Starting phenix.real_space_refine on Wed Feb 12 18:27:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8p_24900/02_2025/7s8p_24900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8p_24900/02_2025/7s8p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8p_24900/02_2025/7s8p_24900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8p_24900/02_2025/7s8p_24900.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8p_24900/02_2025/7s8p_24900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8p_24900/02_2025/7s8p_24900.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} 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: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} 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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} 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: 5.22, per 1000 atoms: 0.65 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: 2.06 Conformation dependent library (CDL) restraints added in 939.6 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: 0.96 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: 2.38 Time building geometry restraints manager: 2.37 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: 0.910 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- 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 8263 Z= 0.351 Angle : 0.749 10.056 11265 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 : 3.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP C 63 HIS 0.007 0.002 HIS B 209 PHE 0.014 0.002 PHE R 225 TYR 0.013 0.002 TYR C 105 ARG 0.005 0.000 ARG R 131 *********************** 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 : 0.843 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: 1.1576 time to fit residues: 221.1644 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 : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.0030 overall best weight: 1.2196 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.114226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095971 restraints weight = 11480.759| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.69 r_work: 0.3146 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8263 Z= 0.314 Angle : 0.714 11.082 11265 Z= 0.371 Chirality : 0.047 0.172 1330 Planarity : 0.005 0.043 1417 Dihedral : 5.286 31.252 1217 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.24 % Allowed : 9.70 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1071 helix: -0.04 (0.26), residues: 357 sheet: 0.28 (0.30), residues: 278 loop : -1.66 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 63 HIS 0.008 0.002 HIS B 209 PHE 0.018 0.002 PHE R 225 TYR 0.020 0.002 TYR R 106 ARG 0.007 0.000 ARG R 201 *********************** 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 175 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.943 Fit side-chains REVERT: B 199 ASP cc_start: 0.7034 (p0) cc_final: 0.6831 (p0) REVERT: B 239 ASN cc_start: 0.8461 (m-40) cc_final: 0.8182 (m110) REVERT: C 61 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8314 (ppp) REVERT: R 226 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8108 (mp) REVERT: R 241 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6155 (mpp-170) outliers start: 18 outliers final: 9 residues processed: 164 average time/residue: 1.2862 time to fit residues: 223.3308 Evaluate side-chains 161 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 178 PHE 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 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.117256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098730 restraints weight = 11684.949| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.72 r_work: 0.3200 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8263 Z= 0.168 Angle : 0.570 9.431 11265 Z= 0.298 Chirality : 0.043 0.152 1330 Planarity : 0.004 0.036 1417 Dihedral : 4.609 25.546 1217 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.99 % Allowed : 12.19 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1071 helix: 0.88 (0.28), residues: 360 sheet: 0.57 (0.31), residues: 271 loop : -1.51 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.011 0.001 PHE B 228 TYR 0.015 0.001 TYR E 178 ARG 0.007 0.000 ARG R 201 *********************** 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 186 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.897 Fit side-chains REVERT: B 194 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7868 (ttm-80) REVERT: B 239 ASN cc_start: 0.8406 (m-40) cc_final: 0.8097 (m110) REVERT: C 61 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8140 (ppp) outliers start: 24 outliers final: 10 residues processed: 175 average time/residue: 1.2481 time to fit residues: 231.2201 Evaluate side-chains 167 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 C residue 61 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN B 144 ASN C 340 ASN E 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095224 restraints weight = 11599.956| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.69 r_work: 0.3141 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8263 Z= 0.328 Angle : 0.681 11.479 11265 Z= 0.354 Chirality : 0.046 0.171 1330 Planarity : 0.004 0.042 1417 Dihedral : 5.051 30.506 1217 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.23 % Allowed : 13.06 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1071 helix: 0.87 (0.28), residues: 360 sheet: 0.53 (0.31), residues: 273 loop : -1.58 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 63 HIS 0.006 0.002 HIS B 209 PHE 0.020 0.002 PHE R 225 TYR 0.016 0.002 TYR R 106 ARG 0.010 0.000 ARG R 201 *********************** 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 193 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.929 Fit side-chains REVERT: B 21 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8290 (tttp) REVERT: B 22 ASN cc_start: 0.8460 (m-40) cc_final: 0.8205 (m110) REVERT: B 25 GLU cc_start: 0.7578 (mp0) cc_final: 0.7233 (mp0) REVERT: