sheet: 0.64 (0.32), residues: 272 loop : -1.39 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 201 TYR 0.014 0.001 TYR E 178 PHE 0.010 0.001 PHE C 241 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8263) covalent geometry : angle 0.54594 (11265) SS BOND : bond 0.00841 ( 3) SS BOND : angle 1.16806 ( 6) hydrogen bonds : bond 0.04220 ( 337) hydrogen bonds : angle 4.08721 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.360 Fit side-chains REVERT: B 21 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8230 (tttp) REVERT: B 25 GLU cc_start: 0.7638 (mp0) cc_final: 0.7264 (mp0) REVERT: B 76 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8121 (t) REVERT: B 194 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7851 (ttm-80) REVERT: C 146 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8692 (mp) REVERT: C 318 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8560 (mt) outliers start: 25 outliers final: 10 residues processed: 173 average time/residue: 0.5079 time to fit residues: 93.0765 Evaluate side-chains 163 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 105 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 60 optimal weight: 0.0270 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 0.0070 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101208 restraints weight = 11714.037| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.72 r_work: 0.3233 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8266 Z= 0.098 Angle : 0.521 8.490 11271 Z= 0.272 Chirality : 0.041 0.141 1330 Planarity : 0.003 0.039 1417 Dihedral : 4.098 21.545 1217 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.11 % Allowed : 14.80 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1071 helix: 1.57 (0.29), residues: 360 sheet: 0.74 (0.32), residues: 281 loop : -1.32 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 201 TYR 0.012 0.001 TYR E 178 PHE 0.009 0.001 PHE C 241 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8263) covalent geometry : angle 0.52058 (11265) SS BOND : bond 0.00747 ( 3) SS BOND : angle 1.06337 ( 6) hydrogen bonds : bond 0.03742 ( 337) hydrogen bonds : angle 3.86445 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.235 Fit side-chains REVERT: B 21 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8197 (tttp) REVERT: B 25 GLU cc_start: 0.7632 (mp0) cc_final: 0.7272 (mp0) REVERT: B 239 ASN cc_start: 0.8405 (m-40) cc_final: 0.8163 (m110) REVERT: B 245 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7788 (mm) REVERT: C 146 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8717 (mt) REVERT: C 318 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8539 (mt) outliers start: 25 outliers final: 13 residues processed: 166 average time/residue: 0.5562 time to fit residues: 97.4512 Evaluate side-chains 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098391 restraints weight = 11634.489| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.72 r_work: 0.3183 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8266 Z= 0.134 Angle : 0.576 7.164 11271 Z= 0.301 Chirality : 0.043 0.151 1330 Planarity : 0.004 0.045 1417 Dihedral : 4.400 21.571 1217 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.73 % Allowed : 15.55 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1071 helix: 1.74 (0.29), residues: 354 sheet: 0.66 (0.32), residues: 274 loop : -1.33 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 201 TYR 0.015 0.002 TYR B 212 PHE 0.014 0.001 PHE R 225 TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8263) covalent geometry : angle 0.57477 (11265) SS BOND : bond 0.01052 ( 3) SS BOND : angle 1.43083 ( 6) hydrogen bonds : bond 0.04686 ( 337) hydrogen bonds : angle 4.07726 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.300 Fit side-chains REVERT: B 21 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8257 (tttp) REVERT: B 25 GLU cc_start: 0.7633 (mp0) cc_final: 0.7293 (mp0) REVERT: B 76 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8134 (t) REVERT: B 194 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7866 (ttm-80) REVERT: C 146 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8716 (mt) REVERT: E 83 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7688 (mtt) outliers start: 30 outliers final: 19 residues processed: 172 average time/residue: 0.5162 time to fit residues: 93.7297 Evaluate side-chains 175 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 340 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098948 restraints weight = 11680.778| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.72 r_work: 0.3194 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8266 Z= 0.123 Angle : 0.568 9.253 11271 Z= 0.296 Chirality : 0.042 0.148 1330 Planarity : 0.004 0.048 1417 Dihedral : 4.377 30.421 1217 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.36 % Allowed : 16.42 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.26), residues: 1071 helix: 1.75 (0.29), residues: 359 sheet: 0.67 (0.32), residues: 274 loop : -1.36 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 201 TYR 0.012 0.001 TYR E 178 PHE 0.011 0.001 PHE R 225 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8263) covalent geometry : angle 0.56784 (11265) SS BOND : bond 0.00961 ( 3) SS BOND : angle 1.30331 ( 6) hydrogen bonds : bond 0.04380 ( 337) hydrogen bonds : angle 4.00695 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.312 Fit side-chains REVERT: B 21 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8234 (tttp) REVERT: B 25 GLU cc_start: 0.7638 (mp0) cc_final: 0.7330 (mp0) REVERT: B 194 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7849 (ttm-80) REVERT: B 245 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7917 (mm) REVERT: C 146 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8707 (mt) REVERT: E 83 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7678 (mtt) outliers start: 27 outliers