B 194 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7836 (ttm-80) REVERT: C 318 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8557 (mp) outliers start: 34 outliers final: 23 residues processed: 171 average time/residue: 1.2134 time to fit residues: 219.7923 Evaluate side-chains 180 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 221 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 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 C residue 322 ASP 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 E residue 233 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 252 HIS 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 25 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098064 restraints weight = 11492.746| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.69 r_work: 0.3178 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8263 Z= 0.199 Angle : 0.594 9.976 11265 Z= 0.308 Chirality : 0.043 0.156 1330 Planarity : 0.004 0.038 1417 Dihedral : 4.637 22.734 1217 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.98 % Allowed : 15.05 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1071 helix: 1.23 (0.29), residues: 360 sheet: 0.51 (0.31), residues: 281 loop : -1.49 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE B 228 TYR 0.015 0.001 TYR R 106 ARG 0.010 0.000 ARG R 201 *********************** 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 188 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.843 Fit side-chains REVERT: B 21 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8270 (tttp) REVERT: B 25 GLU cc_start: 0.7618 (mp0) cc_final: 0.7272 (mp0) REVERT: B 194 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7874 (ttm-80) REVERT: C 61 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8226 (ppp) REVERT: R 201 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7355 (mtp-110) outliers start: 32 outliers final: 21 residues processed: 175 average time/residue: 1.2106 time to fit residues: 224.4688 Evaluate side-chains 178 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 165 THR 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 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 192 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 252 HIS 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 91 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097077 restraints weight = 11508.688| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.71 r_work: 0.3164 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8263 Z= 0.238 Angle : 0.626 10.542 11265 Z= 0.323 Chirality : 0.044 0.160 1330 Planarity : 0.004 0.041 1417 Dihedral : 4.722 22.270 1217 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.73 % Allowed : 15.80 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1071 helix: 1.28 (0.28), residues: 360 sheet: 0.55 (0.31), residues: 280 loop : -1.51 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.002 PHE B 228 TYR 0.014 0.002 TYR R 106 ARG 0.008 0.000 ARG R 201 *********************** 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 194 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.898 Fit side-chains REVERT: B 21 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8270 (tttp) REVERT: B 25 GLU cc_start: 0.7615 (mp0) cc_final: 0.7318 (mp0) REVERT: B 194 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7864 (ttm-80) REVERT: C 61 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8397 (ppp) REVERT: E 83 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7748 (mtt) outliers start: 38 outliers final: 24 residues processed: 175 average time/residue: 1.1818 time to fit residues: 219.7645 Evaluate side-chains 181 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain C residue 61 MET 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 165 THR 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 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 192 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 99 VAL 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 44 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 E 77 ASN E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099075 restraints weight = 11623.289| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.72 r_work: 0.3195 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8263 Z= 0.170 Angle : 0.574 9.646 11265 Z= 0.298 Chirality : 0.042 0.154 1330 Planarity : 0.004 0.047 1417 Dihedral : 4.423 20.010 1217 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.36 % Allowed : 17.04 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1071 helix: 1.56 (0.29), residues: 360 sheet: 0.69 (0.32), residues: 276 loop : -1.48 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 228 TYR 0.014 0.001 TYR E 178 ARG 0.013 0.000 ARG R 201 *********************** 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 186 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.803 Fit side-chains REVERT: B 21 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8260 (tttp) REVERT: B 25 GLU cc_start: 0.7640 (mp0) cc_final: 0.7336 (mp0) REVERT: B 76 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8157 (t) REVERT: B 194 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7822 (ttm-80) REVERT: B 245 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7912 (mm) REVERT: C 61 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8200 (ppp) REVERT: E 83 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7710 (mtt) outliers start: 27 outliers final: 17 residues processed: 176 average time/residue: 1.2338 time to fit residues: 230.0566 Evaluate side-chains 175 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain C residue 61 MET 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 165 THR 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 83 MET 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 99 VAL Chi-restraints excluded: chain R residue 252 HIS 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 79 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 89 optimal weight: 0.0020 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097127 restraints weight = 11715.236| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.73 r_work: 0.3165 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8263 Z= 0.239 Angle : 0.623 10.273 11265 Z= 0.323 Chirality : 0.044 0.158 1330 Planarity : 0.004 0.052 1417 Dihedral : 4.643 21.190 1217 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.23 % Allowed : 17.