final: 20 residues processed: 172 average time/residue: 0.5122 time to fit residues: 92.9756 Evaluate side-chains 179 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100710 restraints weight = 11694.647| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.72 r_work: 0.3223 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8266 Z= 0.101 Angle : 0.528 8.610 11271 Z= 0.276 Chirality : 0.041 0.139 1330 Planarity : 0.004 0.051 1417 Dihedral : 4.111 22.645 1217 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.36 % Allowed : 17.91 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 1071 helix: 1.91 (0.29), residues: 359 sheet: 0.73 (0.32), residues: 274 loop : -1.31 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 201 TYR 0.013 0.001 TYR E 178 PHE 0.009 0.001 PHE C 241 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8263) covalent geometry : angle 0.52797 (11265) SS BOND : bond 0.00758 ( 3) SS BOND : angle 1.09334 ( 6) hydrogen bonds : bond 0.03716 ( 337) hydrogen bonds : angle 3.83713 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.195 Fit side-chains REVERT: B 21 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8225 (tttp) REVERT: B 25 GLU cc_start: 0.7660 (mp0) cc_final: 0.7337 (mp0) REVERT: B 76 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8088 (t) REVERT: B 194 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7786 (ttm-80) REVERT: B 245 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7835 (mm) REVERT: C 146 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8715 (mt) outliers start: 19 outliers final: 13 residues processed: 166 average time/residue: 0.5626 time to fit residues: 98.4297 Evaluate side-chains 166 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 30.0000 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099814 restraints weight = 11609.845| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.72 r_work: 0.3211 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8266 Z= 0.111 Angle : 0.547 8.656 11271 Z= 0.286 Chirality : 0.042 0.141 1330 Planarity : 0.004 0.044 1417 Dihedral : 4.151 22.874 1217 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.99 % Allowed : 17.66 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.27), residues: 1071 helix: 2.05 (0.29), residues: 354 sheet: 0.71 (0.32), residues: 275 loop : -1.29 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 201 TYR 0.012 0.001 TYR C 111 PHE 0.011 0.001 PHE B 228 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8263) covalent geometry : angle 0.54665 (11265) SS BOND : bond 0.00885 ( 3) SS BOND : angle 1.21226 ( 6) hydrogen bonds : bond 0.04043 ( 337) hydrogen bonds : angle 3.89271 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.213 Fit side-chains REVERT: B 21 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8230 (tttp) REVERT: B 25 GLU cc_start: 0.7658 (mp0) cc_final: 0.7360 (mp0) REVERT: B 76 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8089 (t) REVERT: C 146 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (mt) REVERT: E 83 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7700 (mtt) outliers start: 24 outliers final: 16 residues processed: 165 average time/residue: 0.5119 time to fit residues: 89.0700 Evaluate side-chains 168 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 104 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 293 ASN R 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099147 restraints weight = 11721.859| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.73 r_work: 0.3200 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8266 Z= 0.120 Angle : 0.569 8.737 11271 Z= 0.297 Chirality : 0.042 0.146 1330 Planarity : 0.004 0.058 1417 Dihedral : 4.233 22.597 1217 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.11 % Allowed : 18.03 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1071 helix: 2.04 (0.29), residues: 354 sheet: 0.71 (0.32), residues: 274 loop : -1.34 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 201 TYR 0.013 0.001 TYR E 178 PHE 0.011 0.001 PHE R 225 TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8263) covalent geometry : angle 0.56837 (11265) SS BOND : bond 0.00928 ( 3) SS BOND : angle 1.26512 ( 6) hydrogen bonds : bond 0.04190 ( 337) hydrogen bonds : angle 3.92705 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.251 Fit side-chains REVERT: B 21 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8230 (tttp) REVERT: B 25 GLU cc_start: 0.7664 (mp0) cc_final: 0.7362 (mp0) REVERT: B 76 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8095 (t) REVERT: C 146 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8699 (mt) REVERT: E 83 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7726 (mtt) outliers start: 25 outliers final: 18 residues processed: 164 average time/residue: 0.5485 time to fit residues: 94.9495 Evaluate side-chains 166 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098571 restraints weight = 11704.824| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.73 r_work: 0.3189 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8266 Z= 0.130 Angle : 0.584 8.377 11271 Z= 0.305 Chirality : 0.043 0.146 1330 Planarity : 0.004 0.058 1417 Dihedral : 4.330 22.810 1217 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.86 % Allowed : 18.41 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1071 helix: 2.04 (0.29), residues: 354 sheet: 0.61 (0.32), residues: 281 loop : -1.33 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 201 TYR 0.013 0.001 TYR B 212 PHE 0.012 0.001 PHE R 225 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8263) covalent geometry : angle 0.58343 (11265) SS BOND : bond 0.00986 ( 3) SS BOND : angle 1.36338 ( 6) hydrogen bonds : bond 0.04461 ( 337) hydrogen bonds : angle 3.99994 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3274.39 seconds wall clock time: 56 minutes 12.95 seconds (3372.95 seconds total)