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1071 helix: 1.58 (0.29), residues: 355 sheet: 0.61 (0.31), residues: 280 loop : -1.46 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.002 PHE B 228 TYR 0.013 0.002 TYR R 106 ARG 0.011 0.000 ARG R 201 *********************** 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 188 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.920 Fit side-chains REVERT: B 21 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8263 (tttp) REVERT: B 22 ASN cc_start: 0.8426 (m-40) cc_final: 0.8206 (m110) REVERT: B 25 GLU cc_start: 0.7634 (mp0) cc_final: 0.7343 (mp0) REVERT: B 194 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7832 (ttm-80) REVERT: B 245 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7926 (mm) REVERT: C 61 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8393 (ppp) outliers start: 34 outliers final: 23 residues processed: 173 average time/residue: 1.1964 time to fit residues: 219.5702 Evaluate side-chains 177 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 221 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 61 MET 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 165 THR 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 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 99 VAL Chi-restraints excluded: chain R residue 252 HIS 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 20 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097574 restraints weight = 11727.962| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.73 r_work: 0.3173 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8263 Z= 0.218 Angle : 0.616 10.336 11265 Z= 0.319 Chirality : 0.044 0.156 1330 Planarity : 0.004 0.049 1417 Dihedral : 4.580 20.291 1217 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.48 % Allowed : 17.91 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1071 helix: 1.53 (0.29), residues: 360 sheet: 0.61 (0.31), residues: 281 loop : -1.46 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE B 228 TYR 0.014 0.002 TYR E 178 ARG 0.011 0.000 ARG R 201 *********************** 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 181 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.955 Fit side-chains REVERT: B 21 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8270 (tttp) REVERT: B 25 GLU cc_start: 0.7635 (mp0) cc_final: 0.7339 (mp0) REVERT: B 194 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7819 (ttm-80) REVERT: B 245 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7914 (mm) REVERT: C 61 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8270 (ppp) outliers start: 28 outliers final: 23 residues processed: 168 average time/residue: 1.2223 time to fit residues: 217.4841 Evaluate side-chains 178 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 61 MET 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 165 THR 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 117 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 99 VAL 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 1 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097334 restraints weight = 11554.636| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.72 r_work: 0.3169 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8263 Z= 0.230 Angle : 0.622 10.510 11265 Z= 0.321 Chirality : 0.044 0.157 1330 Planarity : 0.004 0.051 1417 Dihedral : 4.612 20.478 1217 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.48 % Allowed : 18.16 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1071 helix: 1.63 (0.29), residues: 355 sheet: 0.63 (0.31), residues: 280 loop : -1.44 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.002 PHE B 228 TYR 0.013 0.002 TYR E 178 ARG 0.010 0.000 ARG R 201 ********************** 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 183 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.967 Fit side-chains REVERT: B 21 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8263 (tttp) REVERT: B 25 GLU cc_start: 0.7625 (mp0) cc_final: 0.7335 (mp0) REVERT: B 194 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7821 (ttm-80) REVERT: B 245 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7919 (mm) REVERT: C 61 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8325 (ppp) outliers start: 28 outliers final: 23 residues processed: 171 average time/residue: 1.2136 time to fit residues: 220.0304 Evaluate side-chains 179 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 61 MET 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 165 THR 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 117 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 99 VAL 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 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098425 restraints weight = 11660.375| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.73 r_work: 0.3186 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8263 Z= 0.189 Angle : 0.593 10.000 11265 Z= 0.307 Chirality : 0.043 0.152 1330 Planarity : 0.004 0.050 1417 Dihedral : 4.448 19.442 1217 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.61 % Allowed : 18.16 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1071 helix: 1.67 (0.29), residues: 361 sheet: 0.66 (0.31), residues: 280 loop : -1.42 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 228 TYR 0.014 0.001 TYR E 178 ARG 0.010 0.000 ARG R 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6951.34 seconds wall clock time: 122 minutes 53.75 seconds (7373.75 seconds total)